diff --git a/404.html b/404.html
index d3a0637..9727451 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://microbiomedb.github.io/MicrobiomeDB/index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 4350344..f0e47ce 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/alphadiv.html b/articles/alphadiv.html
index 7c25c74..e22afe1 100644
--- a/articles/alphadiv.html
+++ b/articles/alphadiv.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -163,11 +163,11 @@ <h3 id="shannon-diversity-index">Shannon Diversity Index<a class="anchor" aria-l
 <span><span class="co">## get an alpha diversity ComputeResult</span></span>
 <span><span class="va">alphaDivOutput</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/alphaDiv-methods.html">alphaDiv</a></span><span class="op">(</span><span class="va">genus</span>, method <span class="op">=</span> <span class="st">'shannon'</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:27.523073 Received df table with 741 samples and 226 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:00.644513 Received df table with 741 samples and 226 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:27.576679 shannon alpha diversity computation complete.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:00.669897 shannon alpha diversity computation complete.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:27.591639 Alpha diversity computation completed with parameters method= shannon</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:37:00.685402 Alpha diversity computation completed with parameters method= shannon</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="simpson-diversity-index">Simpson Diversity Index<a class="anchor" aria-label="anchor" href="#simpson-diversity-index"></a>
@@ -181,11 +181,11 @@ <h3 id="simpson-diversity-index">Simpson Diversity Index<a class="anchor" aria-l
 <span><span class="va">genus</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/getCollection.html">getCollection</a></span><span class="op">(</span><span class="fu">microbiomeData</span><span class="fu">::</span><span class="va"><a href="https://microbiomedb.github.io/microbiomeData/reference/HMP_WGS.html" class="external-link">HMP_WGS</a></span>, <span class="st">'WGS Genus'</span><span class="op">)</span></span>
 <span><span class="va">alphaDivOutput</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/alphaDiv-methods.html">alphaDiv</a></span><span class="op">(</span><span class="va">genus</span>, method <span class="op">=</span> <span class="st">'simpson'</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:27.68364 Received df table with 741 samples and 226 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:00.779723 Received df table with 741 samples and 226 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:27.706332 simpson alpha diversity computation complete.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:00.802822 simpson alpha diversity computation complete.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:27.711408 Alpha diversity computation completed with parameters method= simpson</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:37:00.808237 Alpha diversity computation completed with parameters method= simpson</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="species-evenness">Species Evenness<a class="anchor" aria-label="anchor" href="#species-evenness"></a>
@@ -199,11 +199,11 @@ <h3 id="species-evenness">Species Evenness<a class="anchor" aria-label="anchor"
 <span><span class="va">genus</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/getCollection.html">getCollection</a></span><span class="op">(</span><span class="fu">microbiomeData</span><span class="fu">::</span><span class="va"><a href="https://microbiomedb.github.io/microbiomeData/reference/HMP_WGS.html" class="external-link">HMP_WGS</a></span>, <span class="st">'WGS Genus'</span><span class="op">)</span></span>
 <span><span class="va">alphaDivOutput</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/alphaDiv-methods.html">alphaDiv</a></span><span class="op">(</span><span class="va">genus</span>, method <span class="op">=</span> <span class="st">'evenness'</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:27.796455 Received df table with 741 samples and 226 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:00.894878 Received df table with 741 samples and 226 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:27.814082 evenness alpha diversity computation complete.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:00.913373 evenness alpha diversity computation complete.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:27.817465 Alpha diversity computation completed with parameters method= evenness</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:37:00.916953 Alpha diversity computation completed with parameters method= evenness</span></span></code></pre></div>
 </div>
 </div>
 <div class="section level2">
diff --git a/articles/alphadiv_files/figure-html/unnamed-chunk-5-1.png b/articles/alphadiv_files/figure-html/unnamed-chunk-5-1.png
index 2bcab45..2e80433 100644
Binary files a/articles/alphadiv_files/figure-html/unnamed-chunk-5-1.png and b/articles/alphadiv_files/figure-html/unnamed-chunk-5-1.png differ
diff --git a/articles/betadiv.html b/articles/betadiv.html
index 8c45253..78ae4b6 100644
--- a/articles/betadiv.html
+++ b/articles/betadiv.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -170,13 +170,13 @@ <h4 id="bray-curtis-dissimilarity">Bray-Curtis Dissimilarity<a class="anchor" ar
 <span><span class="co">## get a betaDiv ComputeResult</span></span>
 <span><span class="va">betaDiv</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/betaDiv-methods.html">betaDiv</a></span><span class="op">(</span><span class="va">HMP_WGS_species</span>, method <span class="op">=</span> <span class="st">"bray"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:41.467959 Received df table with 741 samples and 704 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:14.829383 Received df table with 741 samples and 704 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:41.797229 Computed dissimilarity matrix.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:15.155728 Computed dissimilarity matrix.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:42.767674 Finished ordination step.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:16.089393 Finished ordination step.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:42.79767 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = bray , k = 2 , verbose = TRUE</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:37:16.11976 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = bray , k = 2 , verbose = TRUE</span></span></code></pre></div>
 </div>
 <div class="section level4">
 <h4 id="jaccard-dissimilarity">Jaccard Dissimilarity<a class="anchor" aria-label="anchor" href="#jaccard-dissimilarity"></a>
@@ -188,13 +188,13 @@ <h4 id="jaccard-dissimilarity">Jaccard Dissimilarity<a class="anchor" aria-label
 <code class="sourceCode R"><span><span class="va">HMP_WGS_species</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/getCollection.html">getCollection</a></span><span class="op">(</span><span class="fu">microbiomeData</span><span class="fu">::</span><span class="va"><a href="https://microbiomedb.github.io/microbiomeData/reference/HMP_WGS.html" class="external-link">HMP_WGS</a></span>, <span class="st">'WGS Species'</span><span class="op">)</span></span>
 <span><span class="va">betaDiv</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/betaDiv-methods.html">betaDiv</a></span><span class="op">(</span><span class="va">HMP_WGS_species</span>, method <span class="op">=</span> <span class="st">"jaccard"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:42.942731 Received df table with 741 samples and 704 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:16.269667 Received df table with 741 samples and 704 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:43.25124 Computed dissimilarity matrix.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:16.581029 Computed dissimilarity matrix.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:43.443083 Finished ordination step.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:16.769338 Finished ordination step.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:43.454034 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jaccard , k = 2 , verbose = TRUE</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:37:16.780671 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jaccard , k = 2 , verbose = TRUE</span></span></code></pre></div>
 </div>
 <div class="section level4">
 <h4 id="jensen-shannon-divergence-jsd">Jensen-Shannon Divergence (JSD)<a class="anchor" aria-label="anchor" href="#jensen-shannon-divergence-jsd"></a>
@@ -207,13 +207,13 @@ <h4 id="jensen-shannon-divergence-jsd">Jensen-Shannon Divergence (JSD)<a class="
 <code class="sourceCode R"><span><span class="va">HMP_WGS_species</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/getCollection.html">getCollection</a></span><span class="op">(</span><span class="fu">microbiomeData</span><span class="fu">::</span><span class="va"><a href="https://microbiomedb.github.io/microbiomeData/reference/HMP_WGS.html" class="external-link">HMP_WGS</a></span>, <span class="st">'WGS Species'</span><span class="op">)</span></span>
 <span><span class="va">betaDiv</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/betaDiv-methods.html">betaDiv</a></span><span class="op">(</span><span class="va">HMP_WGS_species</span>, method <span class="op">=</span> <span class="st">"jsd"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:43.58537 Received df table with 741 samples and 704 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:16.914771 Received df table with 741 samples and 704 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:50.290221 Computed dissimilarity matrix.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:23.70449 Computed dissimilarity matrix.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:50.485559 Finished ordination step.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:23.903281 Finished ordination step.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:11:50.492093 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jsd , k = 2 , verbose = TRUE</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:37:23.90968 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jsd , k = 2 , verbose = TRUE</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="principal-coordinate-analysis-pcoa">Principal Coordinate Analysis (PCoA):<a class="anchor" aria-label="anchor" href="#principal-coordinate-analysis-pcoa"></a>
diff --git a/articles/betadiv_files/figure-html/unnamed-chunk-5-1.png b/articles/betadiv_files/figure-html/unnamed-chunk-5-1.png
index 91dfdd6..10fb7bf 100644
Binary files a/articles/betadiv_files/figure-html/unnamed-chunk-5-1.png and b/articles/betadiv_files/figure-html/unnamed-chunk-5-1.png differ
diff --git a/articles/correlation.html b/articles/correlation.html
index a1e3cb5..b1f85e7 100644
--- a/articles/correlation.html
+++ b/articles/correlation.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -224,17 +224,17 @@ <h3 id="spearman-correlation">Spearman Correlation<a class="anchor" aria-label="
 <span><span class="co">## it is simply exemplary. Always look at your data!</span></span>
 <span><span class="va">species_vs_metadata</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/correlation-methods.html">correlation</a></span><span class="op">(</span><span class="va">HMP_WGS_species</span>, method <span class="op">=</span> <span class="st">'spearman'</span><span class="op">)</span> </span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:03.565216 Removed 7 records with no data.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:37.301624 Removed 7 records with no data.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:03.593909 Removed 7 records with no data.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:37.331011 Removed 7 records with no data.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:03.62961 Removed 7 records with no data.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:37.367011 Removed 7 records with no data.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:04.960872 Completed correlation with method=spearman. Formatting results.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:38.706018 Completed correlation with method=spearman. Formatting results.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:04.96186 Received df table with 734 samples and 316 features with values.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:38.707003 Received df table with 734 samples and 316 features with values.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:04.966443 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method =  spearman</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:37:38.711433 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method =  spearman</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="pearson-correlation">Pearson Correlation<a class="anchor" aria-label="anchor" href="#pearson-correlation"></a>
@@ -251,21 +251,21 @@ <h3 id="pearson-correlation">Pearson Correlation<a class="anchor" aria-label="an
 <span><span class="co">## it is simply exemplary. Always look at your data!</span></span>
 <span><span class="va">pathway_vs_species</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/correlation-methods.html">correlation</a></span><span class="op">(</span><span class="va">HMP_WGS_species</span>, <span class="va">HMP_WGS_pathways</span>, method <span class="op">=</span> <span class="st">'pearson'</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:05.911691 Removed 7 records with no data.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:39.633612 Removed 7 records with no data.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:05.948013 Removed 7 records with no data.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:39.670784 Removed 7 records with no data.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:06.087085 Removed 7 records with no data.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:39.823658 Removed 7 records with no data.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:06.097721 Received first df table with 734 samples and 319 features with values.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:39.834297 Received first df table with 734 samples and 319 features with values.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:06.098063 Received second df table with 741 samples and 371 features with values.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:39.834609 Received second df table with 741 samples and 371 features with values.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:06.098324 Found 734 samples in common between data1 and data2. Only these samples will be used.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:39.834852 Found 734 samples in common between data1 and data2. Only these samples will be used.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:06.515177 Completed correlation with method=pearson. Formatting results.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:40.250861 Completed correlation with method=pearson. Formatting results.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:06.521023 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method =  pearson</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:37:40.256431 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method =  pearson</span></span></code></pre></div>
 </div>
 </div>
 <div class="section level2">
diff --git a/articles/index.html b/articles/index.html
index 634a55a..7dd2ac5 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/ranked-abundance.html b/articles/ranked-abundance.html
index 9907c76..5e3a216 100644
--- a/articles/ranked-abundance.html
+++ b/articles/ranked-abundance.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -178,35 +178,35 @@ <h2 id="how-to-find-ranked-relative-abundances">How to Find Ranked Relative Abun
 <span><span class="co">## top 10 taxa by max relative abundance across all samples</span></span>
 <span><span class="va">rankedAbund</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/rankedAbundance-methods.html">rankedAbundance</a></span><span class="op">(</span><span class="va">HMP_WGS_species</span>, method <span class="op">=</span> <span class="st">"max"</span>, cutoff <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> </span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:20.822977 Received df table with 741 samples and 704 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:54.182368 Received df table with 741 samples and 704 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:20.854149 Finished ranking taxa</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:54.213604 Finished ranking taxa</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:20.874894 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = max , cutoff = 10 , naToZero =  TRUE , verbose = TRUE</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:54.234347 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = max , cutoff = 10 , naToZero =  TRUE , verbose = TRUE</span></span>
 <span><span class="co">## top 8 taxa by median relative abundance across all samples</span></span>
 <span><span class="va">rankedAbund</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/rankedAbundance-methods.html">rankedAbundance</a></span><span class="op">(</span><span class="va">HMP_WGS_species</span>, method <span class="op">=</span> <span class="st">"median"</span>, cutoff <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:21.658376 Received df table with 741 samples and 704 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:54.955539 Received df table with 741 samples and 704 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:21.679641 Finished ranking taxa</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:54.976285 Finished ranking taxa</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:21.688558 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = median , cutoff = 8 , naToZero =  TRUE , verbose = TRUE</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:54.984991 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = median , cutoff = 8 , naToZero =  TRUE , verbose = TRUE</span></span>
 <span><span class="co">## top 20 taxa by third quartile relative abundance across all samples</span></span>
 <span><span class="va">rankedAbund</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/rankedAbundance-methods.html">rankedAbundance</a></span><span class="op">(</span><span class="va">HMP_WGS_species</span>, method <span class="op">=</span> <span class="st">"q3"</span>, cutoff <span class="op">=</span> <span class="fl">20</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:21.715574 Received df table with 741 samples and 704 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:55.011114 Received df table with 741 samples and 704 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:21.811909 Finished ranking taxa</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:55.118115 Finished ranking taxa</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:21.818515 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = q3 , cutoff = 20 , naToZero =  TRUE , verbose = TRUE</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:55.124598 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = q3 , cutoff = 20 , naToZero =  TRUE , verbose = TRUE</span></span>
 <span><span class="co">## top 10 taxa by greatest variance in relative abundance across all samples</span></span>
 <span><span class="va">rankedAbund</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/rankedAbundance-methods.html">rankedAbundance</a></span><span class="op">(</span><span class="va">HMP_WGS_species</span>, method <span class="op">=</span> <span class="st">"variance"</span>, cutoff <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:21.845605 Received df table with 741 samples and 704 taxa.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:55.150866 Received df table with 741 samples and 704 taxa.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:21.866328 Finished ranking taxa</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:37:55.171238 Finished ranking taxa</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:21.871848 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = variance , cutoff = 10 , naToZero =  TRUE , verbose = TRUE</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:37:55.176685 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = variance , cutoff = 10 , naToZero =  TRUE , verbose = TRUE</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="visualizing-ranked-relative-abundances">Visualizing Ranked Relative Abundances<a class="anchor" aria-label="anchor" href="#visualizing-ranked-relative-abundances"></a>
diff --git a/articles/ranked-abundance_files/figure-html/unnamed-chunk-3-1.png b/articles/ranked-abundance_files/figure-html/unnamed-chunk-3-1.png
index c995cb7..721572f 100644
Binary files a/articles/ranked-abundance_files/figure-html/unnamed-chunk-3-1.png and b/articles/ranked-abundance_files/figure-html/unnamed-chunk-3-1.png differ
diff --git a/articles/self-correlation.html b/articles/self-correlation.html
index d09d5f0..a7d6408 100644
--- a/articles/self-correlation.html
+++ b/articles/self-correlation.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -196,17 +196,17 @@ <h2 id="how-are-correlations-calculated">How are Correlations Calculated?<a clas
 <span><span class="co">## these methods can be used with other data types as well</span></span>
 <span><span class="va">farmm_metabolomics</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/getCollection.html">getCollection</a></span><span class="op">(</span><span class="fu">microbiomeData</span><span class="fu">::</span><span class="va"><a href="https://microbiomedb.github.io/microbiomeData/reference/FARMM.html" class="external-link">FARMM</a></span>, <span class="st">"Metabolomics Mass spectrometry assay"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:35.42818 Integer values detected. Converting collection to AbsoluteAbundanceData</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:38:08.623847 Integer values detected. Converting collection to AbsoluteAbundanceData</span></span>
 <span></span>
 <span><span class="co">## get a self correlation ComputeResult</span></span>
 <span><span class="co">## methods spearman and pearson are options here as well, for data known to not be compositional</span></span>
 <span><span class="va">selfCorrelation_metabolomics</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/selfCorrelation-methods.html">selfCorrelation</a></span><span class="op">(</span><span class="va">farmm_metabolomics</span>, method<span class="op">=</span><span class="st">'spearman'</span><span class="op">)</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:36.768037 Completed correlation with method=spearman. Formatting results.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:38:09.960696 Completed correlation with method=spearman. Formatting results.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:37.649345 Received df table with 150 samples and 479 features with abundances.</span></span>
+<span><span class="co">#&gt; 2024-04-24 17:38:10.821158 Received df table with 150 samples and 479 features with abundances.</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; 2024-04-24 17:12:37.653913 Correlation computation completed with parameters recordIdColumn= Mass_spectrometry_assay_Id , method =  spearman</span></span></code></pre></div>
+<span><span class="co">#&gt; 2024-04-24 17:38:10.825808 Correlation computation completed with parameters recordIdColumn= Mass_spectrometry_assay_Id , method =  spearman</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="interpreting-results">Interpreting Results<a class="anchor" aria-label="anchor" href="#interpreting-results"></a>
diff --git a/authors.html b/authors.html
index 37e1cf8..0b47803 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,13 +65,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Callan D (2024).
 <em>MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org</em>.
-R package version 0.2.0, https://microbiomedb.github.io/MicrobiomeDB/, <a href="https://github.com/microbiomeDB/MicrobiomeDB" class="external-link">https://github.com/microbiomeDB/MicrobiomeDB</a>. 
+R package version 1.0.0, https://microbiomedb.github.io/MicrobiomeDB/, <a href="https://github.com/microbiomeDB/MicrobiomeDB" class="external-link">https://github.com/microbiomeDB/MicrobiomeDB</a>. 
 </p>
       <pre>@Manual{,
   title = {MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org},
   author = {Danielle Callan},
   year = {2024},
-  note = {R package version 0.2.0, https://microbiomedb.github.io/MicrobiomeDB/},
+  note = {R package version 1.0.0, https://microbiomedb.github.io/MicrobiomeDB/},
   url = {https://github.com/microbiomeDB/MicrobiomeDB},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 0a0e0c9..2fa0261 100644
--- a/index.html
+++ b/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index 7b529da..2d686d7 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   correlation: correlation.html
   ranked-abundance: ranked-abundance.html
   self-correlation: self-correlation.html
-last_built: 2024-04-24T16:50Z
+last_built: 2024-04-24T17:16Z
 urls:
   reference: https://microbiomedb.github.io/MicrobiomeDB/reference
   article: https://microbiomedb.github.io/MicrobiomeDB/articles
diff --git a/reference/DESeqDataSetFromCollection.html b/reference/DESeqDataSetFromCollection.html
index e3eee28..7b4490c 100644
--- a/reference/DESeqDataSetFromCollection.html
+++ b/reference/DESeqDataSetFromCollection.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/Maaslin2.html b/reference/Maaslin2.html
index a59653b..88a379a 100644
--- a/reference/Maaslin2.html
+++ b/reference/Maaslin2.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -107,137 +107,137 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output folder"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output feature tables folder"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output fits folder"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.689123 INFO::Writing function arguments to log file</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.704111 INFO::Verifying options selected are valid</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.734445 INFO::Determining format of input files</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.736163 INFO::Input format is data samples as rows and metadata samples as rows</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.750647 INFO::Formula for fixed effects: expr ~  delivery_mode</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.751732 INFO::Filter data based on min abundance and min prevalence</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.752267 INFO::Total samples in data: 3184</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.752756 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.772777 INFO::Total filtered features: 563</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.773912 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.781983 INFO::Total filtered features with variance filtering: 0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.782585 INFO::Filtered feature names from variance filtering:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.783064 INFO::Running selected normalization method: TSS</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.84251 INFO::Applying z-score to standardize continuous metadata</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.851343 INFO::Running selected transform method: LOG</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.914274 INFO::Running selected analysis method: LM</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.920555 INFO::Fitting model to feature number 1, Actinomyces</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.929258 INFO::Fitting model to feature number 2, Agathobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.933501 INFO::Fitting model to feature number 3, Akkermansia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.937621 INFO::Fitting model to feature number 4, Alistipes</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.941725 INFO::Fitting model to feature number 5, Anaerostipes</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.945867 INFO::Fitting model to feature number 6, Atopobium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.949921 INFO::Fitting model to feature number 7, Bacteroides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.954178 INFO::Fitting model to feature number 8, Barnesiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.9583 INFO::Fitting model to feature number 9, Bifidobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.962408 INFO::Fitting model to feature number 10, Bilophila</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.966498 INFO::Fitting model to feature number 11, Blautia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.990195 INFO::Fitting model to feature number 12, Butyricicoccus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.994916 INFO::Fitting model to feature number 13, CAG.352</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:36.99904 INFO::Fitting model to feature number 14, Campylobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.003131 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.007246 INFO::Fitting model to feature number 16, Clostridioides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.011571 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.015681 INFO::Fitting model to feature number 18, Colidextribacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.019885 INFO::Fitting model to feature number 19, Collinsella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.024768 INFO::Fitting model to feature number 20, Coprobacillus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.029115 INFO::Fitting model to feature number 21, Coprococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.033249 INFO::Fitting model to feature number 22, DTU089</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.037397 INFO::Fitting model to feature number 23, Dialister</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.041522 INFO::Fitting model to feature number 24, Dorea</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.045609 INFO::Fitting model to feature number 25, Eggerthella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.04967 INFO::Fitting model to feature number 26, Eisenbergiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.053738 INFO::Fitting model to feature number 27, Enterococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.057915 INFO::Fitting model to feature number 28, Erysipelatoclostridium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.062057 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.066175 INFO::Fitting model to feature number 30, Escherichia.Shigella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.070257 INFO::Fitting model to feature number 31, Faecalibacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.074361 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.078558 INFO::Fitting model to feature number 33, Flavonifractor</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.082631 INFO::Fitting model to feature number 34, Fusicatenibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.086782 INFO::Fitting model to feature number 35, Fusobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.090875 INFO::Fitting model to feature number 36, Gemella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.094934 INFO::Fitting model to feature number 37, Granulicatella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.099094 INFO::Fitting model to feature number 38, Haemophilus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.104082 INFO::Fitting model to feature number 39, Holdemania</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.108351 INFO::Fitting model to feature number 40, Hungatella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.112507 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.11659 INFO::Fitting model to feature number 42, Intestinibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.12853 INFO::Fitting model to feature number 43, Intestinimonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.132896 INFO::Fitting model to feature number 44, Klebsiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.137085 INFO::Fitting model to feature number 45, Lachnoclostridium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.141203 INFO::Fitting model to feature number 46, Lachnospira</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.145363 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.149453 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.153548 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.157645 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.161741 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.165858 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.170027 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.174133 INFO::Fitting model to feature number 54, Lactobacillus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.178273 INFO::Fitting model to feature number 55, Lactococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.182408 INFO::Fitting model to feature number 56, Mannheimia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.186542 INFO::Fitting model to feature number 57, Megasphaera</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.190647 INFO::Fitting model to feature number 58, Monoglobus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.194826 INFO::Fitting model to feature number 59, Neisseria</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.198956 INFO::Fitting model to feature number 60, Odoribacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.203068 INFO::Fitting model to feature number 61, Oscillibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.207123 INFO::Fitting model to feature number 62, Oscillospira</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.211255 INFO::Fitting model to feature number 63, Parabacteroides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.215393 INFO::Fitting model to feature number 64, Parasutterella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.219496 INFO::Fitting model to feature number 65, Prevotella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.223722 INFO::Fitting model to feature number 66, Pseudomonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.227811 INFO::Fitting model to feature number 67, Romboutsia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.231956 INFO::Fitting model to feature number 68, Roseburia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.236034 INFO::Fitting model to feature number 69, Rothia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.240137 INFO::Fitting model to feature number 70, Ruminococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.2442 INFO::Fitting model to feature number 71, Sellimonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.248294 INFO::Fitting model to feature number 72, Solobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.252344 INFO::Fitting model to feature number 73, Staphylococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.264847 INFO::Fitting model to feature number 74, Streptococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.269177 INFO::Fitting model to feature number 75, Subdoligranulum</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.27329 INFO::Fitting model to feature number 76, Sutterella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.277501 INFO::Fitting model to feature number 77, Terrisporobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.281673 INFO::Fitting model to feature number 78, Turicibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.285811 INFO::Fitting model to feature number 79, Tuzzerella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.289967 INFO::Fitting model to feature number 80, Tyzzerella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.294118 INFO::Fitting model to feature number 81, UBA1819</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.298263 INFO::Fitting model to feature number 82, UCG.002</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.30243 INFO::Fitting model to feature number 83, UCG.003</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.306582 INFO::Fitting model to feature number 84, UCG.005</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.310752 INFO::Fitting model to feature number 85, Veillonella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.314917 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.319044 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.323189 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.327366 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.331574 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.335738 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.339885 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.344007 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.348122 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.35227 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.356377 INFO::Fitting model to feature number 96, unclassified.Chloroplast</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.360484 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.364588 INFO::Fitting model to feature number 98, unclassified.Clostridia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.368677 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.372785 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.376869 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.381 INFO::Fitting model to feature number 102, unclassified.Mitochondria</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.393731 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.398149 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.402386 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.4066 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.410811 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.431035 INFO::Counting total values for each feature</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.437077 INFO::Writing filtered data to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/features/filtered_data.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.584518 INFO::Writing filtered, normalized data to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/features/filtered_data_norm.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:37.734916 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/features/filtered_data_norm_transformed.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:38.00878 INFO::Writing residuals to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/fits/residuals.rds</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:38.079005 INFO::Writing fitted values to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/fits/fitted.rds</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:38.103251 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/all_results.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:38.105003 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/significant_results.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.137393 INFO::Writing function arguments to log file</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.152308 INFO::Verifying options selected are valid</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.181968 INFO::Determining format of input files</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.183541 INFO::Input format is data samples as rows and metadata samples as rows</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.197836 INFO::Formula for fixed effects: expr ~  delivery_mode</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.198775 INFO::Filter data based on min abundance and min prevalence</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.199319 INFO::Total samples in data: 3184</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.199795 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.219658 INFO::Total filtered features: 563</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.220761 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.228667 INFO::Total filtered features with variance filtering: 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.229223 INFO::Filtered feature names from variance filtering:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.229697 INFO::Running selected normalization method: TSS</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.288467 INFO::Applying z-score to standardize continuous metadata</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.296834 INFO::Running selected transform method: LOG</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.35947 INFO::Running selected analysis method: LM</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.365472 INFO::Fitting model to feature number 1, Actinomyces</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.374012 INFO::Fitting model to feature number 2, Agathobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.378144 INFO::Fitting model to feature number 3, Akkermansia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.38224 INFO::Fitting model to feature number 4, Alistipes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.386331 INFO::Fitting model to feature number 5, Anaerostipes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.390452 INFO::Fitting model to feature number 6, Atopobium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.3945 INFO::Fitting model to feature number 7, Bacteroides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.398598 INFO::Fitting model to feature number 8, Barnesiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.402634 INFO::Fitting model to feature number 9, Bifidobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.406713 INFO::Fitting model to feature number 10, Bilophila</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.410826 INFO::Fitting model to feature number 11, Blautia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.432689 INFO::Fitting model to feature number 12, Butyricicoccus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.437162 INFO::Fitting model to feature number 13, CAG.352</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.441193 INFO::Fitting model to feature number 14, Campylobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.445297 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.449362 INFO::Fitting model to feature number 16, Clostridioides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.453418 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.457496 INFO::Fitting model to feature number 18, Colidextribacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.46159 INFO::Fitting model to feature number 19, Collinsella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.465642 INFO::Fitting model to feature number 20, Coprobacillus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.46976 INFO::Fitting model to feature number 21, Coprococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.473836 INFO::Fitting model to feature number 22, DTU089</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.477946 INFO::Fitting model to feature number 23, Dialister</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.482205 INFO::Fitting model to feature number 24, Dorea</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.486331 INFO::Fitting model to feature number 25, Eggerthella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.490447 INFO::Fitting model to feature number 26, Eisenbergiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.494556 INFO::Fitting model to feature number 27, Enterococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.498703 INFO::Fitting model to feature number 28, Erysipelatoclostridium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.502821 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.506915 INFO::Fitting model to feature number 30, Escherichia.Shigella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.510962 INFO::Fitting model to feature number 31, Faecalibacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.515036 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.519112 INFO::Fitting model to feature number 33, Flavonifractor</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.523153 INFO::Fitting model to feature number 34, Fusicatenibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.527172 INFO::Fitting model to feature number 35, Fusobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.531253 INFO::Fitting model to feature number 36, Gemella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.535288 INFO::Fitting model to feature number 37, Granulicatella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.539339 INFO::Fitting model to feature number 38, Haemophilus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.543461 INFO::Fitting model to feature number 39, Holdemania</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.547532 INFO::Fitting model to feature number 40, Hungatella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.551624 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.555752 INFO::Fitting model to feature number 42, Intestinibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.567054 INFO::Fitting model to feature number 43, Intestinimonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.571323 INFO::Fitting model to feature number 44, Klebsiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.575483 INFO::Fitting model to feature number 45, Lachnoclostridium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.579586 INFO::Fitting model to feature number 46, Lachnospira</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.58366 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.587696 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.591765 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.595816 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.599863 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.603962 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.608043 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.612105 INFO::Fitting model to feature number 54, Lactobacillus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.616189 INFO::Fitting model to feature number 55, Lactococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.620257 INFO::Fitting model to feature number 56, Mannheimia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.624327 INFO::Fitting model to feature number 57, Megasphaera</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.628387 INFO::Fitting model to feature number 58, Monoglobus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.632524 INFO::Fitting model to feature number 59, Neisseria</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.636647 INFO::Fitting model to feature number 60, Odoribacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.640717 INFO::Fitting model to feature number 61, Oscillibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.644774 INFO::Fitting model to feature number 62, Oscillospira</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.64883 INFO::Fitting model to feature number 63, Parabacteroides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.652919 INFO::Fitting model to feature number 64, Parasutterella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.657008 INFO::Fitting model to feature number 65, Prevotella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.661202 INFO::Fitting model to feature number 66, Pseudomonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.665254 INFO::Fitting model to feature number 67, Romboutsia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.669317 INFO::Fitting model to feature number 68, Roseburia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.673414 INFO::Fitting model to feature number 69, Rothia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.677464 INFO::Fitting model to feature number 70, Ruminococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.681498 INFO::Fitting model to feature number 71, Sellimonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.685598 INFO::Fitting model to feature number 72, Solobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.689627 INFO::Fitting model to feature number 73, Staphylococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.701293 INFO::Fitting model to feature number 74, Streptococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.705551 INFO::Fitting model to feature number 75, Subdoligranulum</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.709659 INFO::Fitting model to feature number 76, Sutterella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.713776 INFO::Fitting model to feature number 77, Terrisporobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.717878 INFO::Fitting model to feature number 78, Turicibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.721924 INFO::Fitting model to feature number 79, Tuzzerella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.72599 INFO::Fitting model to feature number 80, Tyzzerella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.730034 INFO::Fitting model to feature number 81, UBA1819</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.734133 INFO::Fitting model to feature number 82, UCG.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.738212 INFO::Fitting model to feature number 83, UCG.003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.742338 INFO::Fitting model to feature number 84, UCG.005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.746497 INFO::Fitting model to feature number 85, Veillonella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.750615 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.754696 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.758765 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.762878 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.767056 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.771185 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.775296 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.779359 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.783436 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.787523 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.79159 INFO::Fitting model to feature number 96, unclassified.Chloroplast</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.795679 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.799751 INFO::Fitting model to feature number 98, unclassified.Clostridia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.803801 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.807838 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.811925 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.815993 INFO::Fitting model to feature number 102, unclassified.Mitochondria</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.827484 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.831639 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.835698 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.839779 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.843884 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.863447 INFO::Counting total values for each feature</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:17.869231 INFO::Writing filtered data to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/features/filtered_data.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:18.014656 INFO::Writing filtered, normalized data to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/features/filtered_data_norm.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:18.16445 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/features/filtered_data_norm_transformed.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:18.437835 INFO::Writing residuals to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/fits/residuals.rds</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:18.512103 INFO::Writing fitted values to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/fits/fitted.rds</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:18.536584 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin195842d2cad5/all_results.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:18.538183 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin195842d2cad5/significant_results.tsv</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/MbioDataset-class.html b/reference/MbioDataset-class.html
index 6f65447..81fde18 100644
--- a/reference/MbioDataset-class.html
+++ b/reference/MbioDataset-class.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/MbioDataset-methods.html b/reference/MbioDataset-methods.html
index 202a191..06886ea 100644
--- a/reference/MbioDataset-methods.html
+++ b/reference/MbioDataset-methods.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/MicrobiomeDB-package.html b/reference/MicrobiomeDB-package.html
index 701cf8c..d642ad4 100644
--- a/reference/MicrobiomeDB-package.html
+++ b/reference/MicrobiomeDB-package.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/alphaDiv-methods.html b/reference/alphaDiv-methods.html
index 04b3e94..42dea96 100644
--- a/reference/alphaDiv-methods.html
+++ b/reference/alphaDiv-methods.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -93,11 +93,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>     method <span class="op">=</span> <span class="st">"shannon"</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:39.569741 Received df table with 3184 samples and 673 taxa.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:19.888041 Received df table with 3184 samples and 673 taxa.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:39.776032 shannon alpha diversity computation complete.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:20.061473 shannon alpha diversity computation complete.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:39.791467 Alpha diversity computation completed with parameters method= shannon</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:20.07684 Alpha diversity computation completed with parameters method= shannon</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/betaDiv-methods.html b/reference/betaDiv-methods.html
index fdece71..1a04864 100644
--- a/reference/betaDiv-methods.html
+++ b/reference/betaDiv-methods.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -99,13 +99,13 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>     k <span class="op">=</span> <span class="fl">2</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:40.793814 Received df table with 3184 samples and 673 taxa.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:21.020579 Received df table with 3184 samples and 673 taxa.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:46.014705 Computed dissimilarity matrix.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:26.282943 Computed dissimilarity matrix.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:55.804064 Finished ordination step.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:35.655616 Finished ordination step.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:55.814119 Beta diversity computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = bray , k = 2 , verbose = TRUE</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:35.665821 Beta diversity computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = bray , k = 2 , verbose = TRUE</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/correlation-methods.html b/reference/correlation-methods.html
index d537aee..6057bf9 100644
--- a/reference/correlation-methods.html
+++ b/reference/correlation-methods.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -117,9 +117,9 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>     format <span class="op">=</span> <span class="st">'data.table'</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:59.8707 Completed correlation with method=spearman. Formatting results.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:39.709734 Completed correlation with method=spearman. Formatting results.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:50:59.871895 Received df table with 3184 samples and 138 features with values.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:39.710918 Received df table with 3184 samples and 138 features with values.</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">correlationOutput</span> <span class="op">&lt;-</span> <span class="fu">correlation</span><span class="op">(</span></span></span>
 <span class="r-in"><span>     <span class="va">diabImmune_genus</span>, </span></span>
@@ -127,11 +127,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>     format <span class="op">=</span> <span class="st">'ComputeResult'</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:03.71643 Completed correlation with method=spearman. Formatting results.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:43.545779 Completed correlation with method=spearman. Formatting results.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:03.717338 Received df table with 3184 samples and 138 features with values.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:43.546683 Received df table with 3184 samples and 138 features with values.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:03.718841 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  spearman</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:43.548213 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  spearman</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">alsoCorrelationDT</span> <span class="op">&lt;-</span> <span class="fu"><a href="getComputeResult.html">getComputeResult</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>     <span class="va">correlationOutput</span>, </span></span>
diff --git a/reference/correlationNetwork.html b/reference/correlationNetwork.html
index 7539d55..ee79688 100644
--- a/reference/correlationNetwork.html
+++ b/reference/correlationNetwork.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/differentialAbundance-methods.html b/reference/differentialAbundance-methods.html
index e2d0e0a..e492f07 100644
--- a/reference/differentialAbundance-methods.html
+++ b/reference/differentialAbundance-methods.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -171,149 +171,149 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>       verbose<span class="op">=</span><span class="cn">TRUE</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:08.848187 Found NAs in specified variable. Removing these records.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.600773 Found NAs in specified variable. Removing these records.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:08.956962 Received abundance table with 2533 samples and 673 taxa.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.704625 Received abundance table with 2533 samples and 673 taxa.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:08.960321 Found 2533 samples with a value for breastfed_duration_days in either groupA or groupB. The calculation will continue with only these samples.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.707878 Found 2533 samples with a value for breastfed_duration_days in either groupA or groupB. The calculation will continue with only these samples.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output folder"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output feature tables folder"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output fits folder"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.097233 INFO::Writing function arguments to log file</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.100942 INFO::Verifying options selected are valid</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.101454 INFO::Determining format of input files</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.102681 INFO::Input format is data samples as rows and metadata samples as rows</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.114772 INFO::Formula for fixed effects: expr ~  breastfed_duration_days</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.11563 INFO::Filter data based on min abundance and min prevalence</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.116118 INFO::Total samples in data: 2533</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.116576 INFO::Min samples required with min abundance for a feature not to be filtered: 253.300000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.132821 INFO::Total filtered features: 521</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.133829 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Candidatus.Arthromitus, Candidatus.Obscuribacter, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Faecalicoccus, Faecalitalea, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavobacterium, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Marvinbryantia, Massilia, Megamonas, Merdibacter, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Myxococcus, NK4A214.group, Nakamurella, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phaseolibacter, Phocea, Phyllobacterium, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudoflavonifractor, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tetragenococcus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.140342 INFO::Total filtered features with variance filtering: 0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.140897 INFO::Filtered feature names from variance filtering:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.141359 INFO::Running selected normalization method: TSS</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.178366 INFO::Applying z-score to standardize continuous metadata</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.181467 INFO::Running selected transform method: LOG</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.230559 INFO::Running selected analysis method: LM</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.231382 INFO::Fitting model to feature number 1, Actinomyces</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.235458 INFO::Fitting model to feature number 2, Agathobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.239058 INFO::Fitting model to feature number 3, Akkermansia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.242643 INFO::Fitting model to feature number 4, Alistipes</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.2462 INFO::Fitting model to feature number 5, Anaerostipes</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.249805 INFO::Fitting model to feature number 6, Atopobium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.253407 INFO::Fitting model to feature number 7, Bacteroides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.257026 INFO::Fitting model to feature number 8, Barnesiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.260637 INFO::Fitting model to feature number 9, Bifidobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.26428 INFO::Fitting model to feature number 10, Bilophila</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.267891 INFO::Fitting model to feature number 11, Blautia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.271437 INFO::Fitting model to feature number 12, Butyricicoccus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.275046 INFO::Fitting model to feature number 13, CAG.352</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.278639 INFO::Fitting model to feature number 14, Campylobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.282255 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.285869 INFO::Fitting model to feature number 16, Clostridioides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.289578 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.293256 INFO::Fitting model to feature number 18, Colidextribacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.296987 INFO::Fitting model to feature number 19, Collinsella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.300686 INFO::Fitting model to feature number 20, Coprobacillus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.304319 INFO::Fitting model to feature number 21, Coprococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.307947 INFO::Fitting model to feature number 22, DTU089</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.311589 INFO::Fitting model to feature number 23, Dialister</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.315149 INFO::Fitting model to feature number 24, Dorea</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.31872 INFO::Fitting model to feature number 25, Eggerthella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.322355 INFO::Fitting model to feature number 26, Eisenbergiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.325932 INFO::Fitting model to feature number 27, Enterococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.329541 INFO::Fitting model to feature number 28, Erysipelatoclostridium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.333117 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.336723 INFO::Fitting model to feature number 30, Escherichia.Shigella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.340408 INFO::Fitting model to feature number 31, Faecalibacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.344066 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.347683 INFO::Fitting model to feature number 33, Flavonifractor</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.351283 INFO::Fitting model to feature number 34, Fusicatenibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.354934 INFO::Fitting model to feature number 35, Fusobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.358572 INFO::Fitting model to feature number 36, Gemella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.362232 INFO::Fitting model to feature number 37, Granulicatella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.365878 INFO::Fitting model to feature number 38, Haemophilus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.36954 INFO::Fitting model to feature number 39, Holdemania</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.373166 INFO::Fitting model to feature number 40, Hungatella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.376817 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.380442 INFO::Fitting model to feature number 42, Intestinibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.384087 INFO::Fitting model to feature number 43, Intestinimonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.387725 INFO::Fitting model to feature number 44, Klebsiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.391377 INFO::Fitting model to feature number 45, Lachnoclostridium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.395036 INFO::Fitting model to feature number 46, Lachnospira</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.398674 INFO::Fitting model to feature number 47, Lachnospiraceae.ND3007.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.402355 INFO::Fitting model to feature number 48, Lachnospiraceae.NK4A136.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.405987 INFO::Fitting model to feature number 49, Lachnospiraceae.UCG.001</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.409643 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.413275 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.009</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.416945 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.010</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.420584 INFO::Fitting model to feature number 53, Lactobacillus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.424252 INFO::Fitting model to feature number 54, Lactococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.427912 INFO::Fitting model to feature number 55, Mannheimia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.431534 INFO::Fitting model to feature number 56, Megasphaera</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.43524 INFO::Fitting model to feature number 57, Monoglobus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.438893 INFO::Fitting model to feature number 58, Neisseria</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.44252 INFO::Fitting model to feature number 59, Odoribacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.446161 INFO::Fitting model to feature number 60, Oscillibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.449859 INFO::Fitting model to feature number 61, Oscillospira</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.453526 INFO::Fitting model to feature number 62, Parabacteroides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.457191 INFO::Fitting model to feature number 63, Parasutterella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.460818 INFO::Fitting model to feature number 64, Phascolarctobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.464475 INFO::Fitting model to feature number 65, Prevotella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.468174 INFO::Fitting model to feature number 66, Pseudomonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.471798 INFO::Fitting model to feature number 67, Romboutsia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.475381 INFO::Fitting model to feature number 68, Roseburia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.478989 INFO::Fitting model to feature number 69, Rothia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.48265 INFO::Fitting model to feature number 70, Ruminococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.486321 INFO::Fitting model to feature number 71, Sellimonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.490161 INFO::Fitting model to feature number 72, Solobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.493887 INFO::Fitting model to feature number 73, Staphylococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.49755 INFO::Fitting model to feature number 74, Streptococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.501204 INFO::Fitting model to feature number 75, Subdoligranulum</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.504918 INFO::Fitting model to feature number 76, Sutterella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.508616 INFO::Fitting model to feature number 77, Terrisporobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.512367 INFO::Fitting model to feature number 78, Turicibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.516001 INFO::Fitting model to feature number 79, Tuzzerella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.519632 INFO::Fitting model to feature number 80, Tyzzerella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.523212 INFO::Fitting model to feature number 81, UBA1819</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.526892 INFO::Fitting model to feature number 82, UCG.002</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.53056 INFO::Fitting model to feature number 83, UCG.003</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.534178 INFO::Fitting model to feature number 84, UCG.005</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.537856 INFO::Fitting model to feature number 85, Veillonella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.541501 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.545154 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.548755 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.552369 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.555989 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.559635 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.563271 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.5669 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.570566 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.574254 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.578036 INFO::Fitting model to feature number 96, unclassified.Chloroplast</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.581705 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.585328 INFO::Fitting model to feature number 98, unclassified.Clostridia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.588966 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.592642 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.596264 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.599934 INFO::Fitting model to feature number 102, unclassified.Mitochondria</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.603577 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.607156 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.610804 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.614427 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.618058 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.633991 INFO::Counting total values for each feature</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.639237 INFO::Writing filtered data to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/features/filtered_data.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.766118 INFO::Writing filtered, normalized data to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/features/filtered_data_norm.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:09.887297 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/features/filtered_data_norm_transformed.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.103637 INFO::Writing residuals to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/fits/residuals.rds</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.158799 INFO::Writing fitted values to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/fits/fitted.rds</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.177932 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/all_results.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.179755 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/significant_results.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.843086 INFO::Writing function arguments to log file</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.846796 INFO::Verifying options selected are valid</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.847406 INFO::Determining format of input files</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.848624 INFO::Input format is data samples as rows and metadata samples as rows</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.860602 INFO::Formula for fixed effects: expr ~  breastfed_duration_days</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.861377 INFO::Filter data based on min abundance and min prevalence</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.861863 INFO::Total samples in data: 2533</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.862344 INFO::Min samples required with min abundance for a feature not to be filtered: 253.300000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.878531 INFO::Total filtered features: 521</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.879519 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Candidatus.Arthromitus, Candidatus.Obscuribacter, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Faecalicoccus, Faecalitalea, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavobacterium, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Marvinbryantia, Massilia, Megamonas, Merdibacter, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Myxococcus, NK4A214.group, Nakamurella, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phaseolibacter, Phocea, Phyllobacterium, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudoflavonifractor, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tetragenococcus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.885978 INFO::Total filtered features with variance filtering: 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.886525 INFO::Filtered feature names from variance filtering:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.887012 INFO::Running selected normalization method: TSS</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.923679 INFO::Applying z-score to standardize continuous metadata</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.926611 INFO::Running selected transform method: LOG</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.975602 INFO::Running selected analysis method: LM</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.976333 INFO::Fitting model to feature number 1, Actinomyces</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.980361 INFO::Fitting model to feature number 2, Agathobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.98392 INFO::Fitting model to feature number 3, Akkermansia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.987482 INFO::Fitting model to feature number 4, Alistipes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.991061 INFO::Fitting model to feature number 5, Anaerostipes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.994589 INFO::Fitting model to feature number 6, Atopobium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:48.998177 INFO::Fitting model to feature number 7, Bacteroides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.001764 INFO::Fitting model to feature number 8, Barnesiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.00534 INFO::Fitting model to feature number 9, Bifidobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.008974 INFO::Fitting model to feature number 10, Bilophila</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.012591 INFO::Fitting model to feature number 11, Blautia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.016168 INFO::Fitting model to feature number 12, Butyricicoccus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.019768 INFO::Fitting model to feature number 13, CAG.352</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.023367 INFO::Fitting model to feature number 14, Campylobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.02695 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.03051 INFO::Fitting model to feature number 16, Clostridioides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.034149 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.037743 INFO::Fitting model to feature number 18, Colidextribacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.041389 INFO::Fitting model to feature number 19, Collinsella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.044945 INFO::Fitting model to feature number 20, Coprobacillus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.048523 INFO::Fitting model to feature number 21, Coprococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.052146 INFO::Fitting model to feature number 22, DTU089</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.055731 INFO::Fitting model to feature number 23, Dialister</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.059315 INFO::Fitting model to feature number 24, Dorea</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.062861 INFO::Fitting model to feature number 25, Eggerthella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.067444 INFO::Fitting model to feature number 26, Eisenbergiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.072906 INFO::Fitting model to feature number 27, Enterococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.078475 INFO::Fitting model to feature number 28, Erysipelatoclostridium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.084011 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.08941 INFO::Fitting model to feature number 30, Escherichia.Shigella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.092985 INFO::Fitting model to feature number 31, Faecalibacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.096567 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.100204 INFO::Fitting model to feature number 33, Flavonifractor</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.103798 INFO::Fitting model to feature number 34, Fusicatenibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.107383 INFO::Fitting model to feature number 35, Fusobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.110925 INFO::Fitting model to feature number 36, Gemella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.114463 INFO::Fitting model to feature number 37, Granulicatella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.118025 INFO::Fitting model to feature number 38, Haemophilus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.121603 INFO::Fitting model to feature number 39, Holdemania</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.125136 INFO::Fitting model to feature number 40, Hungatella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.128701 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.132299 INFO::Fitting model to feature number 42, Intestinibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.135896 INFO::Fitting model to feature number 43, Intestinimonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.139476 INFO::Fitting model to feature number 44, Klebsiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.143127 INFO::Fitting model to feature number 45, Lachnoclostridium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.146711 INFO::Fitting model to feature number 46, Lachnospira</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.150302 INFO::Fitting model to feature number 47, Lachnospiraceae.ND3007.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.153897 INFO::Fitting model to feature number 48, Lachnospiraceae.NK4A136.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.15763 INFO::Fitting model to feature number 49, Lachnospiraceae.UCG.001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.16134 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.004</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.164931 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.009</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.168539 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.010</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.172123 INFO::Fitting model to feature number 53, Lactobacillus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.175735 INFO::Fitting model to feature number 54, Lactococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.17937 INFO::Fitting model to feature number 55, Mannheimia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.182969 INFO::Fitting model to feature number 56, Megasphaera</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.186574 INFO::Fitting model to feature number 57, Monoglobus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.190192 INFO::Fitting model to feature number 58, Neisseria</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.193823 INFO::Fitting model to feature number 59, Odoribacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.197427 INFO::Fitting model to feature number 60, Oscillibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.20107 INFO::Fitting model to feature number 61, Oscillospira</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.204689 INFO::Fitting model to feature number 62, Parabacteroides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.208342 INFO::Fitting model to feature number 63, Parasutterella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.211993 INFO::Fitting model to feature number 64, Phascolarctobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.215601 INFO::Fitting model to feature number 65, Prevotella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.219189 INFO::Fitting model to feature number 66, Pseudomonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.22276 INFO::Fitting model to feature number 67, Romboutsia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.226463 INFO::Fitting model to feature number 68, Roseburia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.23005 INFO::Fitting model to feature number 69, Rothia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.23365 INFO::Fitting model to feature number 70, Ruminococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.2373 INFO::Fitting model to feature number 71, Sellimonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.240968 INFO::Fitting model to feature number 72, Solobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.244585 INFO::Fitting model to feature number 73, Staphylococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.248228 INFO::Fitting model to feature number 74, Streptococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.251845 INFO::Fitting model to feature number 75, Subdoligranulum</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.255519 INFO::Fitting model to feature number 76, Sutterella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.259158 INFO::Fitting model to feature number 77, Terrisporobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.262745 INFO::Fitting model to feature number 78, Turicibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.266374 INFO::Fitting model to feature number 79, Tuzzerella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.269949 INFO::Fitting model to feature number 80, Tyzzerella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.273539 INFO::Fitting model to feature number 81, UBA1819</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.277157 INFO::Fitting model to feature number 82, UCG.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.280774 INFO::Fitting model to feature number 83, UCG.003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.284424 INFO::Fitting model to feature number 84, UCG.005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.288046 INFO::Fitting model to feature number 85, Veillonella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.291635 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.295258 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.298843 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.302456 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.306091 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.309665 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.313267 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.316923 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.320577 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.324228 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.327848 INFO::Fitting model to feature number 96, unclassified.Chloroplast</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.33145 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.335068 INFO::Fitting model to feature number 98, unclassified.Clostridia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.338648 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.342247 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.345847 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.349469 INFO::Fitting model to feature number 102, unclassified.Mitochondria</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.353108 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.356689 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.360342 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.363909 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.367611 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.383164 INFO::Counting total values for each feature</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.388217 INFO::Writing filtered data to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/features/filtered_data.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.504738 INFO::Writing filtered, normalized data to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/features/filtered_data_norm.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.624761 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/features/filtered_data_norm_transformed.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.839021 INFO::Writing residuals to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/fits/residuals.rds</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.893575 INFO::Writing fitted values to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/fits/fitted.rds</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.912584 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/all_results.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.91421 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/significant_results.tsv</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.181783 Completed method=Maaslin2. Formatting results.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.916079 Completed method=Maaslin2. Formatting results.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.185421 Differential abundance computation completed with parameters recordIdColumn =  16S_rRNA_(V4)_assay_Id , comparatorColName =  breastfed_duration_days , method =  Maaslin2 , groupA = groupA , groupB =  groupB</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:49.919326 Differential abundance computation completed with parameters recordIdColumn =  16S_rRNA_(V4)_assay_Id , comparatorColName =  breastfed_duration_days , method =  Maaslin2 , groupA = groupA , groupB =  groupB</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## a categorical variable with 3 values, one of which we exclude</span></span></span>
 <span class="r-in"><span><span class="va">diffAbundOutput</span> <span class="op">&lt;-</span> <span class="fu">MicrobiomeDB</span><span class="fu">::</span><span class="fu">differentialAbundance</span><span class="op">(</span></span></span>
@@ -327,137 +327,137 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output folder"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output feature tables folder"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output fits folder"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.472175 INFO::Writing function arguments to log file</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.475968 INFO::Verifying options selected are valid</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.476489 INFO::Determining format of input files</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.477783 INFO::Input format is data samples as rows and metadata samples as rows</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.49066 INFO::Formula for fixed effects: expr ~  country</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.491644 INFO::Filter data based on min abundance and min prevalence</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.492133 INFO::Total samples in data: 2692</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.492626 INFO::Min samples required with min abundance for a feature not to be filtered: 269.200000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.509655 INFO::Total filtered features: 521</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.510739 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asticcacaulis, Aureimonas, Bacillus, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Marinilactibacillus, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylobacillus, Methylobacterium.Methylorubrum, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, Paenibacillus, Paeniclostridium, Paludicola, Papillibacter, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Piscinibacter, Planifilum, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinivibrio, Sulfurospirillum, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gastranaerophilales, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.51758 INFO::Total filtered features with variance filtering: 0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.518154 INFO::Filtered feature names from variance filtering:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.518617 INFO::Running selected normalization method: TSS</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.570749 INFO::Applying z-score to standardize continuous metadata</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.573849 INFO::Running selected transform method: LOG</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.626987 INFO::Running selected analysis method: LM</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.627897 INFO::Fitting model to feature number 1, Actinomyces</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.632164 INFO::Fitting model to feature number 2, Agathobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.636015 INFO::Fitting model to feature number 3, Akkermansia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.639817 INFO::Fitting model to feature number 4, Alistipes</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.643527 INFO::Fitting model to feature number 5, Anaerostipes</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.647264 INFO::Fitting model to feature number 6, Atopobium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.651001 INFO::Fitting model to feature number 7, Bacteroides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.654754 INFO::Fitting model to feature number 8, Barnesiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.658484 INFO::Fitting model to feature number 9, Bifidobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.662206 INFO::Fitting model to feature number 10, Bilophila</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.665942 INFO::Fitting model to feature number 11, Blautia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.669673 INFO::Fitting model to feature number 12, Butyricicoccus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.67342 INFO::Fitting model to feature number 13, CAG.352</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.677135 INFO::Fitting model to feature number 14, Campylobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.680911 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.684646 INFO::Fitting model to feature number 16, Clostridioides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.688373 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.692153 INFO::Fitting model to feature number 18, Colidextribacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.695945 INFO::Fitting model to feature number 19, Collinsella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.69971 INFO::Fitting model to feature number 20, Coprobacillus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.703426 INFO::Fitting model to feature number 21, Coprococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.707182 INFO::Fitting model to feature number 22, Corynebacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.710906 INFO::Fitting model to feature number 23, DTU089</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.714686 INFO::Fitting model to feature number 24, Dialister</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.718477 INFO::Fitting model to feature number 25, Dorea</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.722259 INFO::Fitting model to feature number 26, Eggerthella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.72605 INFO::Fitting model to feature number 27, Eisenbergiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.729803 INFO::Fitting model to feature number 28, Enterococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.733574 INFO::Fitting model to feature number 29, Erysipelatoclostridium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.737375 INFO::Fitting model to feature number 30, Erysipelotrichaceae.UCG.003</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.741156 INFO::Fitting model to feature number 31, Escherichia.Shigella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.744953 INFO::Fitting model to feature number 32, Faecalibacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.748741 INFO::Fitting model to feature number 33, Family.XIII.AD3011.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.752519 INFO::Fitting model to feature number 34, Flavonifractor</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.756344 INFO::Fitting model to feature number 35, Fusicatenibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.76017 INFO::Fitting model to feature number 36, Fusobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.764029 INFO::Fitting model to feature number 37, Gemella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.769405 INFO::Fitting model to feature number 38, Gordonibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.775218 INFO::Fitting model to feature number 39, Granulicatella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.781141 INFO::Fitting model to feature number 40, Haemophilus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.78698 INFO::Fitting model to feature number 41, Holdemania</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.791312 INFO::Fitting model to feature number 42, Hungatella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.79505 INFO::Fitting model to feature number 43, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.798803 INFO::Fitting model to feature number 44, Intestinibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.802514 INFO::Fitting model to feature number 45, Intestinimonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.80625 INFO::Fitting model to feature number 46, Klebsiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.809972 INFO::Fitting model to feature number 47, Lachnoclostridium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.813697 INFO::Fitting model to feature number 48, Lachnospira</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.817451 INFO::Fitting model to feature number 49, Lachnospiraceae.ND3007.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.821231 INFO::Fitting model to feature number 50, Lachnospiraceae.NK4A136.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.824974 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.001</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.828727 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.832465 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.009</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.836181 INFO::Fitting model to feature number 54, Lachnospiraceae.UCG.010</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.839871 INFO::Fitting model to feature number 55, Lactobacillus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.843587 INFO::Fitting model to feature number 56, Lactococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.847297 INFO::Fitting model to feature number 57, Mannheimia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.850981 INFO::Fitting model to feature number 58, Megasphaera</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.85479 INFO::Fitting model to feature number 59, Monoglobus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.858541 INFO::Fitting model to feature number 60, Neisseria</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.862243 INFO::Fitting model to feature number 61, Odoribacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.865965 INFO::Fitting model to feature number 62, Oscillibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.869746 INFO::Fitting model to feature number 63, Oscillospira</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.873487 INFO::Fitting model to feature number 64, Parabacteroides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.877286 INFO::Fitting model to feature number 65, Parasutterella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.881036 INFO::Fitting model to feature number 66, Prevotella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.88484 INFO::Fitting model to feature number 67, Pseudomonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.888625 INFO::Fitting model to feature number 68, Romboutsia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.892438 INFO::Fitting model to feature number 69, Roseburia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.89642 INFO::Fitting model to feature number 70, Rothia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.900202 INFO::Fitting model to feature number 71, Ruminococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.904021 INFO::Fitting model to feature number 72, Sellimonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.907835 INFO::Fitting model to feature number 73, Solobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.911615 INFO::Fitting model to feature number 74, Staphylococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.915434 INFO::Fitting model to feature number 75, Streptococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.919264 INFO::Fitting model to feature number 76, Subdoligranulum</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.923058 INFO::Fitting model to feature number 77, Sutterella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.926849 INFO::Fitting model to feature number 78, Terrisporobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.930625 INFO::Fitting model to feature number 79, Turicibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.934417 INFO::Fitting model to feature number 80, Tuzzerella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.938244 INFO::Fitting model to feature number 81, Tyzzerella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.942025 INFO::Fitting model to feature number 82, UBA1819</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.945811 INFO::Fitting model to feature number 83, UCG.002</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.94957 INFO::Fitting model to feature number 84, UCG.003</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.953444 INFO::Fitting model to feature number 85, UCG.005</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.957261 INFO::Fitting model to feature number 86, Veillonella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.961042 INFO::Fitting model to feature number 87, X.Clostridium..innocuum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.964842 INFO::Fitting model to feature number 88, X.Eubacterium..eligens.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.968675 INFO::Fitting model to feature number 89, X.Eubacterium..fissicatena.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.972506 INFO::Fitting model to feature number 90, X.Eubacterium..hallii.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.976315 INFO::Fitting model to feature number 91, X.Eubacterium..siraeum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.98014 INFO::Fitting model to feature number 92, X.Eubacterium..ventriosum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.983917 INFO::Fitting model to feature number 93, X.Eubacterium..xylanophilum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.987715 INFO::Fitting model to feature number 94, X.Ruminococcus..gauvreauii.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.991523 INFO::Fitting model to feature number 95, X.Ruminococcus..gnavus.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.995312 INFO::Fitting model to feature number 96, X.Ruminococcus..torques.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:10.999141 INFO::Fitting model to feature number 97, unclassified.Chloroplast</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.00288 INFO::Fitting model to feature number 98, unclassified.Clostridia.UCG.014</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.006635 INFO::Fitting model to feature number 99, unclassified.Clostridia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.010418 INFO::Fitting model to feature number 100, unclassified.Clostridia.vadinBB60.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.014205 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.018021 INFO::Fitting model to feature number 102, unclassified.Mitochondria</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.021864 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.025646 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.029402 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.033162 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.036959 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.052416 INFO::Counting total values for each feature</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.057658 INFO::Writing filtered data to file /tmp/RtmpXpuOxT/maaslin194e36845449/features/filtered_data.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.18178 INFO::Writing filtered, normalized data to file /tmp/RtmpXpuOxT/maaslin194e36845449/features/filtered_data_norm.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.311745 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpXpuOxT/maaslin194e36845449/features/filtered_data_norm_transformed.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.540246 INFO::Writing residuals to file /tmp/RtmpXpuOxT/maaslin194e36845449/fits/residuals.rds</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.600622 INFO::Writing fitted values to file /tmp/RtmpXpuOxT/maaslin194e36845449/fits/fitted.rds</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.620542 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e36845449/all_results.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.622221 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e36845449/significant_results.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.196045 INFO::Writing function arguments to log file</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.199926 INFO::Verifying options selected are valid</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.200479 INFO::Determining format of input files</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.201769 INFO::Input format is data samples as rows and metadata samples as rows</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.214262 INFO::Formula for fixed effects: expr ~  country</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.21509 INFO::Filter data based on min abundance and min prevalence</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.215583 INFO::Total samples in data: 2692</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.216047 INFO::Min samples required with min abundance for a feature not to be filtered: 269.200000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.232627 INFO::Total filtered features: 521</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.23363 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asticcacaulis, Aureimonas, Bacillus, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Marinilactibacillus, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylobacillus, Methylobacterium.Methylorubrum, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, Paenibacillus, Paeniclostridium, Paludicola, Papillibacter, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Piscinibacter, Planifilum, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinivibrio, Sulfurospirillum, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gastranaerophilales, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.240345 INFO::Total filtered features with variance filtering: 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.240901 INFO::Filtered feature names from variance filtering:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.241369 INFO::Running selected normalization method: TSS</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.292056 INFO::Applying z-score to standardize continuous metadata</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.295007 INFO::Running selected transform method: LOG</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.347621 INFO::Running selected analysis method: LM</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.348336 INFO::Fitting model to feature number 1, Actinomyces</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.352555 INFO::Fitting model to feature number 2, Agathobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.356368 INFO::Fitting model to feature number 3, Akkermansia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.36011 INFO::Fitting model to feature number 4, Alistipes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.363925 INFO::Fitting model to feature number 5, Anaerostipes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.367708 INFO::Fitting model to feature number 6, Atopobium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.371444 INFO::Fitting model to feature number 7, Bacteroides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.375173 INFO::Fitting model to feature number 8, Barnesiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.378835 INFO::Fitting model to feature number 9, Bifidobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.38256 INFO::Fitting model to feature number 10, Bilophila</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.386305 INFO::Fitting model to feature number 11, Blautia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.389993 INFO::Fitting model to feature number 12, Butyricicoccus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.39375 INFO::Fitting model to feature number 13, CAG.352</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.397455 INFO::Fitting model to feature number 14, Campylobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.40119 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.404904 INFO::Fitting model to feature number 16, Clostridioides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.408609 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.412314 INFO::Fitting model to feature number 18, Colidextribacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.416275 INFO::Fitting model to feature number 19, Collinsella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.420022 INFO::Fitting model to feature number 20, Coprobacillus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.423736 INFO::Fitting model to feature number 21, Coprococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.427498 INFO::Fitting model to feature number 22, Corynebacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.431297 INFO::Fitting model to feature number 23, DTU089</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.435004 INFO::Fitting model to feature number 24, Dialister</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.438678 INFO::Fitting model to feature number 25, Dorea</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.442431 INFO::Fitting model to feature number 26, Eggerthella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.446229 INFO::Fitting model to feature number 27, Eisenbergiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.450008 INFO::Fitting model to feature number 28, Enterococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.453808 INFO::Fitting model to feature number 29, Erysipelatoclostridium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.457582 INFO::Fitting model to feature number 30, Erysipelotrichaceae.UCG.003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.461339 INFO::Fitting model to feature number 31, Escherichia.Shigella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.465102 INFO::Fitting model to feature number 32, Faecalibacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.468873 INFO::Fitting model to feature number 33, Family.XIII.AD3011.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.472607 INFO::Fitting model to feature number 34, Flavonifractor</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.476376 INFO::Fitting model to feature number 35, Fusicatenibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.480095 INFO::Fitting model to feature number 36, Fusobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.483825 INFO::Fitting model to feature number 37, Gemella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.487579 INFO::Fitting model to feature number 38, Gordonibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.491306 INFO::Fitting model to feature number 39, Granulicatella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.49501 INFO::Fitting model to feature number 40, Haemophilus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.498741 INFO::Fitting model to feature number 41, Holdemania</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.502461 INFO::Fitting model to feature number 42, Hungatella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.506173 INFO::Fitting model to feature number 43, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.509959 INFO::Fitting model to feature number 44, Intestinibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.51371 INFO::Fitting model to feature number 45, Intestinimonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.517435 INFO::Fitting model to feature number 46, Klebsiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.521145 INFO::Fitting model to feature number 47, Lachnoclostridium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.524839 INFO::Fitting model to feature number 48, Lachnospira</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.528552 INFO::Fitting model to feature number 49, Lachnospiraceae.ND3007.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.53229 INFO::Fitting model to feature number 50, Lachnospiraceae.NK4A136.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.536035 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.539745 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.004</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.543442 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.009</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.547173 INFO::Fitting model to feature number 54, Lachnospiraceae.UCG.010</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.550853 INFO::Fitting model to feature number 55, Lactobacillus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.554646 INFO::Fitting model to feature number 56, Lactococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.558405 INFO::Fitting model to feature number 57, Mannheimia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.562241 INFO::Fitting model to feature number 58, Megasphaera</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.565961 INFO::Fitting model to feature number 59, Monoglobus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.569868 INFO::Fitting model to feature number 60, Neisseria</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.57365 INFO::Fitting model to feature number 61, Odoribacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.577368 INFO::Fitting model to feature number 62, Oscillibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.581139 INFO::Fitting model to feature number 63, Oscillospira</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.584899 INFO::Fitting model to feature number 64, Parabacteroides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.588673 INFO::Fitting model to feature number 65, Parasutterella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.592399 INFO::Fitting model to feature number 66, Prevotella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.596152 INFO::Fitting model to feature number 67, Pseudomonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.599874 INFO::Fitting model to feature number 68, Romboutsia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.603612 INFO::Fitting model to feature number 69, Roseburia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.607336 INFO::Fitting model to feature number 70, Rothia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.611045 INFO::Fitting model to feature number 71, Ruminococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.614707 INFO::Fitting model to feature number 72, Sellimonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.618438 INFO::Fitting model to feature number 73, Solobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.622171 INFO::Fitting model to feature number 74, Staphylococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.625948 INFO::Fitting model to feature number 75, Streptococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.629743 INFO::Fitting model to feature number 76, Subdoligranulum</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.633482 INFO::Fitting model to feature number 77, Sutterella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.637209 INFO::Fitting model to feature number 78, Terrisporobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.640958 INFO::Fitting model to feature number 79, Turicibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.644702 INFO::Fitting model to feature number 80, Tuzzerella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.648438 INFO::Fitting model to feature number 81, Tyzzerella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.652151 INFO::Fitting model to feature number 82, UBA1819</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.655933 INFO::Fitting model to feature number 83, UCG.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.659814 INFO::Fitting model to feature number 84, UCG.003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.663595 INFO::Fitting model to feature number 85, UCG.005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.667338 INFO::Fitting model to feature number 86, Veillonella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.671224 INFO::Fitting model to feature number 87, X.Clostridium..innocuum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.674993 INFO::Fitting model to feature number 88, X.Eubacterium..eligens.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.678745 INFO::Fitting model to feature number 89, X.Eubacterium..fissicatena.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.68253 INFO::Fitting model to feature number 90, X.Eubacterium..hallii.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.686319 INFO::Fitting model to feature number 91, X.Eubacterium..siraeum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.690114 INFO::Fitting model to feature number 92, X.Eubacterium..ventriosum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.693877 INFO::Fitting model to feature number 93, X.Eubacterium..xylanophilum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.697619 INFO::Fitting model to feature number 94, X.Ruminococcus..gauvreauii.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.701468 INFO::Fitting model to feature number 95, X.Ruminococcus..gnavus.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.705246 INFO::Fitting model to feature number 96, X.Ruminococcus..torques.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.709061 INFO::Fitting model to feature number 97, unclassified.Chloroplast</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.712789 INFO::Fitting model to feature number 98, unclassified.Clostridia.UCG.014</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.716518 INFO::Fitting model to feature number 99, unclassified.Clostridia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.720244 INFO::Fitting model to feature number 100, unclassified.Clostridia.vadinBB60.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.723988 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.727733 INFO::Fitting model to feature number 102, unclassified.Mitochondria</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.731469 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.73519 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.738885 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.742623 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.746359 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.761322 INFO::Counting total values for each feature</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.766469 INFO::Writing filtered data to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/features/filtered_data.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:50.889727 INFO::Writing filtered, normalized data to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/features/filtered_data_norm.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.018245 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/features/filtered_data_norm_transformed.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.258202 INFO::Writing residuals to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/fits/residuals.rds</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.318386 INFO::Writing fitted values to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/fits/fitted.rds</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.33811 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/all_results.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.339837 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/significant_results.tsv</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## a categorical variable with 2 values</span></span></span>
 <span class="r-in"><span><span class="va">diffAbundOutput</span> <span class="op">&lt;-</span> <span class="fu">MicrobiomeDB</span><span class="fu">::</span><span class="fu">differentialAbundance</span><span class="op">(</span></span></span>
@@ -469,137 +469,137 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output folder"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output feature tables folder"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Creating output fits folder"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.943767 INFO::Writing function arguments to log file</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.947457 INFO::Verifying options selected are valid</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.948004 INFO::Determining format of input files</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.949487 INFO::Input format is data samples as rows and metadata samples as rows</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.964072 INFO::Formula for fixed effects: expr ~  delivery_mode</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.964972 INFO::Filter data based on min abundance and min prevalence</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.965457 INFO::Total samples in data: 3184</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.965918 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.985696 INFO::Total filtered features: 563</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.986722 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.994362 INFO::Total filtered features with variance filtering: 0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.994928 INFO::Filtered feature names from variance filtering:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:11.995388 INFO::Running selected normalization method: TSS</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.04412 INFO::Applying z-score to standardize continuous metadata</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.047171 INFO::Running selected transform method: LOG</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.11105 INFO::Running selected analysis method: LM</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.11193 INFO::Fitting model to feature number 1, Actinomyces</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.116581 INFO::Fitting model to feature number 2, Agathobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.120772 INFO::Fitting model to feature number 3, Akkermansia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.124941 INFO::Fitting model to feature number 4, Alistipes</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.129074 INFO::Fitting model to feature number 5, Anaerostipes</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.1332 INFO::Fitting model to feature number 6, Atopobium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.137281 INFO::Fitting model to feature number 7, Bacteroides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.141403 INFO::Fitting model to feature number 8, Barnesiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.145457 INFO::Fitting model to feature number 9, Bifidobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.14956 INFO::Fitting model to feature number 10, Bilophila</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.153613 INFO::Fitting model to feature number 11, Blautia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.157671 INFO::Fitting model to feature number 12, Butyricicoccus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.161767 INFO::Fitting model to feature number 13, CAG.352</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.165833 INFO::Fitting model to feature number 14, Campylobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.16993 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.174026 INFO::Fitting model to feature number 16, Clostridioides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.178134 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.18224 INFO::Fitting model to feature number 18, Colidextribacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.186364 INFO::Fitting model to feature number 19, Collinsella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.190536 INFO::Fitting model to feature number 20, Coprobacillus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.194659 INFO::Fitting model to feature number 21, Coprococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.198787 INFO::Fitting model to feature number 22, DTU089</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.202933 INFO::Fitting model to feature number 23, Dialister</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.207039 INFO::Fitting model to feature number 24, Dorea</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.211143 INFO::Fitting model to feature number 25, Eggerthella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.215236 INFO::Fitting model to feature number 26, Eisenbergiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.219383 INFO::Fitting model to feature number 27, Enterococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.223527 INFO::Fitting model to feature number 28, Erysipelatoclostridium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.227646 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.231746 INFO::Fitting model to feature number 30, Escherichia.Shigella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.235831 INFO::Fitting model to feature number 31, Faecalibacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.23993 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.244063 INFO::Fitting model to feature number 33, Flavonifractor</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.248202 INFO::Fitting model to feature number 34, Fusicatenibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.252374 INFO::Fitting model to feature number 35, Fusobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.256522 INFO::Fitting model to feature number 36, Gemella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.26069 INFO::Fitting model to feature number 37, Granulicatella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.26481 INFO::Fitting model to feature number 38, Haemophilus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.268952 INFO::Fitting model to feature number 39, Holdemania</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.273063 INFO::Fitting model to feature number 40, Hungatella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.277163 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.281285 INFO::Fitting model to feature number 42, Intestinibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.285474 INFO::Fitting model to feature number 43, Intestinimonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.289644 INFO::Fitting model to feature number 44, Klebsiella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.293754 INFO::Fitting model to feature number 45, Lachnoclostridium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.297914 INFO::Fitting model to feature number 46, Lachnospira</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.314676 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.319063 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.32337 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.327633 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.33181 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.335998 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.340224 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.344447 INFO::Fitting model to feature number 54, Lactobacillus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.348625 INFO::Fitting model to feature number 55, Lactococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.352767 INFO::Fitting model to feature number 56, Mannheimia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.356889 INFO::Fitting model to feature number 57, Megasphaera</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.361008 INFO::Fitting model to feature number 58, Monoglobus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.36511 INFO::Fitting model to feature number 59, Neisseria</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.369211 INFO::Fitting model to feature number 60, Odoribacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.373294 INFO::Fitting model to feature number 61, Oscillibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.377416 INFO::Fitting model to feature number 62, Oscillospira</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.381511 INFO::Fitting model to feature number 63, Parabacteroides</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.385606 INFO::Fitting model to feature number 64, Parasutterella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.389753 INFO::Fitting model to feature number 65, Prevotella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.393852 INFO::Fitting model to feature number 66, Pseudomonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.397985 INFO::Fitting model to feature number 67, Romboutsia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.402123 INFO::Fitting model to feature number 68, Roseburia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.406248 INFO::Fitting model to feature number 69, Rothia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.410368 INFO::Fitting model to feature number 70, Ruminococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.414539 INFO::Fitting model to feature number 71, Sellimonas</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.418649 INFO::Fitting model to feature number 72, Solobacterium</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.42274 INFO::Fitting model to feature number 73, Staphylococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.426823 INFO::Fitting model to feature number 74, Streptococcus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.430968 INFO::Fitting model to feature number 75, Subdoligranulum</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.435097 INFO::Fitting model to feature number 76, Sutterella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.439275 INFO::Fitting model to feature number 77, Terrisporobacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.44342 INFO::Fitting model to feature number 78, Turicibacter</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.447555 INFO::Fitting model to feature number 79, Tuzzerella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.451684 INFO::Fitting model to feature number 80, Tyzzerella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.455791 INFO::Fitting model to feature number 81, UBA1819</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.459931 INFO::Fitting model to feature number 82, UCG.002</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.464082 INFO::Fitting model to feature number 83, UCG.003</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.468238 INFO::Fitting model to feature number 84, UCG.005</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.472381 INFO::Fitting model to feature number 85, Veillonella</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.476564 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.48072 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.484896 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.489138 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.493288 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.497476 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.501643 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.505765 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.509953 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.51412 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.518234 INFO::Fitting model to feature number 96, unclassified.Chloroplast</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.522321 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.526482 INFO::Fitting model to feature number 98, unclassified.Clostridia</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.530657 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.534753 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.538822 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.542972 INFO::Fitting model to feature number 102, unclassified.Mitochondria</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.547074 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.551182 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.555286 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.55942 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.563591 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.580038 INFO::Counting total values for each feature</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.585433 INFO::Writing filtered data to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/features/filtered_data.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.731498 INFO::Writing filtered, normalized data to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/features/filtered_data_norm.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:12.881629 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/features/filtered_data_norm_transformed.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:13.154268 INFO::Writing residuals to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/fits/residuals.rds</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:13.224374 INFO::Writing fitted values to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/fits/fitted.rds</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:13.248273 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e625efd4a/all_results.tsv</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:13.249922 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e625efd4a/significant_results.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.641871 INFO::Writing function arguments to log file</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.6457 INFO::Verifying options selected are valid</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.646238 INFO::Determining format of input files</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.647745 INFO::Input format is data samples as rows and metadata samples as rows</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.662126 INFO::Formula for fixed effects: expr ~  delivery_mode</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.662966 INFO::Filter data based on min abundance and min prevalence</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.663476 INFO::Total samples in data: 3184</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.663964 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.683603 INFO::Total filtered features: 563</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.684458 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.691984 INFO::Total filtered features with variance filtering: 0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.692518 INFO::Filtered feature names from variance filtering:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.692974 INFO::Running selected normalization method: TSS</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.741262 INFO::Applying z-score to standardize continuous metadata</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.744238 INFO::Running selected transform method: LOG</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.807753 INFO::Running selected analysis method: LM</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.808467 INFO::Fitting model to feature number 1, Actinomyces</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.813009 INFO::Fitting model to feature number 2, Agathobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.817101 INFO::Fitting model to feature number 3, Akkermansia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.821279 INFO::Fitting model to feature number 4, Alistipes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.825387 INFO::Fitting model to feature number 5, Anaerostipes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.829515 INFO::Fitting model to feature number 6, Atopobium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.833546 INFO::Fitting model to feature number 7, Bacteroides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.837641 INFO::Fitting model to feature number 8, Barnesiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.841688 INFO::Fitting model to feature number 9, Bifidobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.84576 INFO::Fitting model to feature number 10, Bilophila</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.849827 INFO::Fitting model to feature number 11, Blautia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.853912 INFO::Fitting model to feature number 12, Butyricicoccus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.857984 INFO::Fitting model to feature number 13, CAG.352</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.862052 INFO::Fitting model to feature number 14, Campylobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.866104 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.870146 INFO::Fitting model to feature number 16, Clostridioides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.874193 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.878295 INFO::Fitting model to feature number 18, Colidextribacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.882366 INFO::Fitting model to feature number 19, Collinsella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.886409 INFO::Fitting model to feature number 20, Coprobacillus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.890463 INFO::Fitting model to feature number 21, Coprococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.894513 INFO::Fitting model to feature number 22, DTU089</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.898586 INFO::Fitting model to feature number 23, Dialister</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.902681 INFO::Fitting model to feature number 24, Dorea</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.906735 INFO::Fitting model to feature number 25, Eggerthella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.910797 INFO::Fitting model to feature number 26, Eisenbergiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.914993 INFO::Fitting model to feature number 27, Enterococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.91906 INFO::Fitting model to feature number 28, Erysipelatoclostridium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.92312 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.927198 INFO::Fitting model to feature number 30, Escherichia.Shigella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.931323 INFO::Fitting model to feature number 31, Faecalibacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.935394 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.939488 INFO::Fitting model to feature number 33, Flavonifractor</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.943558 INFO::Fitting model to feature number 34, Fusicatenibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.947632 INFO::Fitting model to feature number 35, Fusobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.951736 INFO::Fitting model to feature number 36, Gemella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.955823 INFO::Fitting model to feature number 37, Granulicatella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.959917 INFO::Fitting model to feature number 38, Haemophilus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.964061 INFO::Fitting model to feature number 39, Holdemania</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.96823 INFO::Fitting model to feature number 40, Hungatella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.97232 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis.</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.976407 INFO::Fitting model to feature number 42, Intestinibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.980541 INFO::Fitting model to feature number 43, Intestinimonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.984639 INFO::Fitting model to feature number 44, Klebsiella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.988772 INFO::Fitting model to feature number 45, Lachnoclostridium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:51.992852 INFO::Fitting model to feature number 46, Lachnospira</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.00783 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.012055 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.016165 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.020285 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.024375 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.028476 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.032567 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.036638 INFO::Fitting model to feature number 54, Lactobacillus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.040771 INFO::Fitting model to feature number 55, Lactococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.044824 INFO::Fitting model to feature number 56, Mannheimia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.048883 INFO::Fitting model to feature number 57, Megasphaera</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.052965 INFO::Fitting model to feature number 58, Monoglobus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.057095 INFO::Fitting model to feature number 59, Neisseria</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.061193 INFO::Fitting model to feature number 60, Odoribacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.065239 INFO::Fitting model to feature number 61, Oscillibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.069337 INFO::Fitting model to feature number 62, Oscillospira</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.073477 INFO::Fitting model to feature number 63, Parabacteroides</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.077561 INFO::Fitting model to feature number 64, Parasutterella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.081631 INFO::Fitting model to feature number 65, Prevotella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.085779 INFO::Fitting model to feature number 66, Pseudomonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.089899 INFO::Fitting model to feature number 67, Romboutsia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.093973 INFO::Fitting model to feature number 68, Roseburia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.098027 INFO::Fitting model to feature number 69, Rothia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.102139 INFO::Fitting model to feature number 70, Ruminococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.106226 INFO::Fitting model to feature number 71, Sellimonas</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.110327 INFO::Fitting model to feature number 72, Solobacterium</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.114395 INFO::Fitting model to feature number 73, Staphylococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.118479 INFO::Fitting model to feature number 74, Streptococcus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.122612 INFO::Fitting model to feature number 75, Subdoligranulum</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.126734 INFO::Fitting model to feature number 76, Sutterella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.130818 INFO::Fitting model to feature number 77, Terrisporobacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.135185 INFO::Fitting model to feature number 78, Turicibacter</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.139626 INFO::Fitting model to feature number 79, Tuzzerella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.143763 INFO::Fitting model to feature number 80, Tyzzerella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.147933 INFO::Fitting model to feature number 81, UBA1819</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.152114 INFO::Fitting model to feature number 82, UCG.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.156343 INFO::Fitting model to feature number 83, UCG.003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.16053 INFO::Fitting model to feature number 84, UCG.005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.164685 INFO::Fitting model to feature number 85, Veillonella</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.168866 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.172972 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.177117 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.181239 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.185343 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.189446 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.193608 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.197704 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.201757 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.205876 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.209989 INFO::Fitting model to feature number 96, unclassified.Chloroplast</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.214132 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.218226 INFO::Fitting model to feature number 98, unclassified.Clostridia</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.222431 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.226542 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.230672 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.234797 INFO::Fitting model to feature number 102, unclassified.Mitochondria</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.238919 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.243027 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.247104 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.251336 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.255428 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.271535 INFO::Counting total values for each feature</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.276874 INFO::Writing filtered data to file /tmp/RtmpfBGTvS/maaslin195822b50425/features/filtered_data.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.421668 INFO::Writing filtered, normalized data to file /tmp/RtmpfBGTvS/maaslin195822b50425/features/filtered_data_norm.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.619771 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpfBGTvS/maaslin195822b50425/features/filtered_data_norm_transformed.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.892076 INFO::Writing residuals to file /tmp/RtmpfBGTvS/maaslin195822b50425/fits/residuals.rds</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.962332 INFO::Writing fitted values to file /tmp/RtmpfBGTvS/maaslin195822b50425/fits/fitted.rds</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.986202 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin195822b50425/all_results.tsv</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:52.987827 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin195822b50425/significant_results.tsv</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/getCollection.html b/reference/getCollection.html
index 0222023..d497b7f 100644
--- a/reference/getCollection.html
+++ b/reference/getCollection.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getCollectionNames-MbioDataset-method.html b/reference/getCollectionNames-MbioDataset-method.html
index 00fc8ae..f6a0266 100644
--- a/reference/getCollectionNames-MbioDataset-method.html
+++ b/reference/getCollectionNames-MbioDataset-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getCollectionVariableNames-MbioDataset-method.html b/reference/getCollectionVariableNames-MbioDataset-method.html
index 0f68203..9c7577a 100644
--- a/reference/getCollectionVariableNames-MbioDataset-method.html
+++ b/reference/getCollectionVariableNames-MbioDataset-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getComputeResult.html b/reference/getComputeResult.html
index ecc8b04..4dc2a52 100644
--- a/reference/getComputeResult.html
+++ b/reference/getComputeResult.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -116,9 +116,9 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>     verbose<span class="op">=</span><span class="cn">FALSE</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:14.283316 Removed 1 records with no data.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:54.012372 Removed 1 records with no data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:14.29003 Removed 1 records with no data.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:54.019006 Removed 1 records with no data.</span>
 <span class="r-in"><span><span class="va">correlationDT</span> <span class="op">&lt;-</span> <span class="fu">getComputeResult</span><span class="op">(</span><span class="va">correlationOutput</span>, <span class="st">"data.table"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">correlationIGraph</span> <span class="op">&lt;-</span> <span class="fu">getComputeResult</span><span class="op">(</span><span class="va">correlationOutput</span>, <span class="st">"igraph"</span><span class="op">)</span></span></span>
 </code></pre></div>
diff --git a/reference/getComputeResultWithMetadata.html b/reference/getComputeResultWithMetadata.html
index 7cf004c..b56ea75 100644
--- a/reference/getComputeResultWithMetadata.html
+++ b/reference/getComputeResultWithMetadata.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getMetadataVariableNames-MbioDataset-method.html b/reference/getMetadataVariableNames-MbioDataset-method.html
index a53f4d8..99d965d 100644
--- a/reference/getMetadataVariableNames-MbioDataset-method.html
+++ b/reference/getMetadataVariableNames-MbioDataset-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getMetadataVariableSummary-MbioDataset-method.html b/reference/getMetadataVariableSummary-MbioDataset-method.html
index 83c66ef..1cfa8ac 100644
--- a/reference/getMetadataVariableSummary-MbioDataset-method.html
+++ b/reference/getMetadataVariableSummary-MbioDataset-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getSampleMetadata-MbioDataset-method.html b/reference/getSampleMetadata-MbioDataset-method.html
index ffacbd8..a1421a3 100644
--- a/reference/getSampleMetadata-MbioDataset-method.html
+++ b/reference/getSampleMetadata-MbioDataset-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getSampleMetadataIdColumns-MbioDataset-method.html b/reference/getSampleMetadataIdColumns-MbioDataset-method.html
index 96b9ea3..b5ddd33 100644
--- a/reference/getSampleMetadataIdColumns-MbioDataset-method.html
+++ b/reference/getSampleMetadataIdColumns-MbioDataset-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getVariables.html b/reference/getVariables.html
index bbc5d9c..506d704 100644
--- a/reference/getVariables.html
+++ b/reference/getVariables.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -842,7 +842,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>     <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:15.706984 Removed 300 records with no data.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:55.430157 Removed 300 records with no data.</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/index.html b/reference/index.html
index 0d93a26..488daf3 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rankedAbundance-methods.html b/reference/rankedAbundance-methods.html
index d15999e..25368ed 100644
--- a/reference/rankedAbundance-methods.html
+++ b/reference/rankedAbundance-methods.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -98,11 +98,11 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>     method <span class="op">=</span> <span class="st">"median"</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:16.079002 Received df table with 3184 samples and 673 taxa.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:55.798224 Received df table with 3184 samples and 673 taxa.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:16.168237 Finished ranking taxa</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:55.884543 Finished ranking taxa</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:16.178349 Ranked abundance computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = median , cutoff = 10 , naToZero =  TRUE , verbose = TRUE</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:55.894467 Ranked abundance computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = median , cutoff = 10 , naToZero =  TRUE , verbose = TRUE</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/selfCorrelation-methods.html b/reference/selfCorrelation-methods.html
index 1d19710..6f2da8b 100644
--- a/reference/selfCorrelation-methods.html
+++ b/reference/selfCorrelation-methods.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -107,15 +107,15 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>     format <span class="op">=</span> <span class="st">'data.table'</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:16.454713 Removed 1 records with no data.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:56.16955 Removed 1 records with no data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:16.461387 Removed 1 records with no data.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:56.176495 Removed 1 records with no data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 16:51:16.467786 Removed 1 records with no data.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:16:56.182957 Removed 1 records with no data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:01:15.654585 Completed correlation with method=sparcc. Formatting results.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:26:52.297835 Completed correlation with method=sparcc. Formatting results.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:01:15.65553 Received df table with 3183 samples and 21 features with abundances.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:26:52.298797 Received df table with 3183 samples and 21 features with abundances.</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">correlationOutput</span> <span class="op">&lt;-</span> <span class="fu">selfCorrelation</span><span class="op">(</span></span></span>
 <span class="r-in"><span>     <span class="fu"><a href="getCollection.html">getCollection</a></span><span class="op">(</span><span class="fu">microbiomeData</span><span class="fu">::</span><span class="va"><a href="https://microbiomedb.github.io/microbiomeData/reference/DiabImmune.html" class="external-link">DiabImmune</a></span>, <span class="st">"16S (V4) Genus"</span><span class="op">)</span>, </span></span>
@@ -123,17 +123,17 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>     format <span class="op">=</span> <span class="st">'ComputeResult'</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:01:15.792888 Removed 1 records with no data.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:26:52.428313 Removed 1 records with no data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:01:15.79952 Removed 1 records with no data.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:26:52.435343 Removed 1 records with no data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:01:15.80587 Removed 1 records with no data.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:26:52.441997 Removed 1 records with no data.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:11:14.707997 Completed correlation with method=sparcc. Formatting results.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:36:47.871937 Completed correlation with method=sparcc. Formatting results.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:11:14.709201 Received df table with 3183 samples and 21 features with abundances.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:36:47.873227 Received df table with 3183 samples and 21 features with abundances.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:11:14.710412 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  sparcc</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024-04-24 17:36:47.874464 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  sparcc</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">alsoCorrelationDT</span> <span class="op">&lt;-</span> <span class="fu"><a href="getComputeResult.html">getComputeResult</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>     <span class="va">correlationOutput</span>, </span></span>
diff --git a/reference/updateCollectionName.html b/reference/updateCollectionName.html
index f9c96e8..0d2010e 100644
--- a/reference/updateCollectionName.html
+++ b/reference/updateCollectionName.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">MicrobiomeDB</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index d63b758..fe79511 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://microbiomedb.github.io/MicrobiomeDB/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004 <http://www.apache.org/licenses/>","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/MicrobiomeDB/LICENSE.html","id":"id_1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. Definitions","title":"Apache License","text":"“License” shall mean terms conditions use, reproduction, distribution defined Sections 1 9 document. “Licensor” shall mean copyright owner entity authorized copyright owner granting License. “Legal Entity” shall mean union acting entity entities control, controlled , common control entity. purposes definition, “control” means () power, direct indirect, cause direction management entity, whether contract otherwise, (ii) ownership fifty percent (50%) outstanding shares, (iii) beneficial ownership entity. “” (“”) shall mean individual Legal Entity exercising permissions granted License. “Source” form shall mean preferred form making modifications, including limited software source code, documentation source, configuration files. “Object” form shall mean form resulting mechanical transformation translation Source form, including limited compiled object code, generated documentation, conversions media types. “Work” shall mean work authorship, whether Source Object form, made available License, indicated copyright notice included attached work (example provided Appendix ). “Derivative Works” shall mean work, whether Source Object form, based (derived ) Work editorial revisions, annotations, elaborations, modifications represent, whole, original work authorship. purposes License, Derivative Works shall include works remain separable , merely link (bind name) interfaces , Work Derivative Works thereof. “Contribution” shall mean work authorship, including original version Work modifications additions Work Derivative Works thereof, intentionally submitted Licensor inclusion Work copyright owner individual Legal Entity authorized submit behalf copyright owner. purposes definition, “submitted” means form electronic, verbal, written communication sent Licensor representatives, including limited communication electronic mailing lists, source code control systems, issue tracking systems managed , behalf , Licensor purpose discussing improving Work, excluding communication conspicuously marked otherwise designated writing copyright owner “Contribution.” “Contributor” shall mean Licensor individual Legal Entity behalf Contribution received Licensor subsequently incorporated within Work.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/LICENSE.html","id":"id_2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. 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Limitation of Liability","title":"Apache License","text":"event legal theory, whether tort (including negligence), contract, otherwise, unless required applicable law (deliberate grossly negligent acts) agreed writing, shall Contributor liable damages, including direct, indirect, special, incidental, consequential damages character arising result License use inability use Work (including limited damages loss goodwill, work stoppage, computer failure malfunction, commercial damages losses), even Contributor advised possibility damages.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/LICENSE.html","id":"id_9-accepting-warranty-or-additional-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"9. Accepting Warranty or Additional Liability","title":"Apache License","text":"redistributing Work Derivative Works thereof, may choose offer, charge fee , acceptance support, warranty, indemnity, liability obligations /rights consistent License. However, accepting obligations, may act behalf sole responsibility, behalf Contributor, agree indemnify, defend, hold Contributor harmless liability incurred , claims asserted , Contributor reason accepting warranty additional liability. END TERMS CONDITIONS","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/LICENSE.html","id":"appendix-how-to-apply-the-apache-license-to-your-work","dir":"","previous_headings":"","what":"APPENDIX: How to apply the Apache License to your work","title":"Apache License","text":"apply Apache License work, attach following boilerplate notice, fields enclosed brackets [] replaced identifying information. (Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright [yyyy] [name of copyright owner]  Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at    http://www.apache.org/licenses/LICENSE-2.0  Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"what-is-alpha-diversity","dir":"Articles","previous_headings":"","what":"What is Alpha Diversity?","title":"Alpha Diversity","text":"Alpha diversity measures diversity microbial taxa within single sample community. takes account number different taxa (richness) distribution (evenness). Understanding alpha diversity provides insights complexity structure microbial communities local level.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"why-care-about-alpha-diversity","dir":"Articles","previous_headings":"","what":"Why Care About Alpha Diversity?","title":"Alpha Diversity","text":"Researchers interested alpha diversity several reasons: Community Comparisons: Compare diversity microbial communities across different samples conditions. Health Assessments: Assess health stability microbial communities within specific environments host systems. Ecological Understanding: Gain insights ecological dynamics microbial communities local scale.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"how-is-alpha-diversity-calculated","dir":"Articles","previous_headings":"","what":"How is Alpha Diversity Calculated?","title":"Alpha Diversity","text":"package offers three diversity indices calculation: Shannon, Simpson Evenness.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"shannon-diversity-index","dir":"Articles","previous_headings":"How is Alpha Diversity Calculated?","what":"Shannon Diversity Index","title":"Alpha Diversity","text":"Shannon diversity index measures entropy uncertainty predicting identity randomly chosen taxon within sample. can calculated follows:","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::HMP_WGS) #>  [1] \"WGS 4th level EC metagenome abundance data\"               #>  [2] \"WGS Metagenome enzyme pathway abundance data\"             #>  [3] \"WGS Metagenome enzyme pathway coverage data\"              #>  [4] \"WGS Genus\"                                                #>  [5] \"WGS Species\"                                              #>  [6] \"WGS Family\"                                               #>  [7] \"WGS Order\"                                                #>  [8] \"WGS Phylum\"                                               #>  [9] \"WGS Class\"                                                #> [10] \"WGS Normalized number of taxon-specific sequence matches\" #> [11] \"WGS Kingdom\"  ## grab a collection we like genus <- getCollection(microbiomeData::HMP_WGS, 'WGS Genus')  ## get an alpha diversity ComputeResult alphaDivOutput <- alphaDiv(genus, method = 'shannon') #>  #> 2024-04-24 17:11:27.523073 Received df table with 741 samples and 226 taxa. #>  #> 2024-04-24 17:11:27.576679 shannon alpha diversity computation complete. #>  #> 2024-04-24 17:11:27.591639 Alpha diversity computation completed with parameters method= shannon"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"simpson-diversity-index","dir":"Articles","previous_headings":"How is Alpha Diversity Calculated?","what":"Simpson Diversity Index","title":"Alpha Diversity","text":"Simpson diversity index measures probability two individuals randomly selected sample belong different taxa. can calculated follows:","code":"## get an alpha diversity ComputeResult genus <- getCollection(microbiomeData::HMP_WGS, 'WGS Genus') alphaDivOutput <- alphaDiv(genus, method = 'simpson') #>  #> 2024-04-24 17:11:27.68364 Received df table with 741 samples and 226 taxa. #>  #> 2024-04-24 17:11:27.706332 simpson alpha diversity computation complete. #>  #> 2024-04-24 17:11:27.711408 Alpha diversity computation completed with parameters method= simpson"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"species-evenness","dir":"Articles","previous_headings":"How is Alpha Diversity Calculated?","what":"Species Evenness","title":"Alpha Diversity","text":"Species evenness describes distribution abundances across species sample. Species evenness highest species sample abundance approaches zero relative abundances vary.","code":"## get an alpha diversity ComputeResult genus <- getCollection(microbiomeData::HMP_WGS, 'WGS Genus') alphaDivOutput <- alphaDiv(genus, method = 'evenness') #>  #> 2024-04-24 17:11:27.796455 Received df table with 741 samples and 226 taxa. #>  #> 2024-04-24 17:11:27.814082 evenness alpha diversity computation complete. #>  #> 2024-04-24 17:11:27.817465 Alpha diversity computation completed with parameters method= evenness"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"visualizing-alpha-diversity","dir":"Articles","previous_headings":"","what":"Visualizing Alpha Diversity","title":"Alpha Diversity","text":"Alpha Diversity frequently visualized scatter box plots. Creating types plots can done like following:","code":"## choose one or more metadata variables to integrate with the compute result alphaDiv_withMetadata <- getComputeResultWithMetadata(   alphaDivOutput,   microbiomeData::HMP_WGS,   metadataVariables = c('host_body_habitat') )  ## plot the compute result with integrated metadata ggplot(alphaDiv_withMetadata) +   aes(x=alphaDiversity, y=host_body_habitat, fill=host_body_habitat) +   geom_boxplot() +   labs(y= \"Body site\", x = \"Alpha diversity (Shannon)\",         title=\"Alpha diversity by body site\",         caption=paste0(\"produced on \", Sys.time())) +   theme_bw()"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"what-is-beta-diversity","dir":"Articles","previous_headings":"","what":"What is Beta Diversity?","title":"Beta Diversity","text":"Beta diversity measures dissimilarity diversity different microbial communities. context microbiome studies, quantifies microbial compositions vary across samples. Understanding beta diversity allows researchers explore unique features sample identify patterns microbial community structure.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"why-care-about-beta-diversity","dir":"Articles","previous_headings":"","what":"Why Care About Beta Diversity?","title":"Beta Diversity","text":"Researchers interested beta diversity several reasons: Ecological Insights: Beta diversity helps uncover ecological differences microbial communities different environments conditions. Disease Studies: medical research, beta diversity can highlight variations microbial communities associated health disease states. Community Dynamics: Studying beta diversity provides information microbial communities change time response specific factors.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"how-is-beta-diversity-calculated","dir":"Articles","previous_headings":"","what":"How is Beta Diversity Calculated?","title":"Beta Diversity","text":"Beta Diversity can calculated first producing dissimilarity matrix samples applying dimensional reduction technique dissimilarity matrix. package offers flexibility calculating beta diversity providing multiple dissimilarity matrix options:","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"bray-curtis-dissimilarity","dir":"Articles","previous_headings":"How is Beta Diversity Calculated?","what":"Bray-Curtis Dissimilarity","title":"Beta Diversity","text":"Bray-Curtis algorithm measures compositional dissimilarity based presence abundance taxa. calculates normalized absolute differences taxon abundance two samples, providing metric ranges 0 (complete similarity) 1 (complete dissimilarity).","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::HMP_WGS) #>  [1] \"WGS 4th level EC metagenome abundance data\"               #>  [2] \"WGS Metagenome enzyme pathway abundance data\"             #>  [3] \"WGS Metagenome enzyme pathway coverage data\"              #>  [4] \"WGS Genus\"                                                #>  [5] \"WGS Species\"                                              #>  [6] \"WGS Family\"                                               #>  [7] \"WGS Order\"                                                #>  [8] \"WGS Phylum\"                                               #>  [9] \"WGS Class\"                                                #> [10] \"WGS Normalized number of taxon-specific sequence matches\" #> [11] \"WGS Kingdom\"  ## grab a collection we like HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, 'WGS Species')  ## get a betaDiv ComputeResult betaDiv <- betaDiv(HMP_WGS_species, method = \"bray\") #>  #> 2024-04-24 17:11:41.467959 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:11:41.797229 Computed dissimilarity matrix. #>  #> 2024-04-24 17:11:42.767674 Finished ordination step. #>  #> 2024-04-24 17:11:42.79767 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = bray , k = 2 , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"jaccard-dissimilarity","dir":"Articles","previous_headings":"How is Beta Diversity Calculated?","what":"Jaccard Dissimilarity","title":"Beta Diversity","text":"Measures dissimilarity based presence-absence taxa. quantifies proportion taxa shared two samples.","code":"HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, 'WGS Species') betaDiv <- betaDiv(HMP_WGS_species, method = \"jaccard\") #>  #> 2024-04-24 17:11:42.942731 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:11:43.25124 Computed dissimilarity matrix. #>  #> 2024-04-24 17:11:43.443083 Finished ordination step. #>  #> 2024-04-24 17:11:43.454034 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jaccard , k = 2 , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"jensen-shannon-divergence-jsd","dir":"Articles","previous_headings":"How is Beta Diversity Calculated?","what":"Jensen-Shannon Divergence (JSD)","title":"Beta Diversity","text":"Captures dissimilarity considering abundance presence-absence information. symmetric version Kullback-Leibler Divergence, providing measure dissimilarity probability distributions.","code":"HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, 'WGS Species') betaDiv <- betaDiv(HMP_WGS_species, method = \"jsd\") #>  #> 2024-04-24 17:11:43.58537 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:11:50.290221 Computed dissimilarity matrix. #>  #> 2024-04-24 17:11:50.485559 Finished ordination step. #>  #> 2024-04-24 17:11:50.492093 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jsd , k = 2 , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"principal-coordinate-analysis-pcoa","dir":"Articles","previous_headings":"How is Beta Diversity Calculated?","what":"Principal Coordinate Analysis (PCoA):","title":"Beta Diversity","text":"PCoA dimensional reduction technique applied dissimilarity matrix, providing visual representation relationships samples lower-dimensional space. transforms dissimilarity matrix set orthogonal axes (principal coordinates) capture maximum variance data. PCoA plot allows researchers visualize spatial arrangement samples, aiding interpretation beta diversity. MicrobiomeDB package performs PCoA part betaDiv method.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"interpreting-pcoa-results","dir":"Articles","previous_headings":"","what":"Interpreting PCoA Results","title":"Beta Diversity","text":"following code produce PCoA plot:  PCoA plot visually represents dissimilarity samples. point plot corresponds sample, position points reflects relationships based beta diversity. ’s interpret PCoA plot:","code":"## choose one or more metadata variables to integrate with the compute result betaDiv_withMetadata <- getComputeResultWithMetadata(   betaDiv,    microbiomeData::HMP_WGS,    metadataVariables = c('host_body_habitat'))  ## plot beta diversity ggplot2::ggplot(betaDiv_withMetadata) +   aes(x=Axis1, y=Axis2, color=host_body_habitat) +   geom_point() +   labs(y= \"Axis 2\", x = \"Axis 1\",         title=\"Beta diversity by body site\",         caption=paste0(\"produced on \", Sys.time())) +   theme_bw()"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"axes-representation","dir":"Articles","previous_headings":"Interpreting PCoA Results","what":"Axes Representation:","title":"Beta Diversity","text":"axes (principal coordinates) PCoA plot represent dimensions maximum variance dissimilarity matrix. distance points plot reflects dissimilarity corresponding samples. axis explains certain percentage total variation data.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"interpreting-axis-direction","dir":"Articles","previous_headings":"Interpreting PCoA Results","what":"Interpreting Axis Direction:","title":"Beta Diversity","text":"direction axes indicates major patterns dissimilarity data. Samples cluster together plot similar , farther apart dissimilar.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"percentage-of-variance","dir":"Articles","previous_headings":"Interpreting PCoA Results","what":"Percentage of Variance:","title":"Beta Diversity","text":"Check percentage variance explained axis. Higher percentages indicate axis captures information dissimilarity samples.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"biological-interpretation","dir":"Articles","previous_headings":"Interpreting PCoA Results","what":"Biological Interpretation:","title":"Beta Diversity","text":"Interpret biological meaning sample clustering. distinct groups trends data? Color PCoA plot another variable learn patterns!","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"what-is-a-correlation-analysis","dir":"Articles","previous_headings":"","what":"What is a Correlation Analysis?","title":"Correlation","text":"Correlations useful identifying relationships variables. helpful identifying biomarkers functional associations, among things. Biomarkers microbiome data microbial taxa features exhibit significant correlation particular conditions, traits, variables sample metadata. Identifying biomarkers allows researchers uncover associations microbiome external factors, age, disease status, environmental conditions. Biomarkers serve indicators specific biological clinical phenomena within microbial communities. Functional associations microbiome data refer relationships taxonomic relative abundances abundances specific pathways functional features. Understanding associations allows researchers explore taxonomic composition microbial communities influences functional capabilities.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"why-care-about-biomarker-discovery","dir":"Articles","previous_headings":"","what":"Why Care About Biomarker Discovery?","title":"Correlation","text":"Researchers interested biomarker discovery several reasons: Diagnostic Insights: Biomarkers can serve potential diagnostic indicators, helping identify microbial patterns associated specific conditions. Predictive Modeling: Understanding biomarker correlations enables predictive modeling microbial responses external factors. Biological Significance: Biomarkers provide insights biological significance microbial community variations response different conditions.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"why-care-about-functional-associations","dir":"Articles","previous_headings":"","what":"Why Care About Functional Associations?","title":"Correlation","text":"Biological Insights: Explore changes taxonomic composition may impact functional potential microbial communities. Pathway-Level Analysis: Understand specific pathways functional features correlate taxonomic abundance, providing pathway-level insights. Predictive Modeling: Assessing functional associations aids predicting microbial functional responses environmental changes perturbations.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"how-are-correlations-calculated","dir":"Articles","previous_headings":"","what":"How are Correlations Calculated?","title":"Correlation","text":"package employs correlation analysis microbial taxonomic abundances sample metadata abundances pathways functional data using following approach: Users can choose either Spearman Pearson correlation analysis. produce correlation coefficient p-value indicating statistical significance.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"spearman-correlation","dir":"Articles","previous_headings":"How are Correlations Calculated?","what":"Spearman Correlation","title":"Correlation","text":"Use relationship variables monotonic necessarily linear. Suitable non-linear associations.","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::HMP_WGS) #>  [1] \"WGS 4th level EC metagenome abundance data\"               #>  [2] \"WGS Metagenome enzyme pathway abundance data\"             #>  [3] \"WGS Metagenome enzyme pathway coverage data\"              #>  [4] \"WGS Genus\"                                                #>  [5] \"WGS Species\"                                              #>  [6] \"WGS Family\"                                               #>  [7] \"WGS Order\"                                                #>  [8] \"WGS Phylum\"                                               #>  [9] \"WGS Class\"                                                #> [10] \"WGS Normalized number of taxon-specific sequence matches\" #> [11] \"WGS Kingdom\"  ## grab a collection of interest HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, \"WGS Species\", continuousMetadataOnly = TRUE)  ## get a correlation ComputeResult ## this is not necessarily to recommend spearman for metadata.  ## it is simply exemplary. Always look at your data! species_vs_metadata <- correlation(HMP_WGS_species, method = 'spearman')  #>  #> 2024-04-24 17:12:03.565216 Removed 7 records with no data. #>  #> 2024-04-24 17:12:03.593909 Removed 7 records with no data. #>  #> 2024-04-24 17:12:03.62961 Removed 7 records with no data. #>  #> 2024-04-24 17:12:04.960872 Completed correlation with method=spearman. Formatting results. #>  #> 2024-04-24 17:12:04.96186 Received df table with 734 samples and 316 features with values. #>  #> 2024-04-24 17:12:04.966443 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method =  spearman"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"pearson-correlation","dir":"Articles","previous_headings":"How are Correlations Calculated?","what":"Pearson Correlation","title":"Correlation","text":"Use relationship variables linear. Suitable assessing linear associations.","code":"## grab two collections of interest, in this case species level data and pathway abundance data HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, \"WGS Species\") HMP_WGS_pathways <- getCollection(microbiomeData::HMP_WGS, \"WGS Metagenome enzyme pathway abundance data\" )  ## get a correlation ComputeResult ## this is not necessarily to recommend pearson for functional data. ## it is simply exemplary. Always look at your data! pathway_vs_species <- correlation(HMP_WGS_species, HMP_WGS_pathways, method = 'pearson') #>  #> 2024-04-24 17:12:05.911691 Removed 7 records with no data. #>  #> 2024-04-24 17:12:05.948013 Removed 7 records with no data. #>  #> 2024-04-24 17:12:06.087085 Removed 7 records with no data. #>  #> 2024-04-24 17:12:06.097721 Received first df table with 734 samples and 319 features with values. #>  #> 2024-04-24 17:12:06.098063 Received second df table with 741 samples and 371 features with values. #>  #> 2024-04-24 17:12:06.098324 Found 734 samples in common between data1 and data2. Only these samples will be used. #>  #> 2024-04-24 17:12:06.515177 Completed correlation with method=pearson. Formatting results. #>  #> 2024-04-24 17:12:06.521023 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method =  pearson"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"interpreting-results","dir":"Articles","previous_headings":"","what":"Interpreting Results","title":"Correlation","text":"Correlation Coefficients: Assess strength direction correlations. Positive coefficients indicate positive correlations, negative coefficients indicate negative correlations. p-values Adjusted p-values: Identify biomarkers statistically significant correlations, considering adjustments multiple testing. can extract metrics sort filter results : can also visualize custom htmlwidgets: Finally, advanced analysis network, can extract igraph object:","code":"## you can extract network metrics  pathway_vs_species.metrics <- as_tibble(   getComputeResult(     pathway_vs_species,     correlationCoefThreshold = 0.8,     pValueThreshold = 0.05   ) )  ## it's also easy to sort and filter these network metrics ## begin by renaming columns colnames(pathway_vs_species.metrics) <- c('species', 'pathway', 'correlationCoef', 'pValue') pathway_vs_species.metrics %>%   filter(species == \"Faecalibacterium prausnitzii\") %>%   filter(correlationCoef > 0.5) %>%   arrange(desc(correlationCoef)) #> # A tibble: 1 × 4 #>   species                      pathway                    correlationCoef pValue #>   <chr>                        <fct>                                <dbl>  <dbl> #> 1 Faecalibacterium prausnitzii PWY-5177: glutaryl-CoA de…           0.825      0 ## now plot the network ## filters can be applied based on correlation coefficient and p-value ## renders an interactive htmlwidget, using a predetermined layout correlationNetwork(   pathway_vs_species,   correlationCoefThreshold = 0.8,   pValueThreshold = 0.05 ) ## if you extract the network as an igraph object, you can get more detailed metrics pathway_vs_species.igraph <- getComputeResult(pathway_vs_species, format = 'igraph') degree <- degree(pathway_vs_species.igraph) edgeBT <- edge_betweenness(pathway_vs_species.igraph) pgRank <- page_rank(pathway_vs_species.igraph) coords <- layout_with_kk(pathway_vs_species.igraph)  #plot(pathway_vs_species.igraph, layout = coords)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/ranked-abundance.html","id":"what-are-relative-abundances","dir":"Articles","previous_headings":"","what":"What are Relative Abundances","title":"Ranked Relative Abundances","text":"Relative abundances refer proportion percentage taxonomic group microbial species within given sample ecosystem. quantifies contribution taxon overall microbial community, providing insights distribution dominance different organisms. Relative abundances typically determined techniques like amplicon sequencing metagenomic analysis, allowing researchers compare prevalence various taxa across different samples conditions. information crucial understanding structure, dynamics, ecological roles microbial communities.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/ranked-abundance.html","id":"why-compare-or-find-taxa-based-on-relative-abundances","dir":"Articles","previous_headings":"","what":"Why Compare or Find Taxa Based on Relative Abundances?","title":"Ranked Relative Abundances","text":"Researchers drawn comparing finding taxa based relative abundances multitude reasons: Ecosystem Dynamics: Assessing relative abundances allows researchers unravel shifts microbial community structures time response environmental changes, offering insights ecosystem dynamics stability. Biological Significance: Identifying taxa significant shifts relative abundances can unveil roles ecosystem functions, providing valuable clues ecological significance potential impacts ecosystem processes. Disease Associations: Comparing taxa based relative abundances can reveal microbial signatures associated various diseases health conditions, paving way potential biomarker discovery diagnostic insights. Taxonomic Profiling: Understanding relative abundances different taxa provides comprehensive snapshot microbial community compositions, aiding taxonomic profiling classification efforts. deciphering ecological shifts uncovering disease markers, comparing finding taxa based relative abundances offers powerful lens researchers can explore intricate world microbial communities.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/ranked-abundance.html","id":"how-to-find-ranked-relative-abundances","dir":"Articles","previous_headings":"","what":"How to Find Ranked Relative Abundances?","title":"Ranked Relative Abundances","text":"package offers convenience function finding taxa ranking relative abundances metric interest. Available metrics max, median, q3 variance.","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::HMP_WGS) #>  [1] \"WGS 4th level EC metagenome abundance data\"               #>  [2] \"WGS Metagenome enzyme pathway abundance data\"             #>  [3] \"WGS Metagenome enzyme pathway coverage data\"              #>  [4] \"WGS Genus\"                                                #>  [5] \"WGS Species\"                                              #>  [6] \"WGS Family\"                                               #>  [7] \"WGS Order\"                                                #>  [8] \"WGS Phylum\"                                               #>  [9] \"WGS Class\"                                                #> [10] \"WGS Normalized number of taxon-specific sequence matches\" #> [11] \"WGS Kingdom\"  ## grab a collection of interest HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, \"WGS Species\")  ## get a ranked abundance ComputeResult ## top 10 taxa by max relative abundance across all samples rankedAbund <- rankedAbundance(HMP_WGS_species, method = \"max\", cutoff = 10)  #>  #> 2024-04-24 17:12:20.822977 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:12:20.854149 Finished ranking taxa #>  #> 2024-04-24 17:12:20.874894 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = max , cutoff = 10 , naToZero =  TRUE , verbose = TRUE ## top 8 taxa by median relative abundance across all samples rankedAbund <- rankedAbundance(HMP_WGS_species, method = \"median\", cutoff = 8) #>  #> 2024-04-24 17:12:21.658376 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:12:21.679641 Finished ranking taxa #>  #> 2024-04-24 17:12:21.688558 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = median , cutoff = 8 , naToZero =  TRUE , verbose = TRUE ## top 20 taxa by third quartile relative abundance across all samples rankedAbund <- rankedAbundance(HMP_WGS_species, method = \"q3\", cutoff = 20) #>  #> 2024-04-24 17:12:21.715574 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:12:21.811909 Finished ranking taxa #>  #> 2024-04-24 17:12:21.818515 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = q3 , cutoff = 20 , naToZero =  TRUE , verbose = TRUE ## top 10 taxa by greatest variance in relative abundance across all samples rankedAbund <- rankedAbundance(HMP_WGS_species, method = \"variance\", cutoff = 10) #>  #> 2024-04-24 17:12:21.845605 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:12:21.866328 Finished ranking taxa #>  #> 2024-04-24 17:12:21.871848 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = variance , cutoff = 10 , naToZero =  TRUE , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/ranked-abundance.html","id":"visualizing-ranked-relative-abundances","dir":"Articles","previous_headings":"","what":"Visualizing Ranked Relative Abundances","title":"Ranked Relative Abundances","text":"Abundances frequently visualized scatter box plots. Creating types plots can done like following:","code":"## combine ranked abundance result with sample metadata of interest rankedAbund_withMetadata <- getComputeResultWithMetadata(     rankedAbund,      microbiomeData::HMP_WGS,      metadataVariables = c('host_body_habitat'))  ## pivot the dataframe to be able to plot it rankedAbund_withMetadata.pivot <- pivot_longer(rankedAbund_withMetadata, # dataframe to be pivoted                                     cols = 4:13, # column names to be stored as a SINGLE variable                                     names_to = \"taxa\", # name of that new variable (column)                                     values_to = \"abundance\") # name of new variable (column) storing all the values (data)  ## plot the compute result with integrated metadata ggplot2::ggplot(rankedAbund_withMetadata.pivot) +     aes(x=abundance, y=taxa, fill = factor(host_body_habitat)) +     geom_boxplot() +     labs(y= \"Taxon\", x = \"Relative abundance\",         title=\"Relative abudnace of top taxa\",         caption=paste0(\"produced on \", Sys.time())) +     theme_bw()"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/self-correlation.html","id":"what-is-a-correlation-analysis","dir":"Articles","previous_headings":"","what":"What is a Correlation Analysis?","title":"Self Correlation","text":"Correlations useful identifying relationships variables. correlate taxonomic abundance variables , essentially produces microbial network. Producing analyzing networks complicated fact microbiome data inherently compositional. properly accounted , can result lot spurious negative correlations.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/self-correlation.html","id":"why-care-about-microbial-network-analysis","dir":"Articles","previous_headings":"","what":"Why Care About Microbial Network Analysis?","title":"Self Correlation","text":"Scientists delve microbial network analysis large number reasons: Unraveling Complex Interactions: Microbial network analysis unveils intricate relationships microorganisms, shedding light interconnectedness within ecosystems. Diagnostic Potential: Identifying key nodes microbial networks can unveil potential diagnostic markers, offering glimpse microbial dynamics associated various diseases environmental conditions. Insights Functionality: Microbial network analysis elucidates functional roles within microbial communities, offering valuable insights ecological physiological significance. unraveling ecological mysteries informing medical diagnoses, microbial network analysis proves indispensable understanding intricate world microorganisms.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/self-correlation.html","id":"how-are-correlations-calculated","dir":"Articles","previous_headings":"","what":"How are Correlations Calculated?","title":"Self Correlation","text":"package employs SPARCC correlation analysis microbial taxa. SPARCC calculates correlations account compositional nature microbiome data.","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::FARMM) #>  [1] \"Metabolomics Mass spectrometry assay\"                     #>  [2] \"WGS 4th level EC metagenome abundance data\"               #>  [3] \"WGS Metagenome enzyme pathway abundance data\"             #>  [4] \"WGS Metagenome enzyme pathway coverage data\"              #>  [5] \"WGS Genus\"                                                #>  [6] \"WGS Species\"                                              #>  [7] \"WGS Family\"                                               #>  [8] \"WGS Order\"                                                #>  [9] \"WGS Phylum\"                                               #> [10] \"WGS Class\"                                                #> [11] \"WGS Normalized number of taxon-specific sequence matches\" #> [12] \"WGS Kingdom\"  ## grab a collection of interest ## these methods can be used with other data types as well farmm_metabolomics <- getCollection(microbiomeData::FARMM, \"Metabolomics Mass spectrometry assay\") #>  #> 2024-04-24 17:12:35.42818 Integer values detected. Converting collection to AbsoluteAbundanceData  ## get a self correlation ComputeResult ## methods spearman and pearson are options here as well, for data known to not be compositional selfCorrelation_metabolomics <- selfCorrelation(farmm_metabolomics, method='spearman') #>  #> 2024-04-24 17:12:36.768037 Completed correlation with method=spearman. Formatting results. #>  #> 2024-04-24 17:12:37.649345 Received df table with 150 samples and 479 features with abundances. #>  #> 2024-04-24 17:12:37.653913 Correlation computation completed with parameters recordIdColumn= Mass_spectrometry_assay_Id , method =  spearman"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/self-correlation.html","id":"interpreting-results","dir":"Articles","previous_headings":"","what":"Interpreting Results","title":"Self Correlation","text":"Correlation Coefficients: Assess strength direction correlations. Positive coefficients indicate positive correlations, negative coefficients indicate negative correlations. p-values Adjusted p-values: Identify biomarkers statistically significant correlations, considering adjustments multiple testing. can extract metrics sort filter results : can also visualize custom htmlwidgets: Finally, advanced analysis network, can extract igraph object:","code":"## you can extract network metrics  selfCorrelation_metabolomics.metrics <- as_tibble(     getComputeResult(         selfCorrelation_metabolomics,         correlationCoefThreshold = 0.5,         pValueThreshold = 0.05     ) )  ## it's also easy to sort and filter these network metrics ## begin by renaming columns colnames(selfCorrelation_metabolomics.metrics) <- c('metabolite1', 'metabolite2', 'correlationCoef', 'pValue') selfCorrelation_metabolomics.metrics %>%     filter(correlationCoef > 0.5) %>%     arrange(desc(correlationCoef)) #> # A tibble: 11,027 × 4 #>    metabolite1                       metabolite2          correlationCoef pValue #>    <fct>                             <fct>                          <dbl>  <dbl> #>  1 C46:3 TAG +NH4:C8-pos: Metabolite C46:3 TAG:C8-pos: M…           0.999      0 #>  2 C44:1 TAG +NH4:C8-pos: Metabolite C44:1 TAG:C8-pos: M…           0.999      0 #>  3 C16:0 LPC:C8-pos: Metabolite      C20:3 LPC:C8-pos: M…           0.999      0 #>  4 C44:2 TAG +NH4:C8-pos: Metabolite C44:2 TAG:C8-pos: M…           0.999      0 #>  5 C46:2 TAG +NH4:C8-pos: Metabolite C46:2 TAG:C8-pos: M…           0.998      0 #>  6 C52:0 TAG +NH4:C8-pos: Metabolite C52:0 TAG:C8-pos: M…           0.997      0 #>  7 C52:1 TAG +NH4:C8-pos: Metabolite C52:1 TAG:C8-pos: M…           0.997      0 #>  8 C50:0 TAG +NH4:C8-pos: Metabolite C50:0 TAG:C8-pos: M…           0.996      0 #>  9 C42:0 TAG +NH4:C8-pos: Metabolite C42:0 TAG:C8-pos: M…           0.995      0 #> 10 C48:3 TAG +NH4:C8-pos: Metabolite C48:3 TAG:C8-pos: M…           0.995      0 #> # ℹ 11,017 more rows ## now plot the network ## filters can be applied based on correlation coefficient and p-value ## renders an interactive htmlwidget, using a predetermined layout correlationNetwork(     selfCorrelation_metabolomics,     correlationCoefThreshold = 0.5,     pValueThreshold = 0.05 ) ## if you extract the network as an igraph object, you can get more detailed metrics selfCorrelation_metabolomics.igraph <- getComputeResult(selfCorrelation_metabolomics, format = 'igraph') degree <- degree(selfCorrelation_metabolomics.igraph) edgeBT <- edge_betweenness(selfCorrelation_metabolomics.igraph) pgRank <- page_rank(selfCorrelation_metabolomics.igraph) coords <- layout_with_kk(selfCorrelation_metabolomics.igraph)  #plot(selfCorrelation_metabolomics.igraph, coords)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Danielle Callan. Author, maintainer.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Callan D (2024). MicrobiomeDB: Curated Data Analysis Tools MicrobiomeDB.org. R package version 0.2.0, https://microbiomedb.github.io/MicrobiomeDB/, https://github.com/microbiomeDB/MicrobiomeDB.","code":"@Manual{,   title = {MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org},   author = {Danielle Callan},   year = {2024},   note = {R package version 0.2.0, https://microbiomedb.github.io/MicrobiomeDB/},   url = {https://github.com/microbiomeDB/MicrobiomeDB}, }"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"microbiomedb","dir":"","previous_headings":"","what":"Curated Data and Analysis Tools from MicrobiomeDB.org","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"R package containing data MicrobiomeDB.org, tools analyzing visualizing .","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"Use R package remotes install MicrobiomeDB. R command prompt:","code":"remotes::install_github('microbiomeDB/MicrobiomeDB')"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"package intended used explore curated datasets MicrobiomeDB.org, well datasets. comes pre-packaged functions used power analysis tools website. also contains functions facilitate easily transforming data custom objects, phyloseq objects, .biom files can upload website. package paired dedicated data package called micribomeData includes number pre-built MbioDataset objects representing curated data MicrobiomeDB.org website. can see names like: return list names data objects installed package. One dataset ‘DiabImmune’, ’ll use following example. MbioDataset objects contain two things metadata collections. Metadata typically include details samples dataset, age person collected . Collections can group variables represent unified biological concept measured consistent comparable range values. example might relative abundances various genera. myCollection, can start using microbiomeComputations package (installed installed one) fun things like: give ComputeResult object, slots data statistics can explore. objects can difficult parse, ’ve added functions help format results usable exciting ways! called getComputeResult getComputeResultWithMetadata return data.tables (sometimes igraph objects) can use like : can take results data.table object use build plots things ggplot2 tool like. Let us know build something interesting, encounter bugs, just wish something easier . ’d love hear !","code":"remotes::install_github('microbiomeDB/microbiomeData') microbiomeData::getCuratedDatasetNames() getCollectionNames(DiabImmune) # will print the names of collections myCollection <- getCollection(DiabImmune, '16S Species') # NOTE: you can also use the `format` argument here to get these as phyloseq objects alphaDivResults <- alphaDiv(myCollection) correlationResults <- correlation(myCollection) differentialAbundanceResults <- differentialAbundance(   myCollection,    \"breastfed_duration_days\", # see getMetadataVariableNames() and getMetadataVariableSummary()   groupA = function(x) {x < 300},   groupB = function(x) {x >= 300},   method = 'Maaslin2') myCorrelationDT <- getComputeResult(correlationResults) myCorrelationGraph <- getComputeResult(correlationResults, format = 'igraph') MicrobiomeDB::correlationNetwork(myCorrelationDT) # will render a network visualization of the results using widgets from our own `corGraph` project  getMetadataVariableNames(DiabImmune) # will print names of metadata variables you can ask for myAlphaDivDT <- getComputeResultWithMetadata(alphaDivResults, DiabImmune, 'host_body_site')"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"Pull requests welcome. major changes, please open issue first discuss like change. Please make sure update tests appropriate.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"Apache 2.0","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/DESeqDataSetFromCollection.html","id":null,"dir":"Reference","previous_headings":"","what":"DESeqDataSet object from a Collection — DESeqDataSetFromCollection","title":"DESeqDataSet object from a Collection — DESeqDataSetFromCollection","text":"DESeqDataSet subclass RangedSummarizedExperiment, used store input values, intermediate calculations results analysis differential expression.  DESeqDataSet class enforces non-negative integer values \"counts\" matrix stored first element assay list. addition, formula specifies design experiment must provided.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/DESeqDataSetFromCollection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DESeqDataSet object from a Collection — DESeqDataSetFromCollection","text":"","code":"DESeqDataSetFromCollection(data, verbose = c(TRUE, FALSE), ...)  # S4 method for AbsoluteAbundanceData DESeqDataSetFromCollection(data, verbose = c(TRUE, FALSE), ...)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/DESeqDataSetFromCollection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DESeqDataSet object from a Collection — DESeqDataSetFromCollection","text":"data AbsoluteAbundanceData object verbose boolean indicating timed logging desired ... additional arguments passed DESeq2::DESeqDataSetFromMatrix","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/Maaslin2.html","id":null,"dir":"Reference","previous_headings":"","what":"Maaslin2 from a Collection — Maaslin2","title":"Maaslin2 from a Collection — Maaslin2","text":"MaAsLin2 finds associations microbiome meta-omics features complex metadata population-scale epidemiological studies. software includes multiple analysis methods (including support multiple covariates repeated measures) filtering, normalization, transform options customize analysis specific study.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/Maaslin2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maaslin2 from a Collection — Maaslin2","text":"","code":"Maaslin2(data, verbose = c(TRUE, FALSE), ...)  # S4 method for CollectionWithMetadata Maaslin2(data, verbose = c(TRUE, FALSE), ...)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/Maaslin2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maaslin2 from a Collection — Maaslin2","text":"data CollectionWithMetadata verbose boolean indicating timed logging desired ... additional arguments pass Maaslin2::Maaslin2","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/Maaslin2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maaslin2 from a Collection — Maaslin2","text":"","code":"maaslinOutput <- MicrobiomeDB::Maaslin2(        data = getCollection(microbiomeData::DiabImmune, '16S (V4) Genus'),         output = tempfile(\"maaslin\"),        #min_prevalence = 0,        fixed_effects = 'delivery_mode',        analysis_method = \"LM\", # default LM        normalization = \"TSS\", # default TSS        transform = \"LOG\", # default LOG        plot_heatmap = FALSE,        plot_scatter = FALSE) #> [1] \"data.table\" \"data.frame\" #> [1] \"Creating output folder\" #> [1] \"Creating output feature tables folder\" #> [1] \"Creating output fits folder\" #> 2024-04-24 16:50:36.689123 INFO::Writing function arguments to log file #> 2024-04-24 16:50:36.704111 INFO::Verifying options selected are valid #> 2024-04-24 16:50:36.734445 INFO::Determining format of input files #> 2024-04-24 16:50:36.736163 INFO::Input format is data samples as rows and metadata samples as rows #> 2024-04-24 16:50:36.750647 INFO::Formula for fixed effects: expr ~  delivery_mode #> 2024-04-24 16:50:36.751732 INFO::Filter data based on min abundance and min prevalence #> 2024-04-24 16:50:36.752267 INFO::Total samples in data: 3184 #> 2024-04-24 16:50:36.752756 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000 #> 2024-04-24 16:50:36.772777 INFO::Total filtered features: 563 #> 2024-04-24 16:50:36.773912 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97 #> 2024-04-24 16:50:36.781983 INFO::Total filtered features with variance filtering: 0 #> 2024-04-24 16:50:36.782585 INFO::Filtered feature names from variance filtering: #> 2024-04-24 16:50:36.783064 INFO::Running selected normalization method: TSS #> 2024-04-24 16:50:36.84251 INFO::Applying z-score to standardize continuous metadata #> 2024-04-24 16:50:36.851343 INFO::Running selected transform method: LOG #> 2024-04-24 16:50:36.914274 INFO::Running selected analysis method: LM #> 2024-04-24 16:50:36.920555 INFO::Fitting model to feature number 1, Actinomyces #> 2024-04-24 16:50:36.929258 INFO::Fitting model to feature number 2, Agathobacter #> 2024-04-24 16:50:36.933501 INFO::Fitting model to feature number 3, Akkermansia #> 2024-04-24 16:50:36.937621 INFO::Fitting model to feature number 4, Alistipes #> 2024-04-24 16:50:36.941725 INFO::Fitting model to feature number 5, Anaerostipes #> 2024-04-24 16:50:36.945867 INFO::Fitting model to feature number 6, Atopobium #> 2024-04-24 16:50:36.949921 INFO::Fitting model to feature number 7, Bacteroides #> 2024-04-24 16:50:36.954178 INFO::Fitting model to feature number 8, Barnesiella #> 2024-04-24 16:50:36.9583 INFO::Fitting model to feature number 9, Bifidobacterium #> 2024-04-24 16:50:36.962408 INFO::Fitting model to feature number 10, Bilophila #> 2024-04-24 16:50:36.966498 INFO::Fitting model to feature number 11, Blautia #> 2024-04-24 16:50:36.990195 INFO::Fitting model to feature number 12, Butyricicoccus #> 2024-04-24 16:50:36.994916 INFO::Fitting model to feature number 13, CAG.352 #> 2024-04-24 16:50:36.99904 INFO::Fitting model to feature number 14, Campylobacter #> 2024-04-24 16:50:37.003131 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group #> 2024-04-24 16:50:37.007246 INFO::Fitting model to feature number 16, Clostridioides #> 2024-04-24 16:50:37.011571 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 #> 2024-04-24 16:50:37.015681 INFO::Fitting model to feature number 18, Colidextribacter #> 2024-04-24 16:50:37.019885 INFO::Fitting model to feature number 19, Collinsella #> 2024-04-24 16:50:37.024768 INFO::Fitting model to feature number 20, Coprobacillus #> 2024-04-24 16:50:37.029115 INFO::Fitting model to feature number 21, Coprococcus #> 2024-04-24 16:50:37.033249 INFO::Fitting model to feature number 22, DTU089 #> 2024-04-24 16:50:37.037397 INFO::Fitting model to feature number 23, Dialister #> 2024-04-24 16:50:37.041522 INFO::Fitting model to feature number 24, Dorea #> 2024-04-24 16:50:37.045609 INFO::Fitting model to feature number 25, Eggerthella #> 2024-04-24 16:50:37.04967 INFO::Fitting model to feature number 26, Eisenbergiella #> 2024-04-24 16:50:37.053738 INFO::Fitting model to feature number 27, Enterococcus #> 2024-04-24 16:50:37.057915 INFO::Fitting model to feature number 28, Erysipelatoclostridium #> 2024-04-24 16:50:37.062057 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003 #> 2024-04-24 16:50:37.066175 INFO::Fitting model to feature number 30, Escherichia.Shigella #> 2024-04-24 16:50:37.070257 INFO::Fitting model to feature number 31, Faecalibacterium #> 2024-04-24 16:50:37.074361 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group #> 2024-04-24 16:50:37.078558 INFO::Fitting model to feature number 33, Flavonifractor #> 2024-04-24 16:50:37.082631 INFO::Fitting model to feature number 34, Fusicatenibacter #> 2024-04-24 16:50:37.086782 INFO::Fitting model to feature number 35, Fusobacterium #> 2024-04-24 16:50:37.090875 INFO::Fitting model to feature number 36, Gemella #> 2024-04-24 16:50:37.094934 INFO::Fitting model to feature number 37, Granulicatella #> 2024-04-24 16:50:37.099094 INFO::Fitting model to feature number 38, Haemophilus #> 2024-04-24 16:50:37.104082 INFO::Fitting model to feature number 39, Holdemania #> 2024-04-24 16:50:37.108351 INFO::Fitting model to feature number 40, Hungatella #> 2024-04-24 16:50:37.112507 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. #> 2024-04-24 16:50:37.11659 INFO::Fitting model to feature number 42, Intestinibacter #> 2024-04-24 16:50:37.12853 INFO::Fitting model to feature number 43, Intestinimonas #> 2024-04-24 16:50:37.132896 INFO::Fitting model to feature number 44, Klebsiella #> 2024-04-24 16:50:37.137085 INFO::Fitting model to feature number 45, Lachnoclostridium #> 2024-04-24 16:50:37.141203 INFO::Fitting model to feature number 46, Lachnospira #> 2024-04-24 16:50:37.145363 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group #> 2024-04-24 16:50:37.149453 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group #> 2024-04-24 16:50:37.153548 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group #> 2024-04-24 16:50:37.157645 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001 #> 2024-04-24 16:50:37.161741 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004 #> 2024-04-24 16:50:37.165858 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009 #> 2024-04-24 16:50:37.170027 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010 #> 2024-04-24 16:50:37.174133 INFO::Fitting model to feature number 54, Lactobacillus #> 2024-04-24 16:50:37.178273 INFO::Fitting model to feature number 55, Lactococcus #> 2024-04-24 16:50:37.182408 INFO::Fitting model to feature number 56, Mannheimia #> 2024-04-24 16:50:37.186542 INFO::Fitting model to feature number 57, Megasphaera #> 2024-04-24 16:50:37.190647 INFO::Fitting model to feature number 58, Monoglobus #> 2024-04-24 16:50:37.194826 INFO::Fitting model to feature number 59, Neisseria #> 2024-04-24 16:50:37.198956 INFO::Fitting model to feature number 60, Odoribacter #> 2024-04-24 16:50:37.203068 INFO::Fitting model to feature number 61, Oscillibacter #> 2024-04-24 16:50:37.207123 INFO::Fitting model to feature number 62, Oscillospira #> 2024-04-24 16:50:37.211255 INFO::Fitting model to feature number 63, Parabacteroides #> 2024-04-24 16:50:37.215393 INFO::Fitting model to feature number 64, Parasutterella #> 2024-04-24 16:50:37.219496 INFO::Fitting model to feature number 65, Prevotella #> 2024-04-24 16:50:37.223722 INFO::Fitting model to feature number 66, Pseudomonas #> 2024-04-24 16:50:37.227811 INFO::Fitting model to feature number 67, Romboutsia #> 2024-04-24 16:50:37.231956 INFO::Fitting model to feature number 68, Roseburia #> 2024-04-24 16:50:37.236034 INFO::Fitting model to feature number 69, Rothia #> 2024-04-24 16:50:37.240137 INFO::Fitting model to feature number 70, Ruminococcus #> 2024-04-24 16:50:37.2442 INFO::Fitting model to feature number 71, Sellimonas #> 2024-04-24 16:50:37.248294 INFO::Fitting model to feature number 72, Solobacterium #> 2024-04-24 16:50:37.252344 INFO::Fitting model to feature number 73, Staphylococcus #> 2024-04-24 16:50:37.264847 INFO::Fitting model to feature number 74, Streptococcus #> 2024-04-24 16:50:37.269177 INFO::Fitting model to feature number 75, Subdoligranulum #> 2024-04-24 16:50:37.27329 INFO::Fitting model to feature number 76, Sutterella #> 2024-04-24 16:50:37.277501 INFO::Fitting model to feature number 77, Terrisporobacter #> 2024-04-24 16:50:37.281673 INFO::Fitting model to feature number 78, Turicibacter #> 2024-04-24 16:50:37.285811 INFO::Fitting model to feature number 79, Tuzzerella #> 2024-04-24 16:50:37.289967 INFO::Fitting model to feature number 80, Tyzzerella #> 2024-04-24 16:50:37.294118 INFO::Fitting model to feature number 81, UBA1819 #> 2024-04-24 16:50:37.298263 INFO::Fitting model to feature number 82, UCG.002 #> 2024-04-24 16:50:37.30243 INFO::Fitting model to feature number 83, UCG.003 #> 2024-04-24 16:50:37.306582 INFO::Fitting model to feature number 84, UCG.005 #> 2024-04-24 16:50:37.310752 INFO::Fitting model to feature number 85, Veillonella #> 2024-04-24 16:50:37.314917 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group #> 2024-04-24 16:50:37.319044 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group #> 2024-04-24 16:50:37.323189 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group #> 2024-04-24 16:50:37.327366 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group #> 2024-04-24 16:50:37.331574 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group #> 2024-04-24 16:50:37.335738 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group #> 2024-04-24 16:50:37.339885 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group #> 2024-04-24 16:50:37.344007 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group #> 2024-04-24 16:50:37.348122 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group #> 2024-04-24 16:50:37.35227 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group #> 2024-04-24 16:50:37.356377 INFO::Fitting model to feature number 96, unclassified.Chloroplast #> 2024-04-24 16:50:37.360484 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014 #> 2024-04-24 16:50:37.364588 INFO::Fitting model to feature number 98, unclassified.Clostridia #> 2024-04-24 16:50:37.368677 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group #> 2024-04-24 16:50:37.372785 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales #> 2024-04-24 16:50:37.376869 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae #> 2024-04-24 16:50:37.381 INFO::Fitting model to feature number 102, unclassified.Mitochondria #> 2024-04-24 16:50:37.393731 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae #> 2024-04-24 16:50:37.398149 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus #> 2024-04-24 16:50:37.402386 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales #> 2024-04-24 16:50:37.4066 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae #> 2024-04-24 16:50:37.410811 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group #> 2024-04-24 16:50:37.431035 INFO::Counting total values for each feature #> 2024-04-24 16:50:37.437077 INFO::Writing filtered data to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/features/filtered_data.tsv #> 2024-04-24 16:50:37.584518 INFO::Writing filtered, normalized data to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/features/filtered_data_norm.tsv #> 2024-04-24 16:50:37.734916 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/features/filtered_data_norm_transformed.tsv #> 2024-04-24 16:50:38.00878 INFO::Writing residuals to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/fits/residuals.rds #> 2024-04-24 16:50:38.079005 INFO::Writing fitted values to file /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/fits/fitted.rds #> 2024-04-24 16:50:38.103251 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/all_results.tsv #> 2024-04-24 16:50:38.105003 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e5eeb7b1d/significant_results.tsv"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MbioDataset-class.html","id":null,"dir":"Reference","previous_headings":"","what":"MicrobiomeDB Dataset — MbioDataset-class","title":"MicrobiomeDB Dataset — MbioDataset-class","text":"class represents MicrobiomeDB dataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MbioDataset-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Microbiome Dataset — MbioDataset","title":"Create a Microbiome Dataset — MbioDataset","text":"constructor MbioDataset class. creates MbioDataset containing list Collections SampleMetadata object.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MbioDataset-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Microbiome Dataset — MbioDataset","text":"","code":"MbioDataset(collections, metadata, ontology)  # S4 method for missing,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,SampleMetadata,character MbioDataset(collections, metadata, ontology)  # S4 method for Collections,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for Collections,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,list,character MbioDataset(collections, metadata, ontology)  # S4 method for Collections,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for Collections,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,character,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,SampleMetadata,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,list,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,character,character MbioDataset(collections, metadata, ontology)  # S4 method for list,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,SampleMetadata,character MbioDataset(collections, metadata, ontology)  # S4 method for list,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for list,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for list,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,list,character MbioDataset(collections, metadata, ontology)  # S4 method for list,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,character,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,SampleMetadata,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,list,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,character,character MbioDataset(collections, metadata, ontology)  # S4 method for character,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,character,character MbioDataset(collections, metadata, ontology)  # S4 method for character,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,list,character MbioDataset(collections, metadata, ontology)  # S4 method for character,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for character,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for character,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,SampleMetadata,character MbioDataset(collections, metadata, ontology)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MbioDataset-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Microbiome Dataset — MbioDataset","text":"collections list Collection objects, data.frame containing multiple collections, character vector containing one file path(s) metadata SampleMetadata object, data.frame containing sample metadata, list file path(s) ontology data.frame containing ontology dataset, character vector containing file path data.frame","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MicrobiomeDB-package.html","id":null,"dir":"Reference","previous_headings":"","what":"MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org — MicrobiomeDB-package","title":"MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org — MicrobiomeDB-package","text":"package intended used explore curated datasets MicrobiomeDB.org, well datasets. comes pre-packaged functions used power analysis tools website. also contains functions facilitate easily transforming data custom objects, phyloseq objects, .biom files can upload website.","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MicrobiomeDB-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org — MicrobiomeDB-package","text":"Maintainer: Danielle Callan dcallan@upenn.edu","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Alpha diversity — alphaDiv","title":"Alpha diversity — alphaDiv","text":"function returns alpha diversity values sample.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alpha diversity — alphaDiv","text":"","code":"alphaDiv(   data,   method = c(\"shannon\", \"simpson\", \"evenness\"),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alpha diversity — alphaDiv","text":"data AbundanceData object method string defining alpha diversity method. Accepted values 'shannon','simpson', 'evenness' verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alpha diversity — alphaDiv","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Alpha diversity — alphaDiv","text":"","code":"alphaDivOutput <- alphaDiv(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = \"shannon\" ) #>  #> 2024-04-24 16:50:39.569741 Received df table with 3184 samples and 673 taxa. #>  #> 2024-04-24 16:50:39.776032 shannon alpha diversity computation complete. #>  #> 2024-04-24 16:50:39.791467 Alpha diversity computation completed with parameters method= shannon"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Beta diversity — betaDiv","title":"Beta diversity — betaDiv","text":"function returns pcoa coordinates calculated beta diversity dissimilarity matrix.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Beta diversity — betaDiv","text":"","code":"betaDiv(   data,   method = c(\"bray\", \"jaccard\", \"jsd\"),   k = 2,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Beta diversity — betaDiv","text":"data AbundanceData object method string defining beta diversity dissimilarity method. Accepted values 'bray','jaccard', 'jsd' k integer determining number pcoa axes return verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Beta diversity — betaDiv","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Beta diversity — betaDiv","text":"","code":"betaDivOutput <- betaDiv(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = \"bray\",       k = 2 ) #>  #> 2024-04-24 16:50:40.793814 Received df table with 3184 samples and 673 taxa. #>  #> 2024-04-24 16:50:46.014705 Computed dissimilarity matrix. #>  #> 2024-04-24 16:50:55.804064 Finished ordination step. #>  #> 2024-04-24 16:50:55.814119 Beta diversity computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = bray , k = 2 , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation — correlation","title":"Correlation — correlation","text":"function returns correlation coefficients variables one dataset variables second dataset","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation — correlation","text":"","code":"correlation(   data1,   data2,   method,   format = c(\"ComputeResult\", \"data.table\"),   verbose = c(TRUE, FALSE),   ... )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation — correlation","text":"data1 first dataset. data.table data2 second dataset. data.table method string defining type correlation run. currently supported values specific class data1 data2. format string defining desired format result. currently supported values 'data.table' 'ComputeResult'. verbose boolean indicating timed logging desired ... additional parameters","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation — correlation","text":"data.frame correlation coefficients ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation — correlation","text":"","code":"diabImmune_genus <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\",       continuousMetadataOnly = TRUE )  correlationDT <- correlation(      diabImmune_genus,       method = 'spearman',       format = 'data.table' ) #>  #> 2024-04-24 16:50:59.8707 Completed correlation with method=spearman. Formatting results. #>  #> 2024-04-24 16:50:59.871895 Received df table with 3184 samples and 138 features with values.  correlationOutput <- correlation(      diabImmune_genus,       method = 'spearman',       format = 'ComputeResult' ) #>  #> 2024-04-24 16:51:03.71643 Completed correlation with method=spearman. Formatting results. #>  #> 2024-04-24 16:51:03.717338 Received df table with 3184 samples and 138 features with values. #>  #> 2024-04-24 16:51:03.718841 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  spearman  alsoCorrelationDT <- getComputeResult(      correlationOutput,       \"data.table\" )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlationNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation Network Visualization — correlationNetwork","title":"Correlation Network Visualization — correlationNetwork","text":"Visualize correlation result network","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlationNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation Network Visualization — correlationNetwork","text":"","code":"correlationNetwork(   object,   correlationCoefThreshold = 0.5,   pValueThreshold = 0.05,   ... )  # S4 method for ComputeResult correlationNetwork(   object,   correlationCoefThreshold = 0.5,   pValueThreshold = 0.05,   ... )  # S4 method for data.frame correlationNetwork(   object,   correlationCoefThreshold = 0.5,   pValueThreshold = 0.05,   bipartiteNetwork = c(FALSE, TRUE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlationNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation Network Visualization — correlationNetwork","text":"object ComputeResult data.frame correlationCoefThreshold threshold filter edges correlation coefficient. Edges correlation coefficients threshold removed. Default .5 pValueThreshold threshold filter edges p-value. Edges p-values threshold removed. Default .05 ... additional arguments bipartiteNetwork network use bipartite unipartite layout? Defaults unipartite.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlationNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation Network Visualization — correlationNetwork","text":"","code":"correlationOutput <- MicrobiomeDB::correlation(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\", continuousMetadataOnly = TRUE),       method='spearman',       verbose=FALSE ) correlationNetwork(correlationOutput) ## renders html widget  {\"x\":{\"data\":{\"links\":[{\"source\":\"Coprobacter\",\"target\":\"age_at_type_1_diabetes_diagnosis_days\",\"value\":0.524663091444649,\"pValue\":4.676770082312487e-11},{\"source\":\"unclassified Muribaculaceae\",\"target\":\"age_at_type_1_diabetes_diagnosis_days\",\"value\":0.509019797520334,\"pValue\":2.13462136855469e-10},{\"source\":\"Alistipes\",\"target\":\"age_months\",\"value\":0.5397456630921771,\"pValue\":0},{\"source\":\"Colidextribacter\",\"target\":\"age_months\",\"value\":0.5192217431279649,\"pValue\":0},{\"source\":\"Faecalibacterium\",\"target\":\"age_months\",\"value\":0.5564628845629651,\"pValue\":0},{\"source\":\"Lachnospiraceae NK4A136 group\",\"target\":\"age_months\",\"value\":0.5664616643798602,\"pValue\":0},{\"source\":\"Lachnospiraceae UCG-004\",\"target\":\"age_months\",\"value\":0.5013839365679983,\"pValue\":0},{\"source\":\"Oscillibacter\",\"target\":\"age_months\",\"value\":0.5610703084864889,\"pValue\":0},{\"source\":\"Ruminococcus\",\"target\":\"age_months\",\"value\":0.5464471254786487,\"pValue\":0},{\"source\":\"unclassified Lachnospiraceae\",\"target\":\"age_months\",\"value\":0.5141615087602621,\"pValue\":0}],\"column1NodeIds\":[\"Coprobacter\",\"unclassified Muribaculaceae\",\"Alistipes\",\"Colidextribacter\",\"Faecalibacterium\",\"Lachnospiraceae NK4A136 group\",\"Lachnospiraceae UCG-004\",\"Oscillibacter\",\"Ruminococcus\",\"unclassified Lachnospiraceae\"],\"column2NodeIds\":[\"age_at_type_1_diabetes_diagnosis_days\",\"age_months\"]}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential abundance — differentialAbundance","title":"Differential abundance — differentialAbundance","text":"function returns fold change associated p value differential abundance analysis. useful finding taxa abundance strongly differs two groups samples, finding taxa abundance differs skin saliva samples. function allows one recreate results differential abundance analysis MicrobiomeDB.org. However, recognize function makes assumptions data may valid contexts. better support longitudinal studies metabolomic data, example, please see wrapper/ helper methods Maaslin2 (MicrobiomeDB::Maaslin2) DESeq2 (DESeqDataSetFromCollection).","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential abundance — differentialAbundance","text":"","code":"differentialAbundance(   data,   covariate,   groupA,   groupB,   method = c(\"Maaslin2\", \"DESeq2\"),   verbose = c(TRUE, FALSE) )  # S4 method for CollectionWithMetadata,character,missingOrNULL,missingOrNULL differentialAbundance(   data,   covariate,   groupA,   groupB,   method = c(\"Maaslin2\", \"DESeq2\"),   verbose = c(TRUE, FALSE) )  # S4 method for CollectionWithMetadata,character,function,missingOrNULL differentialAbundance(   data,   covariate,   groupA,   groupB,   method = c(\"Maaslin2\", \"DESeq2\"),   verbose = c(TRUE, FALSE) )  # S4 method for CollectionWithMetadata,character,function,function differentialAbundance(   data,   covariate,   groupA,   groupB,   method = c(\"Maaslin2\", \"DESeq2\"),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential abundance — differentialAbundance","text":"data AbundanceData object covariate character vector giving name metadata variable interest. variable two values, need provide functions arguments groupA groupB. groupA function takes vector values returns TRUE FALSE value. used assign samples groupA. groupB function takes vector values returns TRUE FALSE value. used assign samples groupB. provided, groupB complement groupA. method string defining differential abundance method. Accepted values 'DESeq2' 'Maaslin2'. Default 'Maaslin2', 'DESeq2' supports counts. verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential abundance — differentialAbundance","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Differential abundance — differentialAbundance","text":"","code":"## a continuous variable diffAbundOutput <- MicrobiomeDB::differentialAbundance(        getCollection(microbiomeData::DiabImmune, '16S (V4) Genus'),         \"breastfed_duration_days\",         groupA = function(x) {x<300},        groupB = function(x) {x>=300},        method='Maaslin2',         verbose=TRUE ) #>  #> 2024-04-24 16:51:08.848187 Found NAs in specified variable. Removing these records. #>  #> 2024-04-24 16:51:08.956962 Received abundance table with 2533 samples and 673 taxa. #>  #> 2024-04-24 16:51:08.960321 Found 2533 samples with a value for breastfed_duration_days in either groupA or groupB. The calculation will continue with only these samples. #> [1] \"Creating output folder\" #> [1] \"Creating output feature tables folder\" #> [1] \"Creating output fits folder\" #> 2024-04-24 16:51:09.097233 INFO::Writing function arguments to log file #> 2024-04-24 16:51:09.100942 INFO::Verifying options selected are valid #> 2024-04-24 16:51:09.101454 INFO::Determining format of input files #> 2024-04-24 16:51:09.102681 INFO::Input format is data samples as rows and metadata samples as rows #> 2024-04-24 16:51:09.114772 INFO::Formula for fixed effects: expr ~  breastfed_duration_days #> 2024-04-24 16:51:09.11563 INFO::Filter data based on min abundance and min prevalence #> 2024-04-24 16:51:09.116118 INFO::Total samples in data: 2533 #> 2024-04-24 16:51:09.116576 INFO::Min samples required with min abundance for a feature not to be filtered: 253.300000 #> 2024-04-24 16:51:09.132821 INFO::Total filtered features: 521 #> 2024-04-24 16:51:09.133829 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Candidatus.Arthromitus, Candidatus.Obscuribacter, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Faecalicoccus, Faecalitalea, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavobacterium, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Marvinbryantia, Massilia, Megamonas, Merdibacter, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Myxococcus, NK4A214.group, Nakamurella, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phaseolibacter, Phocea, Phyllobacterium, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudoflavonifractor, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tetragenococcus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97 #> 2024-04-24 16:51:09.140342 INFO::Total filtered features with variance filtering: 0 #> 2024-04-24 16:51:09.140897 INFO::Filtered feature names from variance filtering: #> 2024-04-24 16:51:09.141359 INFO::Running selected normalization method: TSS #> 2024-04-24 16:51:09.178366 INFO::Applying z-score to standardize continuous metadata #> 2024-04-24 16:51:09.181467 INFO::Running selected transform method: LOG #> 2024-04-24 16:51:09.230559 INFO::Running selected analysis method: LM #> 2024-04-24 16:51:09.231382 INFO::Fitting model to feature number 1, Actinomyces #> 2024-04-24 16:51:09.235458 INFO::Fitting model to feature number 2, Agathobacter #> 2024-04-24 16:51:09.239058 INFO::Fitting model to feature number 3, Akkermansia #> 2024-04-24 16:51:09.242643 INFO::Fitting model to feature number 4, Alistipes #> 2024-04-24 16:51:09.2462 INFO::Fitting model to feature number 5, Anaerostipes #> 2024-04-24 16:51:09.249805 INFO::Fitting model to feature number 6, Atopobium #> 2024-04-24 16:51:09.253407 INFO::Fitting model to feature number 7, Bacteroides #> 2024-04-24 16:51:09.257026 INFO::Fitting model to feature number 8, Barnesiella #> 2024-04-24 16:51:09.260637 INFO::Fitting model to feature number 9, Bifidobacterium #> 2024-04-24 16:51:09.26428 INFO::Fitting model to feature number 10, Bilophila #> 2024-04-24 16:51:09.267891 INFO::Fitting model to feature number 11, Blautia #> 2024-04-24 16:51:09.271437 INFO::Fitting model to feature number 12, Butyricicoccus #> 2024-04-24 16:51:09.275046 INFO::Fitting model to feature number 13, CAG.352 #> 2024-04-24 16:51:09.278639 INFO::Fitting model to feature number 14, Campylobacter #> 2024-04-24 16:51:09.282255 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group #> 2024-04-24 16:51:09.285869 INFO::Fitting model to feature number 16, Clostridioides #> 2024-04-24 16:51:09.289578 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 #> 2024-04-24 16:51:09.293256 INFO::Fitting model to feature number 18, Colidextribacter #> 2024-04-24 16:51:09.296987 INFO::Fitting model to feature number 19, Collinsella #> 2024-04-24 16:51:09.300686 INFO::Fitting model to feature number 20, Coprobacillus #> 2024-04-24 16:51:09.304319 INFO::Fitting model to feature number 21, Coprococcus #> 2024-04-24 16:51:09.307947 INFO::Fitting model to feature number 22, DTU089 #> 2024-04-24 16:51:09.311589 INFO::Fitting model to feature number 23, Dialister #> 2024-04-24 16:51:09.315149 INFO::Fitting model to feature number 24, Dorea #> 2024-04-24 16:51:09.31872 INFO::Fitting model to feature number 25, Eggerthella #> 2024-04-24 16:51:09.322355 INFO::Fitting model to feature number 26, Eisenbergiella #> 2024-04-24 16:51:09.325932 INFO::Fitting model to feature number 27, Enterococcus #> 2024-04-24 16:51:09.329541 INFO::Fitting model to feature number 28, Erysipelatoclostridium #> 2024-04-24 16:51:09.333117 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003 #> 2024-04-24 16:51:09.336723 INFO::Fitting model to feature number 30, Escherichia.Shigella #> 2024-04-24 16:51:09.340408 INFO::Fitting model to feature number 31, Faecalibacterium #> 2024-04-24 16:51:09.344066 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group #> 2024-04-24 16:51:09.347683 INFO::Fitting model to feature number 33, Flavonifractor #> 2024-04-24 16:51:09.351283 INFO::Fitting model to feature number 34, Fusicatenibacter #> 2024-04-24 16:51:09.354934 INFO::Fitting model to feature number 35, Fusobacterium #> 2024-04-24 16:51:09.358572 INFO::Fitting model to feature number 36, Gemella #> 2024-04-24 16:51:09.362232 INFO::Fitting model to feature number 37, Granulicatella #> 2024-04-24 16:51:09.365878 INFO::Fitting model to feature number 38, Haemophilus #> 2024-04-24 16:51:09.36954 INFO::Fitting model to feature number 39, Holdemania #> 2024-04-24 16:51:09.373166 INFO::Fitting model to feature number 40, Hungatella #> 2024-04-24 16:51:09.376817 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. #> 2024-04-24 16:51:09.380442 INFO::Fitting model to feature number 42, Intestinibacter #> 2024-04-24 16:51:09.384087 INFO::Fitting model to feature number 43, Intestinimonas #> 2024-04-24 16:51:09.387725 INFO::Fitting model to feature number 44, Klebsiella #> 2024-04-24 16:51:09.391377 INFO::Fitting model to feature number 45, Lachnoclostridium #> 2024-04-24 16:51:09.395036 INFO::Fitting model to feature number 46, Lachnospira #> 2024-04-24 16:51:09.398674 INFO::Fitting model to feature number 47, Lachnospiraceae.ND3007.group #> 2024-04-24 16:51:09.402355 INFO::Fitting model to feature number 48, Lachnospiraceae.NK4A136.group #> 2024-04-24 16:51:09.405987 INFO::Fitting model to feature number 49, Lachnospiraceae.UCG.001 #> 2024-04-24 16:51:09.409643 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.004 #> 2024-04-24 16:51:09.413275 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.009 #> 2024-04-24 16:51:09.416945 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.010 #> 2024-04-24 16:51:09.420584 INFO::Fitting model to feature number 53, Lactobacillus #> 2024-04-24 16:51:09.424252 INFO::Fitting model to feature number 54, Lactococcus #> 2024-04-24 16:51:09.427912 INFO::Fitting model to feature number 55, Mannheimia #> 2024-04-24 16:51:09.431534 INFO::Fitting model to feature number 56, Megasphaera #> 2024-04-24 16:51:09.43524 INFO::Fitting model to feature number 57, Monoglobus #> 2024-04-24 16:51:09.438893 INFO::Fitting model to feature number 58, Neisseria #> 2024-04-24 16:51:09.44252 INFO::Fitting model to feature number 59, Odoribacter #> 2024-04-24 16:51:09.446161 INFO::Fitting model to feature number 60, Oscillibacter #> 2024-04-24 16:51:09.449859 INFO::Fitting model to feature number 61, Oscillospira #> 2024-04-24 16:51:09.453526 INFO::Fitting model to feature number 62, Parabacteroides #> 2024-04-24 16:51:09.457191 INFO::Fitting model to feature number 63, Parasutterella #> 2024-04-24 16:51:09.460818 INFO::Fitting model to feature number 64, Phascolarctobacterium #> 2024-04-24 16:51:09.464475 INFO::Fitting model to feature number 65, Prevotella #> 2024-04-24 16:51:09.468174 INFO::Fitting model to feature number 66, Pseudomonas #> 2024-04-24 16:51:09.471798 INFO::Fitting model to feature number 67, Romboutsia #> 2024-04-24 16:51:09.475381 INFO::Fitting model to feature number 68, Roseburia #> 2024-04-24 16:51:09.478989 INFO::Fitting model to feature number 69, Rothia #> 2024-04-24 16:51:09.48265 INFO::Fitting model to feature number 70, Ruminococcus #> 2024-04-24 16:51:09.486321 INFO::Fitting model to feature number 71, Sellimonas #> 2024-04-24 16:51:09.490161 INFO::Fitting model to feature number 72, Solobacterium #> 2024-04-24 16:51:09.493887 INFO::Fitting model to feature number 73, Staphylococcus #> 2024-04-24 16:51:09.49755 INFO::Fitting model to feature number 74, Streptococcus #> 2024-04-24 16:51:09.501204 INFO::Fitting model to feature number 75, Subdoligranulum #> 2024-04-24 16:51:09.504918 INFO::Fitting model to feature number 76, Sutterella #> 2024-04-24 16:51:09.508616 INFO::Fitting model to feature number 77, Terrisporobacter #> 2024-04-24 16:51:09.512367 INFO::Fitting model to feature number 78, Turicibacter #> 2024-04-24 16:51:09.516001 INFO::Fitting model to feature number 79, Tuzzerella #> 2024-04-24 16:51:09.519632 INFO::Fitting model to feature number 80, Tyzzerella #> 2024-04-24 16:51:09.523212 INFO::Fitting model to feature number 81, UBA1819 #> 2024-04-24 16:51:09.526892 INFO::Fitting model to feature number 82, UCG.002 #> 2024-04-24 16:51:09.53056 INFO::Fitting model to feature number 83, UCG.003 #> 2024-04-24 16:51:09.534178 INFO::Fitting model to feature number 84, UCG.005 #> 2024-04-24 16:51:09.537856 INFO::Fitting model to feature number 85, Veillonella #> 2024-04-24 16:51:09.541501 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group #> 2024-04-24 16:51:09.545154 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group #> 2024-04-24 16:51:09.548755 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group #> 2024-04-24 16:51:09.552369 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group #> 2024-04-24 16:51:09.555989 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group #> 2024-04-24 16:51:09.559635 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group #> 2024-04-24 16:51:09.563271 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group #> 2024-04-24 16:51:09.5669 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group #> 2024-04-24 16:51:09.570566 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group #> 2024-04-24 16:51:09.574254 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group #> 2024-04-24 16:51:09.578036 INFO::Fitting model to feature number 96, unclassified.Chloroplast #> 2024-04-24 16:51:09.581705 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014 #> 2024-04-24 16:51:09.585328 INFO::Fitting model to feature number 98, unclassified.Clostridia #> 2024-04-24 16:51:09.588966 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group #> 2024-04-24 16:51:09.592642 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales #> 2024-04-24 16:51:09.596264 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae #> 2024-04-24 16:51:09.599934 INFO::Fitting model to feature number 102, unclassified.Mitochondria #> 2024-04-24 16:51:09.603577 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae #> 2024-04-24 16:51:09.607156 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus #> 2024-04-24 16:51:09.610804 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales #> 2024-04-24 16:51:09.614427 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae #> 2024-04-24 16:51:09.618058 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group #> 2024-04-24 16:51:09.633991 INFO::Counting total values for each feature #> 2024-04-24 16:51:09.639237 INFO::Writing filtered data to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/features/filtered_data.tsv #> 2024-04-24 16:51:09.766118 INFO::Writing filtered, normalized data to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/features/filtered_data_norm.tsv #> 2024-04-24 16:51:09.887297 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/features/filtered_data_norm_transformed.tsv #> 2024-04-24 16:51:10.103637 INFO::Writing residuals to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/fits/residuals.rds #> 2024-04-24 16:51:10.158799 INFO::Writing fitted values to file /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/fits/fitted.rds #> 2024-04-24 16:51:10.177932 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/all_results.tsv #> 2024-04-24 16:51:10.179755 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e4c9d31fb/significant_results.tsv #>  #> 2024-04-24 16:51:10.181783 Completed method=Maaslin2. Formatting results. #>  #> 2024-04-24 16:51:10.185421 Differential abundance computation completed with parameters recordIdColumn =  16S_rRNA_(V4)_assay_Id , comparatorColName =  breastfed_duration_days , method =  Maaslin2 , groupA = groupA , groupB =  groupB  ## a categorical variable with 3 values, one of which we exclude diffAbundOutput <- MicrobiomeDB::differentialAbundance(        getCollection(microbiomeData::DiabImmune, '16S (V4) Genus'),         \"country\",         groupA = function(x) {x==\"Russia\"},        groupB = function(x) {x==\"Finland\"},        method='Maaslin2',         verbose=FALSE ) #> [1] \"Creating output folder\" #> [1] \"Creating output feature tables folder\" #> [1] \"Creating output fits folder\" #> 2024-04-24 16:51:10.472175 INFO::Writing function arguments to log file #> 2024-04-24 16:51:10.475968 INFO::Verifying options selected are valid #> 2024-04-24 16:51:10.476489 INFO::Determining format of input files #> 2024-04-24 16:51:10.477783 INFO::Input format is data samples as rows and metadata samples as rows #> 2024-04-24 16:51:10.49066 INFO::Formula for fixed effects: expr ~  country #> 2024-04-24 16:51:10.491644 INFO::Filter data based on min abundance and min prevalence #> 2024-04-24 16:51:10.492133 INFO::Total samples in data: 2692 #> 2024-04-24 16:51:10.492626 INFO::Min samples required with min abundance for a feature not to be filtered: 269.200000 #> 2024-04-24 16:51:10.509655 INFO::Total filtered features: 521 #> 2024-04-24 16:51:10.510739 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asticcacaulis, Aureimonas, Bacillus, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Marinilactibacillus, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylobacillus, Methylobacterium.Methylorubrum, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, Paenibacillus, Paeniclostridium, Paludicola, Papillibacter, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Piscinibacter, Planifilum, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinivibrio, Sulfurospirillum, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gastranaerophilales, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97 #> 2024-04-24 16:51:10.51758 INFO::Total filtered features with variance filtering: 0 #> 2024-04-24 16:51:10.518154 INFO::Filtered feature names from variance filtering: #> 2024-04-24 16:51:10.518617 INFO::Running selected normalization method: TSS #> 2024-04-24 16:51:10.570749 INFO::Applying z-score to standardize continuous metadata #> 2024-04-24 16:51:10.573849 INFO::Running selected transform method: LOG #> 2024-04-24 16:51:10.626987 INFO::Running selected analysis method: LM #> 2024-04-24 16:51:10.627897 INFO::Fitting model to feature number 1, Actinomyces #> 2024-04-24 16:51:10.632164 INFO::Fitting model to feature number 2, Agathobacter #> 2024-04-24 16:51:10.636015 INFO::Fitting model to feature number 3, Akkermansia #> 2024-04-24 16:51:10.639817 INFO::Fitting model to feature number 4, Alistipes #> 2024-04-24 16:51:10.643527 INFO::Fitting model to feature number 5, Anaerostipes #> 2024-04-24 16:51:10.647264 INFO::Fitting model to feature number 6, Atopobium #> 2024-04-24 16:51:10.651001 INFO::Fitting model to feature number 7, Bacteroides #> 2024-04-24 16:51:10.654754 INFO::Fitting model to feature number 8, Barnesiella #> 2024-04-24 16:51:10.658484 INFO::Fitting model to feature number 9, Bifidobacterium #> 2024-04-24 16:51:10.662206 INFO::Fitting model to feature number 10, Bilophila #> 2024-04-24 16:51:10.665942 INFO::Fitting model to feature number 11, Blautia #> 2024-04-24 16:51:10.669673 INFO::Fitting model to feature number 12, Butyricicoccus #> 2024-04-24 16:51:10.67342 INFO::Fitting model to feature number 13, CAG.352 #> 2024-04-24 16:51:10.677135 INFO::Fitting model to feature number 14, Campylobacter #> 2024-04-24 16:51:10.680911 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group #> 2024-04-24 16:51:10.684646 INFO::Fitting model to feature number 16, Clostridioides #> 2024-04-24 16:51:10.688373 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 #> 2024-04-24 16:51:10.692153 INFO::Fitting model to feature number 18, Colidextribacter #> 2024-04-24 16:51:10.695945 INFO::Fitting model to feature number 19, Collinsella #> 2024-04-24 16:51:10.69971 INFO::Fitting model to feature number 20, Coprobacillus #> 2024-04-24 16:51:10.703426 INFO::Fitting model to feature number 21, Coprococcus #> 2024-04-24 16:51:10.707182 INFO::Fitting model to feature number 22, Corynebacterium #> 2024-04-24 16:51:10.710906 INFO::Fitting model to feature number 23, DTU089 #> 2024-04-24 16:51:10.714686 INFO::Fitting model to feature number 24, Dialister #> 2024-04-24 16:51:10.718477 INFO::Fitting model to feature number 25, Dorea #> 2024-04-24 16:51:10.722259 INFO::Fitting model to feature number 26, Eggerthella #> 2024-04-24 16:51:10.72605 INFO::Fitting model to feature number 27, Eisenbergiella #> 2024-04-24 16:51:10.729803 INFO::Fitting model to feature number 28, Enterococcus #> 2024-04-24 16:51:10.733574 INFO::Fitting model to feature number 29, Erysipelatoclostridium #> 2024-04-24 16:51:10.737375 INFO::Fitting model to feature number 30, Erysipelotrichaceae.UCG.003 #> 2024-04-24 16:51:10.741156 INFO::Fitting model to feature number 31, Escherichia.Shigella #> 2024-04-24 16:51:10.744953 INFO::Fitting model to feature number 32, Faecalibacterium #> 2024-04-24 16:51:10.748741 INFO::Fitting model to feature number 33, Family.XIII.AD3011.group #> 2024-04-24 16:51:10.752519 INFO::Fitting model to feature number 34, Flavonifractor #> 2024-04-24 16:51:10.756344 INFO::Fitting model to feature number 35, Fusicatenibacter #> 2024-04-24 16:51:10.76017 INFO::Fitting model to feature number 36, Fusobacterium #> 2024-04-24 16:51:10.764029 INFO::Fitting model to feature number 37, Gemella #> 2024-04-24 16:51:10.769405 INFO::Fitting model to feature number 38, Gordonibacter #> 2024-04-24 16:51:10.775218 INFO::Fitting model to feature number 39, Granulicatella #> 2024-04-24 16:51:10.781141 INFO::Fitting model to feature number 40, Haemophilus #> 2024-04-24 16:51:10.78698 INFO::Fitting model to feature number 41, Holdemania #> 2024-04-24 16:51:10.791312 INFO::Fitting model to feature number 42, Hungatella #> 2024-04-24 16:51:10.79505 INFO::Fitting model to feature number 43, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. #> 2024-04-24 16:51:10.798803 INFO::Fitting model to feature number 44, Intestinibacter #> 2024-04-24 16:51:10.802514 INFO::Fitting model to feature number 45, Intestinimonas #> 2024-04-24 16:51:10.80625 INFO::Fitting model to feature number 46, Klebsiella #> 2024-04-24 16:51:10.809972 INFO::Fitting model to feature number 47, Lachnoclostridium #> 2024-04-24 16:51:10.813697 INFO::Fitting model to feature number 48, Lachnospira #> 2024-04-24 16:51:10.817451 INFO::Fitting model to feature number 49, Lachnospiraceae.ND3007.group #> 2024-04-24 16:51:10.821231 INFO::Fitting model to feature number 50, Lachnospiraceae.NK4A136.group #> 2024-04-24 16:51:10.824974 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.001 #> 2024-04-24 16:51:10.828727 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.004 #> 2024-04-24 16:51:10.832465 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.009 #> 2024-04-24 16:51:10.836181 INFO::Fitting model to feature number 54, Lachnospiraceae.UCG.010 #> 2024-04-24 16:51:10.839871 INFO::Fitting model to feature number 55, Lactobacillus #> 2024-04-24 16:51:10.843587 INFO::Fitting model to feature number 56, Lactococcus #> 2024-04-24 16:51:10.847297 INFO::Fitting model to feature number 57, Mannheimia #> 2024-04-24 16:51:10.850981 INFO::Fitting model to feature number 58, Megasphaera #> 2024-04-24 16:51:10.85479 INFO::Fitting model to feature number 59, Monoglobus #> 2024-04-24 16:51:10.858541 INFO::Fitting model to feature number 60, Neisseria #> 2024-04-24 16:51:10.862243 INFO::Fitting model to feature number 61, Odoribacter #> 2024-04-24 16:51:10.865965 INFO::Fitting model to feature number 62, Oscillibacter #> 2024-04-24 16:51:10.869746 INFO::Fitting model to feature number 63, Oscillospira #> 2024-04-24 16:51:10.873487 INFO::Fitting model to feature number 64, Parabacteroides #> 2024-04-24 16:51:10.877286 INFO::Fitting model to feature number 65, Parasutterella #> 2024-04-24 16:51:10.881036 INFO::Fitting model to feature number 66, Prevotella #> 2024-04-24 16:51:10.88484 INFO::Fitting model to feature number 67, Pseudomonas #> 2024-04-24 16:51:10.888625 INFO::Fitting model to feature number 68, Romboutsia #> 2024-04-24 16:51:10.892438 INFO::Fitting model to feature number 69, Roseburia #> 2024-04-24 16:51:10.89642 INFO::Fitting model to feature number 70, Rothia #> 2024-04-24 16:51:10.900202 INFO::Fitting model to feature number 71, Ruminococcus #> 2024-04-24 16:51:10.904021 INFO::Fitting model to feature number 72, Sellimonas #> 2024-04-24 16:51:10.907835 INFO::Fitting model to feature number 73, Solobacterium #> 2024-04-24 16:51:10.911615 INFO::Fitting model to feature number 74, Staphylococcus #> 2024-04-24 16:51:10.915434 INFO::Fitting model to feature number 75, Streptococcus #> 2024-04-24 16:51:10.919264 INFO::Fitting model to feature number 76, Subdoligranulum #> 2024-04-24 16:51:10.923058 INFO::Fitting model to feature number 77, Sutterella #> 2024-04-24 16:51:10.926849 INFO::Fitting model to feature number 78, Terrisporobacter #> 2024-04-24 16:51:10.930625 INFO::Fitting model to feature number 79, Turicibacter #> 2024-04-24 16:51:10.934417 INFO::Fitting model to feature number 80, Tuzzerella #> 2024-04-24 16:51:10.938244 INFO::Fitting model to feature number 81, Tyzzerella #> 2024-04-24 16:51:10.942025 INFO::Fitting model to feature number 82, UBA1819 #> 2024-04-24 16:51:10.945811 INFO::Fitting model to feature number 83, UCG.002 #> 2024-04-24 16:51:10.94957 INFO::Fitting model to feature number 84, UCG.003 #> 2024-04-24 16:51:10.953444 INFO::Fitting model to feature number 85, UCG.005 #> 2024-04-24 16:51:10.957261 INFO::Fitting model to feature number 86, Veillonella #> 2024-04-24 16:51:10.961042 INFO::Fitting model to feature number 87, X.Clostridium..innocuum.group #> 2024-04-24 16:51:10.964842 INFO::Fitting model to feature number 88, X.Eubacterium..eligens.group #> 2024-04-24 16:51:10.968675 INFO::Fitting model to feature number 89, X.Eubacterium..fissicatena.group #> 2024-04-24 16:51:10.972506 INFO::Fitting model to feature number 90, X.Eubacterium..hallii.group #> 2024-04-24 16:51:10.976315 INFO::Fitting model to feature number 91, X.Eubacterium..siraeum.group #> 2024-04-24 16:51:10.98014 INFO::Fitting model to feature number 92, X.Eubacterium..ventriosum.group #> 2024-04-24 16:51:10.983917 INFO::Fitting model to feature number 93, X.Eubacterium..xylanophilum.group #> 2024-04-24 16:51:10.987715 INFO::Fitting model to feature number 94, X.Ruminococcus..gauvreauii.group #> 2024-04-24 16:51:10.991523 INFO::Fitting model to feature number 95, X.Ruminococcus..gnavus.group #> 2024-04-24 16:51:10.995312 INFO::Fitting model to feature number 96, X.Ruminococcus..torques.group #> 2024-04-24 16:51:10.999141 INFO::Fitting model to feature number 97, unclassified.Chloroplast #> 2024-04-24 16:51:11.00288 INFO::Fitting model to feature number 98, unclassified.Clostridia.UCG.014 #> 2024-04-24 16:51:11.006635 INFO::Fitting model to feature number 99, unclassified.Clostridia #> 2024-04-24 16:51:11.010418 INFO::Fitting model to feature number 100, unclassified.Clostridia.vadinBB60.group #> 2024-04-24 16:51:11.014205 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae #> 2024-04-24 16:51:11.018021 INFO::Fitting model to feature number 102, unclassified.Mitochondria #> 2024-04-24 16:51:11.021864 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae #> 2024-04-24 16:51:11.025646 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus #> 2024-04-24 16:51:11.029402 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales #> 2024-04-24 16:51:11.033162 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae #> 2024-04-24 16:51:11.036959 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group #> 2024-04-24 16:51:11.052416 INFO::Counting total values for each feature #> 2024-04-24 16:51:11.057658 INFO::Writing filtered data to file /tmp/RtmpXpuOxT/maaslin194e36845449/features/filtered_data.tsv #> 2024-04-24 16:51:11.18178 INFO::Writing filtered, normalized data to file /tmp/RtmpXpuOxT/maaslin194e36845449/features/filtered_data_norm.tsv #> 2024-04-24 16:51:11.311745 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpXpuOxT/maaslin194e36845449/features/filtered_data_norm_transformed.tsv #> 2024-04-24 16:51:11.540246 INFO::Writing residuals to file /tmp/RtmpXpuOxT/maaslin194e36845449/fits/residuals.rds #> 2024-04-24 16:51:11.600622 INFO::Writing fitted values to file /tmp/RtmpXpuOxT/maaslin194e36845449/fits/fitted.rds #> 2024-04-24 16:51:11.620542 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e36845449/all_results.tsv #> 2024-04-24 16:51:11.622221 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e36845449/significant_results.tsv  ## a categorical variable with 2 values diffAbundOutput <- MicrobiomeDB::differentialAbundance(        getCollection(microbiomeData::DiabImmune, '16S (V4) Genus'),        \"delivery_mode\",        method='Maaslin2',         verbose=FALSE )  #> [1] \"Creating output folder\" #> [1] \"Creating output feature tables folder\" #> [1] \"Creating output fits folder\" #> 2024-04-24 16:51:11.943767 INFO::Writing function arguments to log file #> 2024-04-24 16:51:11.947457 INFO::Verifying options selected are valid #> 2024-04-24 16:51:11.948004 INFO::Determining format of input files #> 2024-04-24 16:51:11.949487 INFO::Input format is data samples as rows and metadata samples as rows #> 2024-04-24 16:51:11.964072 INFO::Formula for fixed effects: expr ~  delivery_mode #> 2024-04-24 16:51:11.964972 INFO::Filter data based on min abundance and min prevalence #> 2024-04-24 16:51:11.965457 INFO::Total samples in data: 3184 #> 2024-04-24 16:51:11.965918 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000 #> 2024-04-24 16:51:11.985696 INFO::Total filtered features: 563 #> 2024-04-24 16:51:11.986722 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97 #> 2024-04-24 16:51:11.994362 INFO::Total filtered features with variance filtering: 0 #> 2024-04-24 16:51:11.994928 INFO::Filtered feature names from variance filtering: #> 2024-04-24 16:51:11.995388 INFO::Running selected normalization method: TSS #> 2024-04-24 16:51:12.04412 INFO::Applying z-score to standardize continuous metadata #> 2024-04-24 16:51:12.047171 INFO::Running selected transform method: LOG #> 2024-04-24 16:51:12.11105 INFO::Running selected analysis method: LM #> 2024-04-24 16:51:12.11193 INFO::Fitting model to feature number 1, Actinomyces #> 2024-04-24 16:51:12.116581 INFO::Fitting model to feature number 2, Agathobacter #> 2024-04-24 16:51:12.120772 INFO::Fitting model to feature number 3, Akkermansia #> 2024-04-24 16:51:12.124941 INFO::Fitting model to feature number 4, Alistipes #> 2024-04-24 16:51:12.129074 INFO::Fitting model to feature number 5, Anaerostipes #> 2024-04-24 16:51:12.1332 INFO::Fitting model to feature number 6, Atopobium #> 2024-04-24 16:51:12.137281 INFO::Fitting model to feature number 7, Bacteroides #> 2024-04-24 16:51:12.141403 INFO::Fitting model to feature number 8, Barnesiella #> 2024-04-24 16:51:12.145457 INFO::Fitting model to feature number 9, Bifidobacterium #> 2024-04-24 16:51:12.14956 INFO::Fitting model to feature number 10, Bilophila #> 2024-04-24 16:51:12.153613 INFO::Fitting model to feature number 11, Blautia #> 2024-04-24 16:51:12.157671 INFO::Fitting model to feature number 12, Butyricicoccus #> 2024-04-24 16:51:12.161767 INFO::Fitting model to feature number 13, CAG.352 #> 2024-04-24 16:51:12.165833 INFO::Fitting model to feature number 14, Campylobacter #> 2024-04-24 16:51:12.16993 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group #> 2024-04-24 16:51:12.174026 INFO::Fitting model to feature number 16, Clostridioides #> 2024-04-24 16:51:12.178134 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 #> 2024-04-24 16:51:12.18224 INFO::Fitting model to feature number 18, Colidextribacter #> 2024-04-24 16:51:12.186364 INFO::Fitting model to feature number 19, Collinsella #> 2024-04-24 16:51:12.190536 INFO::Fitting model to feature number 20, Coprobacillus #> 2024-04-24 16:51:12.194659 INFO::Fitting model to feature number 21, Coprococcus #> 2024-04-24 16:51:12.198787 INFO::Fitting model to feature number 22, DTU089 #> 2024-04-24 16:51:12.202933 INFO::Fitting model to feature number 23, Dialister #> 2024-04-24 16:51:12.207039 INFO::Fitting model to feature number 24, Dorea #> 2024-04-24 16:51:12.211143 INFO::Fitting model to feature number 25, Eggerthella #> 2024-04-24 16:51:12.215236 INFO::Fitting model to feature number 26, Eisenbergiella #> 2024-04-24 16:51:12.219383 INFO::Fitting model to feature number 27, Enterococcus #> 2024-04-24 16:51:12.223527 INFO::Fitting model to feature number 28, Erysipelatoclostridium #> 2024-04-24 16:51:12.227646 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003 #> 2024-04-24 16:51:12.231746 INFO::Fitting model to feature number 30, Escherichia.Shigella #> 2024-04-24 16:51:12.235831 INFO::Fitting model to feature number 31, Faecalibacterium #> 2024-04-24 16:51:12.23993 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group #> 2024-04-24 16:51:12.244063 INFO::Fitting model to feature number 33, Flavonifractor #> 2024-04-24 16:51:12.248202 INFO::Fitting model to feature number 34, Fusicatenibacter #> 2024-04-24 16:51:12.252374 INFO::Fitting model to feature number 35, Fusobacterium #> 2024-04-24 16:51:12.256522 INFO::Fitting model to feature number 36, Gemella #> 2024-04-24 16:51:12.26069 INFO::Fitting model to feature number 37, Granulicatella #> 2024-04-24 16:51:12.26481 INFO::Fitting model to feature number 38, Haemophilus #> 2024-04-24 16:51:12.268952 INFO::Fitting model to feature number 39, Holdemania #> 2024-04-24 16:51:12.273063 INFO::Fitting model to feature number 40, Hungatella #> 2024-04-24 16:51:12.277163 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. #> 2024-04-24 16:51:12.281285 INFO::Fitting model to feature number 42, Intestinibacter #> 2024-04-24 16:51:12.285474 INFO::Fitting model to feature number 43, Intestinimonas #> 2024-04-24 16:51:12.289644 INFO::Fitting model to feature number 44, Klebsiella #> 2024-04-24 16:51:12.293754 INFO::Fitting model to feature number 45, Lachnoclostridium #> 2024-04-24 16:51:12.297914 INFO::Fitting model to feature number 46, Lachnospira #> 2024-04-24 16:51:12.314676 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group #> 2024-04-24 16:51:12.319063 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group #> 2024-04-24 16:51:12.32337 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group #> 2024-04-24 16:51:12.327633 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001 #> 2024-04-24 16:51:12.33181 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004 #> 2024-04-24 16:51:12.335998 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009 #> 2024-04-24 16:51:12.340224 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010 #> 2024-04-24 16:51:12.344447 INFO::Fitting model to feature number 54, Lactobacillus #> 2024-04-24 16:51:12.348625 INFO::Fitting model to feature number 55, Lactococcus #> 2024-04-24 16:51:12.352767 INFO::Fitting model to feature number 56, Mannheimia #> 2024-04-24 16:51:12.356889 INFO::Fitting model to feature number 57, Megasphaera #> 2024-04-24 16:51:12.361008 INFO::Fitting model to feature number 58, Monoglobus #> 2024-04-24 16:51:12.36511 INFO::Fitting model to feature number 59, Neisseria #> 2024-04-24 16:51:12.369211 INFO::Fitting model to feature number 60, Odoribacter #> 2024-04-24 16:51:12.373294 INFO::Fitting model to feature number 61, Oscillibacter #> 2024-04-24 16:51:12.377416 INFO::Fitting model to feature number 62, Oscillospira #> 2024-04-24 16:51:12.381511 INFO::Fitting model to feature number 63, Parabacteroides #> 2024-04-24 16:51:12.385606 INFO::Fitting model to feature number 64, Parasutterella #> 2024-04-24 16:51:12.389753 INFO::Fitting model to feature number 65, Prevotella #> 2024-04-24 16:51:12.393852 INFO::Fitting model to feature number 66, Pseudomonas #> 2024-04-24 16:51:12.397985 INFO::Fitting model to feature number 67, Romboutsia #> 2024-04-24 16:51:12.402123 INFO::Fitting model to feature number 68, Roseburia #> 2024-04-24 16:51:12.406248 INFO::Fitting model to feature number 69, Rothia #> 2024-04-24 16:51:12.410368 INFO::Fitting model to feature number 70, Ruminococcus #> 2024-04-24 16:51:12.414539 INFO::Fitting model to feature number 71, Sellimonas #> 2024-04-24 16:51:12.418649 INFO::Fitting model to feature number 72, Solobacterium #> 2024-04-24 16:51:12.42274 INFO::Fitting model to feature number 73, Staphylococcus #> 2024-04-24 16:51:12.426823 INFO::Fitting model to feature number 74, Streptococcus #> 2024-04-24 16:51:12.430968 INFO::Fitting model to feature number 75, Subdoligranulum #> 2024-04-24 16:51:12.435097 INFO::Fitting model to feature number 76, Sutterella #> 2024-04-24 16:51:12.439275 INFO::Fitting model to feature number 77, Terrisporobacter #> 2024-04-24 16:51:12.44342 INFO::Fitting model to feature number 78, Turicibacter #> 2024-04-24 16:51:12.447555 INFO::Fitting model to feature number 79, Tuzzerella #> 2024-04-24 16:51:12.451684 INFO::Fitting model to feature number 80, Tyzzerella #> 2024-04-24 16:51:12.455791 INFO::Fitting model to feature number 81, UBA1819 #> 2024-04-24 16:51:12.459931 INFO::Fitting model to feature number 82, UCG.002 #> 2024-04-24 16:51:12.464082 INFO::Fitting model to feature number 83, UCG.003 #> 2024-04-24 16:51:12.468238 INFO::Fitting model to feature number 84, UCG.005 #> 2024-04-24 16:51:12.472381 INFO::Fitting model to feature number 85, Veillonella #> 2024-04-24 16:51:12.476564 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group #> 2024-04-24 16:51:12.48072 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group #> 2024-04-24 16:51:12.484896 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group #> 2024-04-24 16:51:12.489138 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group #> 2024-04-24 16:51:12.493288 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group #> 2024-04-24 16:51:12.497476 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group #> 2024-04-24 16:51:12.501643 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group #> 2024-04-24 16:51:12.505765 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group #> 2024-04-24 16:51:12.509953 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group #> 2024-04-24 16:51:12.51412 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group #> 2024-04-24 16:51:12.518234 INFO::Fitting model to feature number 96, unclassified.Chloroplast #> 2024-04-24 16:51:12.522321 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014 #> 2024-04-24 16:51:12.526482 INFO::Fitting model to feature number 98, unclassified.Clostridia #> 2024-04-24 16:51:12.530657 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group #> 2024-04-24 16:51:12.534753 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales #> 2024-04-24 16:51:12.538822 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae #> 2024-04-24 16:51:12.542972 INFO::Fitting model to feature number 102, unclassified.Mitochondria #> 2024-04-24 16:51:12.547074 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae #> 2024-04-24 16:51:12.551182 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus #> 2024-04-24 16:51:12.555286 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales #> 2024-04-24 16:51:12.55942 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae #> 2024-04-24 16:51:12.563591 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group #> 2024-04-24 16:51:12.580038 INFO::Counting total values for each feature #> 2024-04-24 16:51:12.585433 INFO::Writing filtered data to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/features/filtered_data.tsv #> 2024-04-24 16:51:12.731498 INFO::Writing filtered, normalized data to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/features/filtered_data_norm.tsv #> 2024-04-24 16:51:12.881629 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/features/filtered_data_norm_transformed.tsv #> 2024-04-24 16:51:13.154268 INFO::Writing residuals to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/fits/residuals.rds #> 2024-04-24 16:51:13.224374 INFO::Writing fitted values to file /tmp/RtmpXpuOxT/maaslin194e625efd4a/fits/fitted.rds #> 2024-04-24 16:51:13.248273 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e625efd4a/all_results.tsv #> 2024-04-24 16:51:13.249922 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpXpuOxT/maaslin194e625efd4a/significant_results.tsv"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Collection — getCollection","title":"Get Microbiome Dataset Collection — getCollection","text":"Get collection Microbiome Dataset. collection returned AbundanceData, phyloseq, Collection object.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Collection — getCollection","text":"","code":"getCollection(   object,   collectionName,   format = c(\"AbundanceData\", \"phyloseq\", \"Collection\"),   continuousMetadataOnly = c(FALSE, TRUE) )  # S4 method for MbioDataset getCollection(   object,   collectionName = character(0),   format = c(\"AbundanceData\", \"phyloseq\", \"Collection\"),   continuousMetadataOnly = c(FALSE, TRUE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Collection — getCollection","text":"object Microbiome Dataset collectionName name collection return format format collection return. Currently supported options \"AbundanceData\", \"phyloseq\" \"Collection\". continuousMetadataOnly TRUE, continuous metadata returned. FALSE, metadata returned.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Collection — getCollection","text":"AbundanceData, phyloseq, Collection object representing collection associated study metadata","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Collection — getCollection","text":"","code":"genus <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\" )  genus_phyloseq <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\",       format = \"phyloseq\" )  ## to pass to correlation method, we want only continuous metadata genus_continuous <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\",       continuousMetadataOnly = TRUE )   ## with no metadata genus_collection <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\",       format = \"Collection\" )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Names of Collections — getCollectionNames,MbioDataset-method","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"Get names collections MbioDataset object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getCollectionNames(object)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"object MbioDataset","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"character vector collection names","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"","code":"getCollectionNames(microbiomeData::DiabImmune) #>  [1] \"16S (V4) Order\"                                           #>  [2] \"16S (V4) Genus\"                                           #>  [3] \"16S (V4) Family\"                                          #>  [4] \"16S (V4) Species\"                                         #>  [5] \"16S (V4) Class\"                                           #>  [6] \"16S (V4) Phylum\"                                          #>  [7] \"16S (V4) Kingdom\"                                         #>  [8] \"WGS 4th level EC metagenome abundance data\"               #>  [9] \"WGS Metagenome enzyme pathway abundance data\"             #> [10] \"WGS Metagenome enzyme pathway coverage data\"              #> [11] \"WGS Genus\"                                                #> [12] \"WGS Species\"                                              #> [13] \"WGS Family\"                                               #> [14] \"WGS Order\"                                                #> [15] \"WGS Phylum\"                                               #> [16] \"WGS Class\"                                                #> [17] \"WGS Kingdom\"                                              #> [18] \"WGS Normalized number of taxon-specific sequence matches\""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"Get variable names collection Microbiome Dataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getCollectionVariableNames(object, collectionName)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"object Microbiome Dataset collectionName name collection return variable names ","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"character vector variable names requested collection","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"","code":"variableNames <- getCollectionVariableNames(microbiomeData::DiabImmune, \"16S (V4) Genus\")"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Compute Result — getComputeResult","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"Get compute result Microbiome Dataset particular format. formats may supported compute results.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"","code":"getComputeResult(object, format = c(\"data.table\"), ...)  # S4 method for ComputeResult getComputeResult(object, format = c(\"data.table\", \"igraph\"), ...)  # S4 method for CorrelationResult getComputeResult(   object,   format = c(\"data.table\", \"igraph\"),   correlationCoefThreshold = 0.5,   pValueThreshold = 0.05 )  # S4 method for DifferentialAbundanceResult getComputeResult(object, format = c(\"data.table\"))"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"object Microbiome Dataset format format compute result. Currently \"data.table\" \"igraph\" supported. ... additional arguments passed getComputeResult method subclasses ComputeResult correlationCoefThreshold threshold filter edges correlation coefficient. Edges correlation coefficients threshold removed. Default .5 pValueThreshold threshold filter edges p-value. Edges p-values threshold removed. Default .05","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"compute result specified format","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"","code":"correlationOutput <- MicrobiomeDB::selfCorrelation(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method='spearman',       verbose=FALSE ) #>  #> 2024-04-24 16:51:14.283316 Removed 1 records with no data. #>  #> 2024-04-24 16:51:14.29003 Removed 1 records with no data. correlationDT <- getComputeResult(correlationOutput, \"data.table\") correlationIGraph <- getComputeResult(correlationOutput, \"igraph\")"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"Get compute result Microbiome Dataset particular format metadata.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"","code":"getComputeResultWithMetadata(   object,   dataset,   format = c(\"data.table\"),   metadataVariables = NULL )  # S4 method for ComputeResult,MbioDataset getComputeResultWithMetadata(   object,   dataset = NULL,   format = c(\"data.table\"),   metadataVariables = NULL )  # S4 method for ComputeResult,Collection getComputeResultWithMetadata(   object,   dataset = NULL,   format = c(\"data.table\"),   metadataVariables = NULL )  # S4 method for ComputeResult,AbundanceData getComputeResultWithMetadata(   object,   dataset = NULL,   format = c(\"data.table\"),   metadataVariables = NULL )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"object Microbiome Dataset dataset MbioDataset, AbundanceData Collection object compute result obtained. format format want compute result . Currently \"data.table\" supported. metadataVariables metadata variables include compute result. NULL, metadata variables included.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"compute result specified format","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"","code":"alphaDivOutput <- MicrobiomeDB::alphaDiv(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method='shannon',       verbose=FALSE )  alphaDivDT <- getComputeResultWithMetadata(      alphaDivOutput,       microbiomeData::DiabImmune,       metadataVariables = c('country', 'delivery_mode') )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"Get names metadata variables MbioDataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getMetadataVariableNames(object)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"object MbioDataset","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"character vector metadata variable names","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"","code":"getMetadataVariableNames(microbiomeData::DiabImmune) #>  [1] \"Participant_Id\"                                       #>  [2] \"Participant_repeated_measure_Id\"                      #>  [3] \"age_1st_animal_milk_or_solids_given_days\"             #>  [4] \"age_1st_given_apple_months\"                           #>  [5] \"age_1st_given_banana_months\"                          #>  [6] \"age_1st_given_barley_months\"                          #>  [7] \"age_1st_given_beef_months\"                            #>  [8] \"age_1st_given_berries_months\"                         #>  [9] \"age_1st_given_cabbs_months\"                           #> [10] \"age_1st_given_carrot_months\"                          #> [11] \"age_1st_given_corn_months\"                            #> [12] \"age_1st_given_cowsmilk_months\"                        #> [13] \"age_1st_given_egg_months\"                             #> [14] \"age_1st_given_fish_months\"                            #> [15] \"age_1st_given_milk_products_months\"                   #> [16] \"age_1st_given_oat_months\"                             #> [17] \"age_1st_given_pear_months\"                            #> [18] \"age_1st_given_peas_months\"                            #> [19] \"age_1st_given_plum_months\"                            #> [20] \"age_1st_given_pork_months\"                            #> [21] \"age_1st_given_potato_months\"                          #> [22] \"age_1st_given_poultry_months\"                         #> [23] \"age_1st_given_rice_months\"                            #> [24] \"age_1st_given_rye_months\"                             #> [25] \"age_1st_given_sweet_potato_months\"                    #> [26] \"age_1st_given_tomato_months\"                          #> [27] \"age_1st_given_wheat_months\"                           #> [28] \"age_at_anthropometry_days\"                            #> [29] \"age_at_two_autoantibodies_positive_days\"              #> [30] \"age_at_type_1_diabetes_diagnosis_days\"                #> [31] \"antibiotics_before_delivery_by_maternal_report\"       #> [32] \"bmi_minus_for_minus_age_z_minus_score\"                #> [33] \"breastfed_duration_days\"                              #> [34] \"country\"                                              #> [35] \"delivery_mode\"                                        #> [36] \"diet_in_first_three_days\"                             #> [37] \"exclusive_breastfed_duration_days\"                    #> [38] \"gestational_diabetes_by_maternal_report\"              #> [39] \"glutamic_acid_decarboxylase_autoantibodies\"           #> [40] \"hla_risk_by_hla_haplotyping\"                          #> [41] \"height_minus_for_minus_age_z_minus_score\"             #> [42] \"insulin_autoantibodies\"                               #> [43] \"insulinoma_minus_associated_protein_2_autoantibodies\" #> [44] \"islet_cell_autoantibodies\"                            #> [45] \"linear_growth_during_1st_year_cm\"                     #> [46] \"maternal_age_at_birth_months\"                         #> [47] \"mean_linear_growth_during_1st_3_years\"                #> [48] \"mean_weight_gain_during_1st_3_years\"                  #> [49] \"sex\"                                                  #> [50] \"study_group\"                                          #> [51] \"type_1_diabetes_diagnosed\"                            #> [52] \"urban_or_rural_site\"                                  #> [53] \"weight_gain_during_1st_year_kg\"                       #> [54] \"weight_minus_for_minus_age_z_minus_score\"             #> [55] \"zinc_transporter_8_autoantibodies\"                    #> [56] \"age_months\"                                           #> [57] \"Sample_Id\"                                            #> [58] \"habitat\"                                              #> [59] \"host_body_habitat\"                                    #> [60] \"host_body_product\"                                    #> [61] \"host_body_site\"                                       #> [62] \"sample_type\""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"Get summary requested metadata variable MbioDataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getMetadataVariableSummary(object, variable)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"object MbioDataset variable character vector representing name metadata variable summarize","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"table summarizing values requested metadata variable","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"","code":"getMetadataVariableSummary(microbiomeData::DiabImmune, \"age_months\") #>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.  #>    0.00    8.00   15.00   15.62   22.00   38.00  getMetadataVariableSummary(microbiomeData::DiabImmune, \"sex\") #> Female   Male  #>   1475   1874  getMetadataVariableSummary(microbiomeData::DiabImmune, \"country\") #> Estonia Finland  Russia  #>     555    2142     652"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"Returns data.table sample metadata","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getSampleMetadata(   object,   asCopy = c(TRUE, FALSE),   includeIds = c(TRUE, FALSE),   metadataVariables = NULL )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"object MbioDataset asCopy boolean indicating whether return data copy reference includeIds boolean indicating whether include recordIdColumn ancestorIdColumns metadataVariables metadata variables include sample metadata. NULL, metadata variables included.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"data.table sample metadata","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"","code":"getSampleMetadata(microbiomeData::DiabImmune) #>         Participant_Id Participant_repeated_measure_Id #>                 <char>                          <char> #>    1: E000823 (Source)              E000823_1 (Source) #>    2: E000823 (Source)             E000823_10 (Source) #>    3: E000823 (Source)             E000823_12 (Source) #>    4: E000823 (Source)             E000823_13 (Source) #>    5: E000823 (Source)             E000823_15 (Source) #>   ---                                                  #> 3345: T029922 (Source)             T029922_14 (Source) #> 3346: T029922 (Source)             T029922_16 (Source) #> 3347: T029922 (Source)             T029922_19 (Source) #> 3348: T029922 (Source)             T029922_22 (Source) #> 3349: T029922 (Source)              T029922_7 (Source) #>       age_1st_animal_milk_or_solids_given_days age_1st_given_apple_months #>                                          <num>                      <num> #>    1:                                        5                          6 #>    2:                                        5                          6 #>    3:                                        5                          6 #>    4:                                        5                          6 #>    5:                                        5                          6 #>   ---                                                                     #> 3345:                                        4                          4 #> 3346:                                        4                          4 #> 3347:                                        4                          4 #> 3348:                                        4                          4 #> 3349:                                        4                          4 #>       age_1st_given_banana_months age_1st_given_barley_months #>                             <num>                       <num> #>    1:                           6                          11 #>    2:                           6                          11 #>    3:                           6                          11 #>    4:                           6                          11 #>    5:                           6                          11 #>   ---                                                         #> 3345:                           4                          10 #> 3346:                           4                          10 #> 3347:                           4                          10 #> 3348:                           4                          10 #> 3349:                           4                          10 #>       age_1st_given_beef_months age_1st_given_berries_months #>                           <num>                        <num> #>    1:                       6.0                          6.0 #>    2:                       6.0                          6.0 #>    3:                       6.0                          6.0 #>    4:                       6.0                          6.0 #>    5:                       6.0                          6.0 #>   ---                                                        #> 3345:                       5.5                          7.5 #> 3346:                       5.5                          7.5 #> 3347:                       5.5                          7.5 #> 3348:                       5.5                          7.5 #> 3349:                       5.5                          7.5 #>       age_1st_given_cabbs_months age_1st_given_carrot_months #>                            <num>                       <num> #>    1:                          7                           5 #>    2:                          7                           5 #>    3:                          7                           5 #>    4:                          7                           5 #>    5:                          7                           5 #>   ---                                                        #> 3345:                          5                           4 #> 3346:                          5                           4 #> 3347:                          5                           4 #> 3348:                          5                           4 #> 3349:                          5                           4 #>       age_1st_given_corn_months age_1st_given_cowsmilk_months #>                           <num>                         <num> #>    1:                         6                          12.0 #>    2:                         6                          12.0 #>    3:                         6                          12.0 #>    4:                         6                          12.0 #>    5:                         6                          12.0 #>   ---                                                         #> 3345:                         5                           8.5 #> 3346:                         5                           8.5 #> 3347:                         5                           8.5 #> 3348:                         5                           8.5 #> 3349:                         5                           8.5 #>       age_1st_given_egg_months age_1st_given_fish_months #>                          <num>                     <num> #>    1:                        8                         7 #>    2:                        8                         7 #>    3:                        8                         7 #>    4:                        8                         7 #>    5:                        8                         7 #>   ---                                                    #> 3345:                       11                         6 #> 3346:                       11                         6 #> 3347:                       11                         6 #> 3348:                       11                         6 #> 3349:                       11                         6 #>       age_1st_given_milk_products_months age_1st_given_oat_months #>                                    <num>                    <num> #>    1:                                 10                        5 #>    2:                                 10                        5 #>    3:                                 10                        5 #>    4:                                 10                        5 #>    5:                                 10                        5 #>   ---                                                             #> 3345:                                  7                        5 #> 3346:                                  7                        5 #> 3347:                                  7                        5 #> 3348:                                  7                        5 #> 3349:                                  7                        5 #>       age_1st_given_pear_months age_1st_given_peas_months #>                           <num>                     <num> #>    1:                      10.0                       6.5 #>    2:                      10.0                       6.5 #>    3:                      10.0                       6.5 #>    4:                      10.0                       6.5 #>    5:                      10.0                       6.5 #>   ---                                                     #> 3345:                       4.5                       5.0 #> 3346:                       4.5                       5.0 #> 3347:                       4.5                       5.0 #> 3348:                       4.5                       5.0 #> 3349:                       4.5                       5.0 #>       age_1st_given_plum_months age_1st_given_pork_months #>                           <num>                     <num> #>    1:                       5.0                         7 #>    2:                       5.0                         7 #>    3:                       5.0                         7 #>    4:                       5.0                         7 #>    5:                       5.0                         7 #>   ---                                                     #> 3345:                       4.5                         8 #> 3346:                       4.5                         8 #> 3347:                       4.5                         8 #> 3348:                       4.5                         8 #> 3349:                       4.5                         8 #>       age_1st_given_potato_months age_1st_given_poultry_months #>                             <num>                        <num> #>    1:                           5                            6 #>    2:                           5                            6 #>    3:                           5                            6 #>    4:                           5                            6 #>    5:                           5                            6 #>   ---                                                          #> 3345:                           5                            5 #> 3346:                           5                            5 #> 3347:                           5                            5 #> 3348:                           5                            5 #> 3349:                           5                            5 #>       age_1st_given_rice_months age_1st_given_rye_months #>                           <num>                    <num> #>    1:                       5.0                     11.0 #>    2:                       5.0                     11.0 #>    3:                       5.0                     11.0 #>    4:                       5.0                     11.0 #>    5:                       5.0                     11.0 #>   ---                                                    #> 3345:                       4.5                      7.5 #> 3346:                       4.5                      7.5 #> 3347:                       4.5                      7.5 #> 3348:                       4.5                      7.5 #> 3349:                       4.5                      7.5 #>       age_1st_given_sweet_potato_months age_1st_given_tomato_months #>                                   <num>                       <num> #>    1:                                NA                           9 #>    2:                                NA                           9 #>    3:                                NA                           9 #>    4:                                NA                           9 #>    5:                                NA                           9 #>   ---                                                               #> 3345:                                NA                           6 #> 3346:                                NA                           6 #> 3347:                                NA                           6 #> 3348:                                NA                           6 #> 3349:                                NA                           6 #>       age_1st_given_wheat_months age_at_anthropometry_days #>                            <num>                     <int> #>    1:                         12                      1110 #>    2:                         12                      1110 #>    3:                         12                      1110 #>    4:                         12                      1110 #>    5:                         12                      1110 #>   ---                                                      #> 3345:                          6                      1123 #> 3346:                          6                      1123 #> 3347:                          6                      1123 #> 3348:                          6                      1123 #> 3349:                          6                      1123 #>       age_at_two_autoantibodies_positive_days #>                                         <int> #>    1:                                      NA #>    2:                                      NA #>    3:                                      NA #>    4:                                      NA #>    5:                                      NA #>   ---                                         #> 3345:                                      NA #> 3346:                                      NA #> 3347:                                      NA #> 3348:                                      NA #> 3349:                                      NA #>       age_at_type_1_diabetes_diagnosis_days #>                                       <int> #>    1:                                    NA #>    2:                                    NA #>    3:                                    NA #>    4:                                    NA #>    5:                                    NA #>   ---                                       #> 3345:                                    NA #> 3346:                                    NA #> 3347:                                    NA #> 3348:                                    NA #> 3349:                                    NA #>       antibiotics_before_delivery_by_maternal_report #>                                               <char> #>    1:                                             No #>    2:                                             No #>    3:                                             No #>    4:                                             No #>    5:                                             No #>   ---                                                #> 3345:                                                #> 3346:                                                #> 3347:                                                #> 3348:                                                #> 3349:                                                #>       bmi_minus_for_minus_age_z_minus_score breastfed_duration_days country #>                                       <num>                   <int>  <char> #>    1:                                  1.62                     397 Finland #>    2:                                  1.62                     397 Finland #>    3:                                  1.62                     397 Finland #>    4:                                  1.62                     397 Finland #>    5:                                  1.62                     397 Finland #>   ---                                                                       #> 3345:                                  0.63                      83 Estonia #> 3346:                                  0.63                      83 Estonia #> 3347:                                  0.63                      83 Estonia #> 3348:                                  0.63                      83 Estonia #> 3349:                                  0.63                      83 Estonia #>       delivery_mode diet_in_first_three_days exclusive_breastfed_duration_days #>              <char>                   <char>                             <int> #>    1:       Vaginal     Mother's breast milk                               150 #>    2:       Vaginal     Mother's breast milk                               150 #>    3:       Vaginal     Mother's breast milk                               150 #>    4:       Vaginal     Mother's breast milk                               150 #>    5:       Vaginal     Mother's breast milk                               150 #>   ---                                                                          #> 3345:      Cesarean     Mother's breast milk                                 1 #> 3346:      Cesarean     Mother's breast milk                                 1 #> 3347:      Cesarean     Mother's breast milk                                 1 #> 3348:      Cesarean     Mother's breast milk                                 1 #> 3349:      Cesarean     Mother's breast milk                                 1 #>       gestational_diabetes_by_maternal_report #>                                        <char> #>    1:                                      No #>    2:                                      No #>    3:                                      No #>    4:                                      No #>    5:                                      No #>   ---                                         #> 3345:                                      No #> 3346:                                      No #> 3347:                                      No #> 3348:                                      No #> 3349:                                      No #>       glutamic_acid_decarboxylase_autoantibodies hla_risk_by_hla_haplotyping #>                                           <char>                       <int> #>    1:                                         No                           2 #>    2:                                         No                           2 #>    3:                                         No                           2 #>    4:                                         No                           2 #>    5:                                         No                           2 #>   ---                                                                        #> 3345:                                         No                           3 #> 3346:                                         No                           3 #> 3347:                                         No                           3 #> 3348:                                         No                           3 #> 3349:                                         No                           3 #>       height_minus_for_minus_age_z_minus_score insulin_autoantibodies #>                                          <num>                 <char> #>    1:                                     1.46                     No #>    2:                                     1.46                     No #>    3:                                     1.46                     No #>    4:                                     1.46                     No #>    5:                                     1.46                     No #>   ---                                                                 #> 3345:                                    -0.25                     No #> 3346:                                    -0.25                     No #> 3347:                                    -0.25                     No #> 3348:                                    -0.25                     No #> 3349:                                    -0.25                     No #>       insulinoma_minus_associated_protein_2_autoantibodies #>                                                     <char> #>    1:                                                   No #>    2:                                                   No #>    3:                                                   No #>    4:                                                   No #>    5:                                                   No #>   ---                                                      #> 3345:                                                   No #> 3346:                                                   No #> 3347:                                                   No #> 3348:                                                   No #> 3349:                                                   No #>       islet_cell_autoantibodies linear_growth_during_1st_year_cm #>                          <char>                            <num> #>    1:                        No                         29.83651 #>    2:                        No                         29.83651 #>    3:                        No                         29.83651 #>    4:                        No                         29.83651 #>    5:                        No                         29.83651 #>   ---                                                            #> 3345:                        No                         31.48248 #> 3346:                        No                         31.48248 #> 3347:                        No                         31.48248 #> 3348:                        No                         31.48248 #> 3349:                        No                         31.48248 #>       maternal_age_at_birth_months mean_linear_growth_during_1st_3_years #>                              <num>                                 <num> #>    1:                     35.75342                              16.77027 #>    2:                     35.75342                              16.77027 #>    3:                     35.75342                              16.77027 #>    4:                     35.75342                              16.77027 #>    5:                     35.75342                              16.77027 #>   ---                                                                    #> 3345:                     36.23288                              16.47863 #> 3346:                     36.23288                              16.47863 #> 3347:                     36.23288                              16.47863 #> 3348:                     36.23288                              16.47863 #> 3349:                     36.23288                              16.47863 #>       mean_weight_gain_during_1st_3_years    sex                    study_group #>                                     <num> <char>                         <char> #>    1:                            4.876532   Male             Antibiotics cohort #>    2:                            4.876532   Male             Antibiotics cohort #>    3:                            4.876532   Male             Antibiotics cohort #>    4:                            4.876532   Male             Antibiotics cohort #>    5:                            4.876532   Male             Antibiotics cohort #>   ---                                                                           #> 3345:                            4.059528   Male Three country cohort (Karelia) #> 3346:                            4.059528   Male Three country cohort (Karelia) #> 3347:                            4.059528   Male Three country cohort (Karelia) #> 3348:                            4.059528   Male Three country cohort (Karelia) #> 3349:                            4.059528   Male Three country cohort (Karelia) #>       type_1_diabetes_diagnosed urban_or_rural_site #>                          <char>              <char> #>    1:                        No               Rural #>    2:                        No               Rural #>    3:                        No               Rural #>    4:                        No               Rural #>    5:                        No               Rural #>   ---                                               #> 3345:                        No               Urban #> 3346:                        No               Urban #> 3347:                        No               Urban #> 3348:                        No               Urban #> 3349:                        No               Urban #>       weight_gain_during_1st_year_kg weight_minus_for_minus_age_z_minus_score #>                                <num>                                    <num> #>    1:                       7.886785                                     2.06 #>    2:                       7.886785                                     2.06 #>    3:                       7.886785                                     2.06 #>    4:                       7.886785                                     2.06 #>    5:                       7.886785                                     2.06 #>   ---                                                                         #> 3345:                       8.942992                                     0.29 #> 3346:                       8.942992                                     0.29 #> 3347:                       8.942992                                     0.29 #> 3348:                       8.942992                                     0.29 #> 3349:                       8.942992                                     0.29 #>       zinc_transporter_8_autoantibodies age_months Sample_Id habitat #>                                  <char>      <int>     <int>  <char> #>    1:                                No          1   3000150   Human #>    2:                                No         10   3102722   Human #>    3:                                No         12   3106237   Human #>    4:                                No         13   3106238   Human #>    5:                                No         15   3106239   Human #>   ---                                                                #> 3345:                                No         14   3117645   Human #> 3346:                                No         16   3117647   Human #> 3347:                                No         19   3119973   Human #> 3348:                                No         22   3119976   Human #> 3349:                                No          7   3116926   Human #>       host_body_habitat host_body_product host_body_site sample_type #>                  <char>            <char>         <char>      <char> #>    1:             Colon             Feces          Colon       Stool #>    2:             Colon             Feces          Colon       Stool #>    3:             Colon             Feces          Colon       Stool #>    4:             Colon             Feces          Colon       Stool #>    5:             Colon             Feces          Colon       Stool #>   ---                                                                #> 3345:             Colon             Feces          Colon       Stool #> 3346:             Colon             Feces          Colon       Stool #> 3347:             Colon             Feces          Colon       Stool #> 3348:             Colon             Feces          Colon       Stool #> 3349:             Colon             Feces          Colon       Stool getSampleMetadata(microbiomeData::DiabImmune, metadataVariables = c(\"age_months\", \"sex\")) #>       Sample_Id   Participant_Id Participant_repeated_measure_Id age_months #>           <int>           <char>                          <char>      <int> #>    1:   3000150 E000823 (Source)              E000823_1 (Source)          1 #>    2:   3102722 E000823 (Source)             E000823_10 (Source)         10 #>    3:   3106237 E000823 (Source)             E000823_12 (Source)         12 #>    4:   3106238 E000823 (Source)             E000823_13 (Source)         13 #>    5:   3106239 E000823 (Source)             E000823_15 (Source)         15 #>   ---                                                                       #> 3345:   3117645 T029922 (Source)             T029922_14 (Source)         14 #> 3346:   3117647 T029922 (Source)             T029922_16 (Source)         16 #> 3347:   3119973 T029922 (Source)             T029922_19 (Source)         19 #> 3348:   3119976 T029922 (Source)             T029922_22 (Source)         22 #> 3349:   3116926 T029922 (Source)              T029922_7 (Source)          7 #>          sex #>       <char> #>    1:   Male #>    2:   Male #>    3:   Male #>    4:   Male #>    5:   Male #>   ---        #> 3345:   Male #> 3346:   Male #> 3347:   Male #> 3348:   Male #> 3349:   Male"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadataIdColumns-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","title":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","text":"Get names record ancestor id columns sample metadata MbioDataset object.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadataIdColumns-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getSampleMetadataIdColumns(object)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadataIdColumns-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","text":"object MbioDataset","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadataIdColumns-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","text":"character vector id column names","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Variables — getVariables","title":"Get Microbiome Dataset Variables — getVariables","text":"Get variables Microbiome Dataset names. requested variables belong collection metadata. returned data.table contain requested variables columns appropriate identifiers. one requested variables returned, warning printed.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Variables — getVariables","text":"","code":"getVariables(object, variables)  # S4 method for MbioDataset getVariables(object, variables)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Variables — getVariables","text":"object Microbiome Dataset variables names variables return. named list names collection names values variable names collection. case metadata variables, name \"metadata\".","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Variables — getVariables","text":"data.table requested variables","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Variables — getVariables","text":"","code":"getCollectionVariableNames(microbiomeData::DiabImmune, \"16S (V4) Genus\") #>   [1] \"28-4\"                                                                                                                       #>   [2] \"Abiotrophia\"                                                                                                                #>   [3] \"Acetanaerobacterium\"                                                                                                        #>   [4] \"Acetobacter\"                                                                                                                #>   [5] \"Achromobacter\"                                                                                                              #>   [6] \"Acidaminococcus\"                                                                                                            #>   [7] \"Acidibacter\"                                                                                                                #>   [8] \"Acidiphilium\"                                                                                                               #>   [9] \"Acidipropionibacterium\"                                                                                                     #>  [10] \"Acidocella\"                                                                                                                 #>  [11] \"Acidovorax\"                                                                                                                 #>  [12] \"Acinetobacter\"                                                                                                              #>  [13] \"Actinobacillus\"                                                                                                             #>  [14] \"Actinobaculum\"                                                                                                              #>  [15] \"Actinomyces\"                                                                                                                #>  [16] \"Actinotignum\"                                                                                                               #>  [17] \"Adlercreutzia\"                                                                                                              #>  [18] \"Aerococcus\"                                                                                                                 #>  [19] \"Aeromonas\"                                                                                                                  #>  [20] \"Afipia\"                                                                                                                     #>  [21] \"Agathobacter\"                                                                                                               #>  [22] \"Aggregatibacter\"                                                                                                            #>  [23] \"Akkermansia\"                                                                                                                #>  [24] \"Alcaligenes\"                                                                                                                #>  [25] \"Alicycliphilus\"                                                                                                             #>  [26] \"Alistipes\"                                                                                                                  #>  [27] \"Allisonella\"                                                                                                                #>  [28] \"Allobaculum\"                                                                                                                #>  [29] \"Alloprevotella\"                                                                                                             #>  [30] \"Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium\"                                                                         #>  [31] \"Alloscardovia\"                                                                                                              #>  [32] \"Amaricoccus\"                                                                                                                #>  [33] \"Amnibacterium\"                                                                                                              #>  [34] \"Anaerobium\"                                                                                                                 #>  [35] \"Anaerocolumna\"                                                                                                              #>  [36] \"Anaerofilum\"                                                                                                                #>  [37] \"Anaerofustis\"                                                                                                               #>  [38] \"Anaeroglobus\"                                                                                                               #>  [39] \"Anaeromyxobacter\"                                                                                                           #>  [40] \"Anaeroplasma\"                                                                                                               #>  [41] \"Anaerosporobacter\"                                                                                                          #>  [42] \"Anaerosporomusa\"                                                                                                            #>  [43] \"Anaerostignum\"                                                                                                              #>  [44] \"Anaerostipes\"                                                                                                               #>  [45] \"Anaerotruncus\"                                                                                                              #>  [46] \"Angelakisella\"                                                                                                              #>  [47] \"Angustibacter\"                                                                                                              #>  [48] \"Anoxybacillus\"                                                                                                              #>  [49] \"Aquabacterium\"                                                                                                              #>  [50] \"Aquamonas\"                                                                                                                  #>  [51] \"Arcanobacterium\"                                                                                                            #>  [52] \"Arcticibacter\"                                                                                                              #>  [53] \"Asaccharospora\"                                                                                                             #>  [54] \"Asaia\"                                                                                                                      #>  [55] \"Asinibacterium\"                                                                                                             #>  [56] \"Asteroleplasma\"                                                                                                             #>  [57] \"Asticcacaulis\"                                                                                                              #>  [58] \"Atopobium\"                                                                                                                  #>  [59] \"Aureimonas\"                                                                                                                 #>  [60] \"Azospira\"                                                                                                                   #>  [61] \"Bacillus\"                                                                                                                   #>  [62] \"Bacteriovorax\"                                                                                                              #>  [63] \"Bacteroides\"                                                                                                                #>  [64] \"Barnesiella\"                                                                                                                #>  [65] \"Bdellovibrio\"                                                                                                               #>  [66] \"Belnapia\"                                                                                                                   #>  [67] \"Bergeyella\"                                                                                                                 #>  [68] \"Bifidobacterium\"                                                                                                            #>  [69] \"Bilophila\"                                                                                                                  #>  [70] \"Blastomonas\"                                                                                                                #>  [71] \"Blautia\"                                                                                                                    #>  [72] \"Bordetella\"                                                                                                                 #>  [73] \"Bosea\"                                                                                                                      #>  [74] \"Brachybacterium\"                                                                                                            #>  [75] \"Bradyrhizobium\"                                                                                                             #>  [76] \"Brevibacterium\"                                                                                                             #>  [77] \"Brevundimonas\"                                                                                                              #>  [78] \"Brucella\"                                                                                                                   #>  [79] \"Bulleidia\"                                                                                                                  #>  [80] \"Burkholderia-Caballeronia-Paraburkholderia\"                                                                                 #>  [81] \"Buttiauxella\"                                                                                                               #>  [82] \"Butyricicoccus\"                                                                                                             #>  [83] \"Butyricimonas\"                                                                                                              #>  [84] \"CAG-352\"                                                                                                                    #>  [85] \"CAG-56\"                                                                                                                     #>  [86] \"CAG-873\"                                                                                                                    #>  [87] \"CHKCI001\"                                                                                                                   #>  [88] \"CHKCI002\"                                                                                                                   #>  [89] \"CL500-29 marine group\"                                                                                                      #>  [90] \"Caloribacterium\"                                                                                                            #>  [91] \"Campylobacter\"                                                                                                              #>  [92] \"Candidatus Arthromitus\"                                                                                                     #>  [93] \"Candidatus Metachlamydia\"                                                                                                   #>  [94] \"Candidatus Obscuribacter\"                                                                                                   #>  [95] \"Candidatus Phytoplasma\"                                                                                                     #>  [96] \"Candidatus Soleaferrea\"                                                                                                     #>  [97] \"Candidatus Stoquefichus\"                                                                                                    #>  [98] \"Capnocytophaga\"                                                                                                             #>  [99] \"Caproiciproducens\"                                                                                                          #> [100] \"Cardiobacterium\"                                                                                                            #> [101] \"Carnobacterium\"                                                                                                             #> [102] \"Caryophanon\"                                                                                                                #> [103] \"Castellaniella\"                                                                                                             #> [104] \"Catabacter\"                                                                                                                 #> [105] \"Catenibacillus\"                                                                                                             #> [106] \"Catenibacterium\"                                                                                                            #> [107] \"Catenisphaera\"                                                                                                              #> [108] \"Catonella\"                                                                                                                  #> [109] \"Caulobacter\"                                                                                                                #> [110] \"Cellulomonas\"                                                                                                               #> [111] \"Cellulosilyticum\"                                                                                                           #> [112] \"Cellvibrio\"                                                                                                                 #> [113] \"Centipeda\"                                                                                                                  #> [114] \"Cetobacterium\"                                                                                                              #> [115] \"Christensenella\"                                                                                                            #> [116] \"Christensenellaceae R-7 group\"                                                                                              #> [117] \"Chryseobacterium\"                                                                                                           #> [118] \"Chryseomicrobium\"                                                                                                           #> [119] \"Chungangia\"                                                                                                                 #> [120] \"Citrobacter\"                                                                                                                #> [121] \"Clavibacter\"                                                                                                                #> [122] \"Cloacibacillus\"                                                                                                             #> [123] \"Cloacibacterium\"                                                                                                            #> [124] \"Clostridioides\"                                                                                                             #> [125] \"Clostridium sensu stricto 1\"                                                                                                #> [126] \"Clostridium sensu stricto 12\"                                                                                               #> [127] \"Clostridium sensu stricto 13\"                                                                                               #> [128] \"Clostridium sensu stricto 15\"                                                                                               #> [129] \"Clostridium sensu stricto 18\"                                                                                               #> [130] \"Clostridium sensu stricto 2\"                                                                                                #> [131] \"Clostridium sensu stricto 3\"                                                                                                #> [132] \"Clostridium sensu stricto 4\"                                                                                                #> [133] \"Clostridium sensu stricto 6\"                                                                                                #> [134] \"Colidextribacter\"                                                                                                           #> [135] \"Collinsella\"                                                                                                                #> [136] \"Comamonas\"                                                                                                                  #> [137] \"Conexibacter\"                                                                                                               #> [138] \"Conservatibacter\"                                                                                                           #> [139] \"Coprobacillus\"                                                                                                              #> [140] \"Coprobacter\"                                                                                                                #> [141] \"Coprococcus\"                                                                                                                #> [142] \"Coriobacteriaceae UCG-002\"                                                                                                  #> [143] \"Corynebacterium\"                                                                                                            #> [144] \"Cosenzaea\"                                                                                                                  #> [145] \"Criibacterium\"                                                                                                              #> [146] \"Cryptobacterium\"                                                                                                            #> [147] \"Curvibacter\"                                                                                                                #> [148] \"Cutibacterium\"                                                                                                              #> [149] \"Cytophaga\"                                                                                                                  #> [150] \"DNF00809\"                                                                                                                   #> [151] \"DSSD61\"                                                                                                                     #> [152] \"DTU089\"                                                                                                                     #> [153] \"Dechloromonas\"                                                                                                              #> [154] \"Defluviicoccus\"                                                                                                             #> [155] \"Defluviitaleaceae UCG-011\"                                                                                                  #> [156] \"Delftia\"                                                                                                                    #> [157] \"Denitrobacterium\"                                                                                                           #> [158] \"Dermabacter\"                                                                                                                #> [159] \"Desemzia\"                                                                                                                   #> [160] \"Desulfovibrio\"                                                                                                              #> [161] \"Devosia\"                                                                                                                    #> [162] \"Dialister\"                                                                                                                  #> [163] \"Diaphorobacter\"                                                                                                             #> [164] \"Dickeya\"                                                                                                                    #> [165] \"Dielma\"                                                                                                                     #> [166] \"Dietzia\"                                                                                                                    #> [167] \"Dinghuibacter\"                                                                                                              #> [168] \"Diplosphaera\"                                                                                                               #> [169] \"Dolosigranulum\"                                                                                                             #> [170] \"Dorea\"                                                                                                                      #> [171] \"Duganella\"                                                                                                                  #> [172] \"Dysgonomonas\"                                                                                                               #> [173] \"Edaphobaculum\"                                                                                                              #> [174] \"Eggerthella\"                                                                                                                #> [175] \"Eikenella\"                                                                                                                  #> [176] \"Eisenbergiella\"                                                                                                             #> [177] \"Empedobacter\"                                                                                                               #> [178] \"Endobacter\"                                                                                                                 #> [179] \"Enhydrobacter\"                                                                                                              #> [180] \"Enterobacter\"                                                                                                               #> [181] \"Enterococcus\"                                                                                                               #> [182] \"Enterorhabdus\"                                                                                                              #> [183] \"Enteroscipio\"                                                                                                               #> [184] \"Epulopiscium\"                                                                                                               #> [185] \"Erwinia\"                                                                                                                    #> [186] \"Erysipelatoclostridium\"                                                                                                     #> [187] \"Erysipelotrichaceae UCG-003\"                                                                                                #> [188] \"Erysipelotrichaceae UCG-006\"                                                                                                #> [189] \"Escherichia/Shigella\"                                                                                                       #> [190] \"Eubacterium\"                                                                                                                #> [191] \"Exiguobacterium\"                                                                                                            #> [192] \"Extensimonas\"                                                                                                               #> [193] \"F0058\"                                                                                                                      #> [194] \"F0332\"                                                                                                                      #> [195] \"FD2005\"                                                                                                                     #> [196] \"Facklamia\"                                                                                                                  #> [197] \"Faecalibacterium\"                                                                                                           #> [198] \"Faecalicoccus\"                                                                                                              #> [199] \"Faecalitalea\"                                                                                                               #> [200] \"Falsochrobactrum\"                                                                                                           #> [201] \"Family XIII AD3011 group\"                                                                                                   #> [202] \"Family XIII UCG-001\"                                                                                                        #> [203] \"Fictibacillus\"                                                                                                              #> [204] \"Flaviflexus\"                                                                                                                #> [205] \"Flavihumibacter\"                                                                                                            #> [206] \"Flavobacterium\"                                                                                                             #> [207] \"Flavonifractor\"                                                                                                             #> [208] \"Floricoccus\"                                                                                                                #> [209] \"Fluviicola\"                                                                                                                 #> [210] \"Fournierella\"                                                                                                               #> [211] \"Fretibacterium\"                                                                                                             #> [212] \"Frisingicoccus\"                                                                                                             #> [213] \"Fructobacillus\"                                                                                                             #> [214] \"Fusicatenibacter\"                                                                                                           #> [215] \"Fusobacterium\"                                                                                                              #> [216] \"GCA-900066575\"                                                                                                              #> [217] \"GCA-900066755\"                                                                                                              #> [218] \"Galbibacter\"                                                                                                                #> [219] \"Garciella\"                                                                                                                  #> [220] \"Gemella\"                                                                                                                    #> [221] \"Gemmata\"                                                                                                                    #> [222] \"Geobacillus\"                                                                                                                #> [223] \"Gluconobacter\"                                                                                                              #> [224] \"Glutamicibacter\"                                                                                                            #> [225] \"Gordonia\"                                                                                                                   #> [226] \"Gordonibacter\"                                                                                                              #> [227] \"Granulicatella\"                                                                                                             #> [228] \"Gulbenkiania\"                                                                                                               #> [229] \"Haemophilus\"                                                                                                                #> [230] \"Hafnia-Obesumbacterium\"                                                                                                     #> [231] \"Halomonas\"                                                                                                                  #> [232] \"Haoranjiania\"                                                                                                               #> [233] \"Harryflintia\"                                                                                                               #> [234] \"Helicobacter\"                                                                                                               #> [235] \"Hephaestia\"                                                                                                                 #> [236] \"Herbaspirillum\"                                                                                                             #> [237] \"Herbinix\"                                                                                                                   #> [238] \"Holdemanella\"                                                                                                               #> [239] \"Holdemania\"                                                                                                                 #> [240] \"Howardella\"                                                                                                                 #> [241] \"Hungatella\"                                                                                                                 #> [242] \"Hydrocarboniphaga\"                                                                                                          #> [243] \"Hydrogenophilus\"                                                                                                            #> [244] \"Hymenobacter\"                                                                                                               #> [245] \"Iamia\"                                                                                                                      #> [246] \"Ignavigranum\"                                                                                                               #> [247] \"Incertae Sedis [EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis]\"               #> [248] \"Incertae Sedis [EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis]\"              #> [249] \"Incertae Sedis [EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis]\"    #> [250] \"Incertae Sedis [EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis]\" #> [251] \"Intestinibacter\"                                                                                                            #> [252] \"Intestinimonas\"                                                                                                             #> [253] \"Janthinobacterium\"                                                                                                          #> [254] \"Jeotgalicoccus\"                                                                                                             #> [255] \"Johnsonella\"                                                                                                                #> [256] \"Kingella\"                                                                                                                   #> [257] \"Klebsiella\"                                                                                                                 #> [258] \"Knoellia\"                                                                                                                   #> [259] \"Kocuria\"                                                                                                                    #> [260] \"Kosakonia\"                                                                                                                  #> [261] \"Lachnoanaerobaculum\"                                                                                                        #> [262] \"Lachnobacterium\"                                                                                                            #> [263] \"Lachnoclostridium\"                                                                                                          #> [264] \"Lachnospira\"                                                                                                                #> [265] \"Lachnospiraceae AC2044 group\"                                                                                               #> [266] \"Lachnospiraceae FCS020 group\"                                                                                               #> [267] \"Lachnospiraceae FE2018 group\"                                                                                               #> [268] \"Lachnospiraceae NC2004 group\"                                                                                               #> [269] \"Lachnospiraceae ND3007 group\"                                                                                               #> [270] \"Lachnospiraceae NK4A136 group\"                                                                                              #> [271] \"Lachnospiraceae UCG-001\"                                                                                                    #> [272] \"Lachnospiraceae UCG-002\"                                                                                                    #> [273] \"Lachnospiraceae UCG-003\"                                                                                                    #> [274] \"Lachnospiraceae UCG-004\"                                                                                                    #> [275] \"Lachnospiraceae UCG-008\"                                                                                                    #> [276] \"Lachnospiraceae UCG-009\"                                                                                                    #> [277] \"Lachnospiraceae UCG-010\"                                                                                                    #> [278] \"Lachnospiraceae XPB1014 group\"                                                                                              #> [279] \"Lachnotalea\"                                                                                                                #> [280] \"Lactobacillus\"                                                                                                              #> [281] \"Lactococcus\"                                                                                                                #> [282] \"Lactonifactor\"                                                                                                              #> [283] \"Lautropia\"                                                                                                                  #> [284] \"Lawsonella\"                                                                                                                 #> [285] \"Legionella\"                                                                                                                 #> [286] \"Leptotrichia\"                                                                                                               #> [287] \"Leuconostoc\"                                                                                                                #> [288] \"Libanicoccus\"                                                                                                               #> [289] \"Luteimonas\"                                                                                                                 #> [290] \"Luteolibacter\"                                                                                                              #> [291] \"Macellibacteroides\"                                                                                                         #> [292] \"Macrococcus\"                                                                                                                #> [293] \"Mailhella\"                                                                                                                  #> [294] \"Mannheimia\"                                                                                                                 #> [295] \"Marinilactibacillus\"                                                                                                        #> [296] \"Marmoricola\"                                                                                                                #> [297] \"Martelella\"                                                                                                                 #> [298] \"Marvinbryantia\"                                                                                                             #> [299] \"Massilia\"                                                                                                                   #> [300] \"Megamonas\"                                                                                                                  #> [301] \"Megasphaera\"                                                                                                                #> [302] \"Merdibacter\"                                                                                                                #> [303] \"Mesorhizobium\"                                                                                                              #> [304] \"Methanobrevibacter\"                                                                                                         #> [305] \"Methylibium\"                                                                                                                #> [306] \"Methylobacillus\"                                                                                                            #> [307] \"Methylobacterium-Methylorubrum\"                                                                                             #> [308] \"Methylorosula\"                                                                                                              #> [309] \"Methylotenera\"                                                                                                              #> [310] \"Micrococcus\"                                                                                                                #> [311] \"Mitsuokella\"                                                                                                                #> [312] \"Mobiluncus\"                                                                                                                 #> [313] \"Mogibacterium\"                                                                                                              #> [314] \"Moheibacter\"                                                                                                                #> [315] \"Mongoliitalea\"                                                                                                              #> [316] \"Monoglobus\"                                                                                                                 #> [317] \"Moraxella\"                                                                                                                  #> [318] \"Morganella\"                                                                                                                 #> [319] \"Moryella\"                                                                                                                   #> [320] \"Mucilaginibacter\"                                                                                                           #> [321] \"Muribaculum\"                                                                                                                #> [322] \"Murimonas\"                                                                                                                  #> [323] \"Mycobacterium\"                                                                                                              #> [324] \"Mycoplasma\"                                                                                                                 #> [325] \"Myxococcus\"                                                                                                                 #> [326] \"NK4A214 group\"                                                                                                              #> [327] \"Nakamurella\"                                                                                                                #> [328] \"Nannocystis\"                                                                                                                #> [329] \"Necropsobacter\"                                                                                                             #> [330] \"Negativibacillus\"                                                                                                           #> [331] \"Negativicoccus\"                                                                                                             #> [332] \"Neisseria\"                                                                                                                  #> [333] \"Neochlamydia\"                                                                                                               #> [334] \"Neomegalonema\"                                                                                                              #> [335] \"Neorhizobium\"                                                                                                               #> [336] \"Neoscardovia\"                                                                                                               #> [337] \"Nesterenkonia\"                                                                                                              #> [338] \"Nocardioides\"                                                                                                               #> [339] \"Nocardiopsis\"                                                                                                               #> [340] \"Novosphingobium\"                                                                                                            #> [341] \"Oceanivirga\"                                                                                                                #> [342] \"Oceanobacillus\"                                                                                                             #> [343] \"Ochrobactrum\"                                                                                                               #> [344] \"Odoribacter\"                                                                                                                #> [345] \"Olsenella\"                                                                                                                  #> [346] \"Oribacterium\"                                                                                                               #> [347] \"Oscillibacter\"                                                                                                              #> [348] \"Oscillospira\"                                                                                                               #> [349] \"Ottowia\"                                                                                                                    #> [350] \"Oxalobacter\"                                                                                                                #> [351] \"Oxobacter\"                                                                                                                  #> [352] \"P3OB-42\"                                                                                                                    #> [353] \"Paenibacillus\"                                                                                                              #> [354] \"Paeniclostridium\"                                                                                                           #> [355] \"Paenisporosarcina\"                                                                                                          #> [356] \"Paludicola\"                                                                                                                 #> [357] \"Papillibacter\"                                                                                                              #> [358] \"Parabacteroides\"                                                                                                            #> [359] \"Paraclostridium\"                                                                                                            #> [360] \"Paracoccus\"                                                                                                                 #> [361] \"Paramesorhizobium\"                                                                                                          #> [362] \"Paraprevotella\"                                                                                                             #> [363] \"Parapusillimonas\"                                                                                                           #> [364] \"Parascardovia\"                                                                                                              #> [365] \"Parasutterella\"                                                                                                             #> [366] \"Parvibacter\"                                                                                                                #> [367] \"Pasteurella\"                                                                                                                #> [368] \"Paucibacter\"                                                                                                                #> [369] \"Pediococcus\"                                                                                                                #> [370] \"Pedobacter\"                                                                                                                 #> [371] \"Peptoclostridium\"                                                                                                           #> [372] \"Peptococcus\"                                                                                                                #> [373] \"Peptostreptococcus\"                                                                                                         #> [374] \"Perlucidibaca\"                                                                                                              #> [375] \"Phascolarctobacterium\"                                                                                                      #> [376] \"Phaseolibacter\"                                                                                                             #> [377] \"Phocea\"                                                                                                                     #> [378] \"Phoenicibacter\"                                                                                                             #> [379] \"Phyllobacterium\"                                                                                                            #> [380] \"Piscinibacter\"                                                                                                              #> [381] \"Planifilum\"                                                                                                                 #> [382] \"Plesiomonas\"                                                                                                                #> [383] \"Plot4-2H12\"                                                                                                                 #> [384] \"Pluralibacter\"                                                                                                              #> [385] \"Polaromonas\"                                                                                                                #> [386] \"Porphyromonas\"                                                                                                              #> [387] \"Prevotella\"                                                                                                                 #> [388] \"Prevotellaceae NK3B31 group\"                                                                                                #> [389] \"Prevotellaceae UCG-001\"                                                                                                     #> [390] \"Propionibacterium\"                                                                                                          #> [391] \"Prosthecobacter\"                                                                                                            #> [392] \"Proteus\"                                                                                                                    #> [393] \"Providencia\"                                                                                                                #> [394] \"Pseudacidovorax\"                                                                                                            #> [395] \"Pseudaminobacter\"                                                                                                           #> [396] \"Pseudocitrobacter\"                                                                                                          #> [397] \"Pseudoflavonifractor\"                                                                                                       #> [398] \"Pseudoglutamicibacter\"                                                                                                      #> [399] \"Pseudomonas\"                                                                                                                #> [400] \"Pseudoramibacter\"                                                                                                           #> [401] \"Pseudoxanthomonas\"                                                                                                          #> [402] \"Psychrobacter\"                                                                                                              #> [403] \"Pygmaiobacter\"                                                                                                              #> [404] \"Pyramidobacter\"                                                                                                             #> [405] \"Qipengyuania\"                                                                                                               #> [406] \"Ralstonia\"                                                                                                                  #> [407] \"Raoultella\"                                                                                                                 #> [408] \"Raoultibacter\"                                                                                                              #> [409] \"Reyranella\"                                                                                                                 #> [410] \"Rhizorhapis\"                                                                                                                #> [411] \"Rhodanobacter\"                                                                                                              #> [412] \"Rhodobacter\"                                                                                                                #> [413] \"Rhodococcus\"                                                                                                                #> [414] \"Rikenella\"                                                                                                                  #> [415] \"Rikenellaceae RC9 gut group\"                                                                                                #> [416] \"Rivicola\"                                                                                                                   #> [417] \"Robinsoniella\"                                                                                                              #> [418] \"Rodentibacter\"                                                                                                              #> [419] \"Romboutsia\"                                                                                                                 #> [420] \"Roseburia\"                                                                                                                  #> [421] \"Roseisolibacter\"                                                                                                            #> [422] \"Rothia\"                                                                                                                     #> [423] \"Rubellimicrobium\"                                                                                                           #> [424] \"Ruminococcus\"                                                                                                               #> [425] \"Rummeliibacillus\"                                                                                                           #> [426] \"S5-A14a\"                                                                                                                    #> [427] \"SH-PL14\"                                                                                                                    #> [428] \"Saccharothrix\"                                                                                                              #> [429] \"Salinimicrobium\"                                                                                                            #> [430] \"Salinisphaera\"                                                                                                              #> [431] \"Salipaludibacillus\"                                                                                                         #> [432] \"Salmonella\"                                                                                                                 #> [433] \"Sanguibacteroides\"                                                                                                          #> [434] \"Sarcina\"                                                                                                                    #> [435] \"Scardovia\"                                                                                                                  #> [436] \"Sedimentibacter\"                                                                                                            #> [437] \"Segetibacter\"                                                                                                               #> [438] \"Selenomonas\"                                                                                                                #> [439] \"Sellimonas\"                                                                                                                 #> [440] \"Senegalimassilia\"                                                                                                           #> [441] \"Serratia\"                                                                                                                   #> [442] \"Shimwellia\"                                                                                                                 #> [443] \"Shuttleworthia\"                                                                                                             #> [444] \"Slackia\"                                                                                                                    #> [445] \"Sneathia\"                                                                                                                   #> [446] \"Solibacillus\"                                                                                                               #> [447] \"Solobacterium\"                                                                                                              #> [448] \"Sphingoaurantiacus\"                                                                                                         #> [449] \"Sphingobacterium\"                                                                                                           #> [450] \"Sphingobium\"                                                                                                                #> [451] \"Sphingomonas\"                                                                                                               #> [452] \"Sphingopyxis\"                                                                                                               #> [453] \"Sporolactobacillus\"                                                                                                         #> [454] \"Staphylococcus\"                                                                                                             #> [455] \"Stenotrophomonas\"                                                                                                           #> [456] \"Stomatobaculum\"                                                                                                             #> [457] \"Streptobacillus\"                                                                                                            #> [458] \"Streptococcus\"                                                                                                              #> [459] \"Subdoligranulum\"                                                                                                            #> [460] \"Succinatimonas\"                                                                                                             #> [461] \"Succiniclasticum\"                                                                                                           #> [462] \"Succinivibrio\"                                                                                                              #> [463] \"Sulfurospirillum\"                                                                                                           #> [464] \"Sutterella\"                                                                                                                 #> [465] \"Synergistes\"                                                                                                                #> [466] \"TM7x\"                                                                                                                       #> [467] \"Tannerella\"                                                                                                                 #> [468] \"Tatumella\"                                                                                                                  #> [469] \"Tepidimonas\"                                                                                                                #> [470] \"Tepidiphilus\"                                                                                                               #> [471] \"Terrisporobacter\"                                                                                                           #> [472] \"Tetragenococcus\"                                                                                                            #> [473] \"Thermus\"                                                                                                                    #> [474] \"Timonella\"                                                                                                                  #> [475] \"Tolumonas\"                                                                                                                  #> [476] \"Trabulsiella\"                                                                                                               #> [477] \"Tropheryma\"                                                                                                                 #> [478] \"Trueperella\"                                                                                                                #> [479] \"Turicibacter\"                                                                                                               #> [480] \"Tuzzerella\"                                                                                                                 #> [481] \"Tyzzerella\"                                                                                                                 #> [482] \"UBA1819\"                                                                                                                    #> [483] \"UC5-1-2E3\"                                                                                                                  #> [484] \"UCG-002\"                                                                                                                    #> [485] \"UCG-003\"                                                                                                                    #> [486] \"UCG-004\"                                                                                                                    #> [487] \"UCG-005\"                                                                                                                    #> [488] \"UCG-007\"                                                                                                                    #> [489] \"UCG-008\"                                                                                                                    #> [490] \"UCG-009\"                                                                                                                    #> [491] \"Ureibacillus\"                                                                                                               #> [492] \"Varibaculum\"                                                                                                                #> [493] \"Variovorax\"                                                                                                                 #> [494] \"Veillonella\"                                                                                                                #> [495] \"Verticiella\"                                                                                                                #> [496] \"Victivallis\"                                                                                                                #> [497] \"Vulcaniibacterium\"                                                                                                          #> [498] \"Weissella\"                                                                                                                  #> [499] \"Xanthomonas\"                                                                                                                #> [500] \"Yersinia\"                                                                                                                   #> [501] \"Yokenella\"                                                                                                                  #> [502] \"Zoogloea\"                                                                                                                   #> [503] \"[Bacteroides] pectinophilus group\"                                                                                          #> [504] \"[Clostridium] innocuum group\"                                                                                               #> [505] \"[Eubacterium] brachy group\"                                                                                                 #> [506] \"[Eubacterium] eligens group\"                                                                                                #> [507] \"[Eubacterium] fissicatena group\"                                                                                            #> [508] \"[Eubacterium] hallii group\"                                                                                                 #> [509] \"[Eubacterium] nodatum group\"                                                                                                #> [510] \"[Eubacterium] oxidoreducens group\"                                                                                          #> [511] \"[Eubacterium] ruminantium group\"                                                                                            #> [512] \"[Eubacterium] siraeum group\"                                                                                                #> [513] \"[Eubacterium] ventriosum group\"                                                                                             #> [514] \"[Eubacterium] xylanophilum group\"                                                                                           #> [515] \"[Ruminococcus] gauvreauii group\"                                                                                            #> [516] \"[Ruminococcus] gnavus group\"                                                                                                #> [517] \"[Ruminococcus] torques group\"                                                                                               #> [518] \"unclassified 0319-6G20\"                                                                                                     #> [519] \"unclassified 67-14\"                                                                                                         #> [520] \"unclassified A0839\"                                                                                                         #> [521] \"unclassified Acetobacteraceae\"                                                                                              #> [522] \"unclassified Acidaminococcaceae\"                                                                                            #> [523] \"unclassified Actinobacteria\"                                                                                                #> [524] \"unclassified Actinomycetaceae\"                                                                                              #> [525] \"unclassified Aeromonadales\"                                                                                                 #> [526] \"unclassified Anaerococcus\"                                                                                                  #> [527] \"unclassified Anaerosalibacter\"                                                                                              #> [528] \"unclassified Anaerovoracaceae\"                                                                                              #> [529] \"unclassified Armatimonadales\"                                                                                               #> [530] \"unclassified Atopobiaceae\"                                                                                                  #> [531] \"unclassified Bacillaceae\"                                                                                                   #> [532] \"unclassified Bacillales\"                                                                                                    #> [533] \"unclassified Bacilli\"                                                                                                       #> [534] \"unclassified Bacteroidales\"                                                                                                 #> [535] \"unclassified Bacteroidia\"                                                                                                   #> [536] \"unclassified Barnesiellaceae\"                                                                                               #> [537] \"unclassified Bifidobacteriaceae\"                                                                                            #> [538] \"unclassified Burkholderiales\"                                                                                               #> [539] \"unclassified Butyricicoccaceae\"                                                                                             #> [540] \"unclassified Caloramatoraceae\"                                                                                              #> [541] \"unclassified Carnobacteriaceae\"                                                                                             #> [542] \"unclassified Caulobacteraceae\"                                                                                              #> [543] \"unclassified Chloroplast\"                                                                                                   #> [544] \"unclassified Christensenellaceae\"                                                                                           #> [545] \"unclassified Chroococcidiopsaceae\"                                                                                          #> [546] \"unclassified Clostridia UCG-014\"                                                                                            #> [547] \"unclassified Clostridia\"                                                                                                    #> [548] \"unclassified Clostridia vadinBB60 group\"                                                                                    #> [549] \"unclassified Clostridiaceae\"                                                                                                #> [550] \"unclassified Clostridiales\"                                                                                                 #> [551] \"unclassified Comamonadaceae\"                                                                                                #> [552] \"unclassified Coriobacteriales Incertae Sedis\"                                                                               #> [553] \"unclassified Coriobacteriales\"                                                                                              #> [554] \"unclassified Corynebacteriaceae\"                                                                                            #> [555] \"unclassified Desulfovibrionaceae\"                                                                                           #> [556] \"unclassified Devosiaceae\"                                                                                                   #> [557] \"unclassified Diplorickettsiaceae\"                                                                                           #> [558] \"unclassified Eggerthellaceae\"                                                                                               #> [559] \"unclassified Enterobacterales\"                                                                                              #> [560] \"unclassified Enterobacteriaceae\"                                                                                            #> [561] \"unclassified Enterococcaceae\"                                                                                               #> [562] \"unclassified Erwiniaceae\"                                                                                                   #> [563] \"unclassified Erysipelatoclostridiaceae\"                                                                                     #> [564] \"unclassified Erysipelotrichaceae\"                                                                                           #> [565] \"unclassified Erysipelotrichales\"                                                                                            #> [566] \"unclassified Ethanoligenenaceae\"                                                                                            #> [567] \"unclassified Eubacteriaceae\"                                                                                                #> [568] \"unclassified Ezakiella\"                                                                                                     #> [569] \"unclassified Fastidiosipila\"                                                                                                #> [570] \"unclassified Fenollaria\"                                                                                                    #> [571] \"unclassified Fimbriimonadaceae\"                                                                                             #> [572] \"unclassified Finegoldia\"                                                                                                    #> [573] \"unclassified Firmicutes\"                                                                                                    #> [574] \"unclassified Flavobacteriaceae\"                                                                                             #> [575] \"unclassified Flavobacteriales\"                                                                                              #> [576] \"unclassified Fusobacteriaceae\"                                                                                              #> [577] \"unclassified Gaiellales\"                                                                                                    #> [578] \"unclassified Gallicola\"                                                                                                     #> [579] \"unclassified Gammaproteobacteria\"                                                                                           #> [580] \"unclassified Gastranaerophilales\"                                                                                           #> [581] \"unclassified Gemmataceae\"                                                                                                   #> [582] \"unclassified Hungateiclostridiaceae\"                                                                                        #> [583] \"unclassified Hydrogenoanaerobacterium\"                                                                                      #> [584] \"unclassified Izemoplasmatales\"                                                                                              #> [585] \"unclassified JI49D030\"                                                                                                      #> [586] \"unclassified KD3-93\"                                                                                                        #> [587] \"unclassified Kapabacteriales\"                                                                                               #> [588] \"unclassified Lachnospiraceae\"                                                                                               #> [589] \"unclassified Lachnospirales\"                                                                                                #> [590] \"unclassified Lactobacillales\"                                                                                               #> [591] \"unclassified Leuconostocaceae\"                                                                                              #> [592] \"unclassified Lineage IV\"                                                                                                    #> [593] \"unclassified MAT-CR-H4-C10\"                                                                                                 #> [594] \"unclassified Methylococcaceae\"                                                                                              #> [595] \"unclassified Micavibrionales\"                                                                                               #> [596] \"unclassified Microbacteriaceae\"                                                                                             #> [597] \"unclassified Micrococcaceae\"                                                                                                #> [598] \"unclassified Micrococcales\"                                                                                                 #> [599] \"unclassified Mitochondria\"                                                                                                  #> [600] \"unclassified Moraxellaceae\"                                                                                                 #> [601] \"unclassified Murdochiella\"                                                                                                  #> [602] \"unclassified Muribaculaceae\"                                                                                                #> [603] \"unclassified NS9 marine group\"                                                                                              #> [604] \"unclassified Neisseriaceae\"                                                                                                 #> [605] \"unclassified OLB14\"                                                                                                         #> [606] \"unclassified Opitutales\"                                                                                                    #> [607] \"unclassified Oscillospiraceae\"                                                                                              #> [608] \"unclassified Oscillospirales\"                                                                                               #> [609] \"unclassified Oxalobacteraceae\"                                                                                              #> [610] \"unclassified P5D1-392\"                                                                                                      #> [611] \"unclassified PLTA13\"                                                                                                        #> [612] \"unclassified Paenibacillaceae\"                                                                                              #> [613] \"unclassified Paracaedibacteraceae\"                                                                                          #> [614] \"unclassified Parachlamydiaceae\"                                                                                             #> [615] \"unclassified Parvimonas\"                                                                                                    #> [616] \"unclassified Pasteurellaceae\"                                                                                               #> [617] \"unclassified Peptococcaceae\"                                                                                                #> [618] \"unclassified Peptoniphilus\"                                                                                                 #> [619] \"unclassified Peptostreptococcaceae\"                                                                                         #> [620] \"unclassified Peptostreptococcales-Tissierellales\"                                                                           #> [621] \"unclassified Planctomycetales\"                                                                                              #> [622] \"unclassified Planococcaceae\"                                                                                                #> [623] \"unclassified Prevotellaceae\"                                                                                                #> [624] \"unclassified Promicromonosporaceae\"                                                                                         #> [625] \"unclassified Propionibacteriaceae\"                                                                                          #> [626] \"unclassified Proteobacteria\"                                                                                                #> [627] \"unclassified Pseudomonadaceae\"                                                                                              #> [628] \"unclassified Puniceicoccaceae\"                                                                                              #> [629] \"unclassified RF39\"                                                                                                          #> [630] \"unclassified Rhizobiaceae\"                                                                                                  #> [631] \"unclassified Rhizobiales Incertae Sedis\"                                                                                    #> [632] \"unclassified Rhizobiales\"                                                                                                   #> [633] \"unclassified Rhodobacteraceae\"                                                                                              #> [634] \"unclassified Rhodocyclaceae\"                                                                                                #> [635] \"unclassified Rhodospirillales\"                                                                                              #> [636] \"unclassified Rickettsiales\"                                                                                                 #> [637] \"unclassified Rikenellaceae\"                                                                                                 #> [638] \"unclassified Ruminiclostridium\"                                                                                             #> [639] \"unclassified Ruminococcaceae\"                                                                                               #> [640] \"unclassified ST-12K33\"                                                                                                      #> [641] \"unclassified Saccharimonadales\"                                                                                             #> [642] \"unclassified Sandaracinaceae\"                                                                                               #> [643] \"unclassified Selenomonadaceae\"                                                                                              #> [644] \"unclassified Simkaniaceae\"                                                                                                  #> [645] \"unclassified Solimonadaceae\"                                                                                                #> [646] \"unclassified Sphingobacteriales\"                                                                                            #> [647] \"unclassified Sphingomonadaceae\"                                                                                             #> [648] \"unclassified Staphylococcaceae\"                                                                                             #> [649] \"unclassified Streptococcaceae\"                                                                                              #> [650] \"unclassified Succinivibrionaceae\"                                                                                           #> [651] \"unclassified Sutterellaceae\"                                                                                                #> [652] \"unclassified TRA3-20\"                                                                                                       #> [653] \"unclassified Tannerellaceae\"                                                                                                #> [654] \"unclassified Tepidimicrobium\"                                                                                               #> [655] \"unclassified UCG-010\"                                                                                                       #> [656] \"unclassified UCG-011\"                                                                                                       #> [657] \"unclassified Veillonellaceae\"                                                                                               #> [658] \"unclassified Veillonellales-Selenomonadales\"                                                                                #> [659] \"unclassified Vermiphilaceae\"                                                                                                #> [660] \"unclassified Verrucomicrobiales\"                                                                                            #> [661] \"unclassified Verrucomicrobiota\"                                                                                             #> [662] \"unclassified Victivallaceae\"                                                                                                #> [663] \"unclassified W5053\"                                                                                                         #> [664] \"unclassified WPS-2\"                                                                                                         #> [665] \"unclassified Weeksellaceae\"                                                                                                 #> [666] \"unclassified Xanthobacteraceae\"                                                                                             #> [667] \"unclassified Yersiniaceae\"                                                                                                  #> [668] \"unclassified [Clostridium] methylpentosum group\"                                                                            #> [669] \"unclassified [Eubacterium] coprostanoligenes group\"                                                                         #> [670] \"unclassified vadinBE97\"                                                                                                     getMetadataVariableNames(microbiomeData::DiabImmune) #>  [1] \"Participant_Id\"                                       #>  [2] \"Participant_repeated_measure_Id\"                      #>  [3] \"age_1st_animal_milk_or_solids_given_days\"             #>  [4] \"age_1st_given_apple_months\"                           #>  [5] \"age_1st_given_banana_months\"                          #>  [6] \"age_1st_given_barley_months\"                          #>  [7] \"age_1st_given_beef_months\"                            #>  [8] \"age_1st_given_berries_months\"                         #>  [9] \"age_1st_given_cabbs_months\"                           #> [10] \"age_1st_given_carrot_months\"                          #> [11] \"age_1st_given_corn_months\"                            #> [12] \"age_1st_given_cowsmilk_months\"                        #> [13] \"age_1st_given_egg_months\"                             #> [14] \"age_1st_given_fish_months\"                            #> [15] \"age_1st_given_milk_products_months\"                   #> [16] \"age_1st_given_oat_months\"                             #> [17] \"age_1st_given_pear_months\"                            #> [18] \"age_1st_given_peas_months\"                            #> [19] \"age_1st_given_plum_months\"                            #> [20] \"age_1st_given_pork_months\"                            #> [21] \"age_1st_given_potato_months\"                          #> [22] \"age_1st_given_poultry_months\"                         #> [23] \"age_1st_given_rice_months\"                            #> [24] \"age_1st_given_rye_months\"                             #> [25] \"age_1st_given_sweet_potato_months\"                    #> [26] \"age_1st_given_tomato_months\"                          #> [27] \"age_1st_given_wheat_months\"                           #> [28] \"age_at_anthropometry_days\"                            #> [29] \"age_at_two_autoantibodies_positive_days\"              #> [30] \"age_at_type_1_diabetes_diagnosis_days\"                #> [31] \"antibiotics_before_delivery_by_maternal_report\"       #> [32] \"bmi_minus_for_minus_age_z_minus_score\"                #> [33] \"breastfed_duration_days\"                              #> [34] \"country\"                                              #> [35] \"delivery_mode\"                                        #> [36] \"diet_in_first_three_days\"                             #> [37] \"exclusive_breastfed_duration_days\"                    #> [38] \"gestational_diabetes_by_maternal_report\"              #> [39] \"glutamic_acid_decarboxylase_autoantibodies\"           #> [40] \"hla_risk_by_hla_haplotyping\"                          #> [41] \"height_minus_for_minus_age_z_minus_score\"             #> [42] \"insulin_autoantibodies\"                               #> [43] \"insulinoma_minus_associated_protein_2_autoantibodies\" #> [44] \"islet_cell_autoantibodies\"                            #> [45] \"linear_growth_during_1st_year_cm\"                     #> [46] \"maternal_age_at_birth_months\"                         #> [47] \"mean_linear_growth_during_1st_3_years\"                #> [48] \"mean_weight_gain_during_1st_3_years\"                  #> [49] \"sex\"                                                  #> [50] \"study_group\"                                          #> [51] \"type_1_diabetes_diagnosed\"                            #> [52] \"urban_or_rural_site\"                                  #> [53] \"weight_gain_during_1st_year_kg\"                       #> [54] \"weight_minus_for_minus_age_z_minus_score\"             #> [55] \"zinc_transporter_8_autoantibodies\"                    #> [56] \"age_months\"                                           #> [57] \"Sample_Id\"                                            #> [58] \"habitat\"                                              #> [59] \"host_body_habitat\"                                    #> [60] \"host_body_product\"                                    #> [61] \"host_body_site\"                                       #> [62] \"sample_type\"                                          variablesDT <- getVariables(      microbiomeData::DiabImmune,       list(\"metadata\" = c(\"age_months\", \"sex\"),           \"16S (V4) Genus\" = \"Bacteroides\",            \"WGS Metagenome enzyme pathway abundance data\" = \"ANAGLYCOLYSIS-PWY: glycolysis III (from glucose)\"      ) ) #>  #> 2024-04-24 16:51:15.706984 Removed 300 records with no data."},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Ranked abundance — rankedAbundance","title":"Ranked abundance — rankedAbundance","text":"function returns abundances, ranked selected ranking function","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ranked abundance — rankedAbundance","text":"","code":"rankedAbundance(   data,   method = c(\"median\", \"max\", \"q3\", \"variance\"),   cutoff = 10,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ranked abundance — rankedAbundance","text":"data AbundanceData object method string defining ranking strategy order taxa. Accepted values 'median','max','q3','variance'. Note taxa return value 0 given method included results. cutoff integer indicating maximium number taxa kept ranking. verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ranked abundance — rankedAbundance","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Ranked abundance — rankedAbundance","text":"","code":"rankedAbundOutput <- rankedAbundance(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = \"median\" ) #>  #> 2024-04-24 16:51:16.079002 Received df table with 3184 samples and 673 taxa. #>  #> 2024-04-24 16:51:16.168237 Finished ranking taxa #>  #> 2024-04-24 16:51:16.178349 Ranked abundance computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = median , cutoff = 10 , naToZero =  TRUE , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Self Correlation — selfCorrelation","title":"Self Correlation — selfCorrelation","text":"function returns correlation coefficients variables one AbundanceData object . generally serves convenience wrapper around veupathUtils::correlation, exception additionally supports sparcc.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Self Correlation — selfCorrelation","text":"","code":"selfCorrelation(   data,   method = c(\"spearman\", \"pearson\", \"sparcc\"),   format = c(\"ComputeResult\", \"data.table\"),   verbose = c(TRUE, FALSE),   ... )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Self Correlation — selfCorrelation","text":"data AbundanceData object method string defining type correlation run. currently supported values 'spearman','pearson' 'sparcc' format string defining desired format result. currently supported values 'data.table' 'ComputeResult'. verbose boolean indicating timed logging desired ... additional parameters","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Self Correlation — selfCorrelation","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Self Correlation — selfCorrelation","text":"","code":"correlationDT <- selfCorrelation(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = 'sparcc',       format = 'data.table' ) #>  #> 2024-04-24 16:51:16.454713 Removed 1 records with no data. #>  #> 2024-04-24 16:51:16.461387 Removed 1 records with no data. #>  #> 2024-04-24 16:51:16.467786 Removed 1 records with no data. #>  #> 2024-04-24 17:01:15.654585 Completed correlation with method=sparcc. Formatting results. #>  #> 2024-04-24 17:01:15.65553 Received df table with 3183 samples and 21 features with abundances.  correlationOutput <- selfCorrelation(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = 'sparcc',       format = 'ComputeResult' ) #>  #> 2024-04-24 17:01:15.792888 Removed 1 records with no data. #>  #> 2024-04-24 17:01:15.79952 Removed 1 records with no data. #>  #> 2024-04-24 17:01:15.80587 Removed 1 records with no data. #>  #> 2024-04-24 17:11:14.707997 Completed correlation with method=sparcc. Formatting results. #>  #> 2024-04-24 17:11:14.709201 Received df table with 3183 samples and 21 features with abundances. #>  #> 2024-04-24 17:11:14.710412 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  sparcc  alsoCorrelationDT <- getComputeResult(      correlationOutput,       \"data.table\" )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Microbiome Dataset Collection Name — updateCollectionName","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"Update name collection Microbiome Dataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"","code":"updateCollectionName(object, oldName, newName)  # S4 method for MbioDataset updateCollectionName(object, oldName, newName)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"object Microbiome Dataset oldName name collection update newName new name collection","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"Microbiome Dataset updated collection name","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"","code":"myCopyOfDiabImmune <- microbiomeData::DiabImmune myCopyOfDiabImmune <- updateCollectionName(myCopyOfDiabImmune, \"16S (V4) Genus\", \"16S Genus\")"}]
+[{"path":"https://microbiomedb.github.io/MicrobiomeDB/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004 <http://www.apache.org/licenses/>","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/MicrobiomeDB/LICENSE.html","id":"id_1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. Definitions","title":"Apache License","text":"“License” shall mean terms conditions use, reproduction, distribution defined Sections 1 9 document. “Licensor” shall mean copyright owner entity authorized copyright owner granting License. “Legal Entity” shall mean union acting entity entities control, controlled , common control entity. purposes definition, “control” means () power, direct indirect, cause direction management entity, whether contract otherwise, (ii) ownership fifty percent (50%) outstanding shares, (iii) beneficial ownership entity. “” (“”) shall mean individual Legal Entity exercising permissions granted License. “Source” form shall mean preferred form making modifications, including limited software source code, documentation source, configuration files. “Object” form shall mean form resulting mechanical transformation translation Source form, including limited compiled object code, generated documentation, conversions media types. “Work” shall mean work authorship, whether Source Object form, made available License, indicated copyright notice included attached work (example provided Appendix ). “Derivative Works” shall mean work, whether Source Object form, based (derived ) Work editorial revisions, annotations, elaborations, modifications represent, whole, original work authorship. purposes License, Derivative Works shall include works remain separable , merely link (bind name) interfaces , Work Derivative Works thereof. “Contribution” shall mean work authorship, including original version Work modifications additions Work Derivative Works thereof, intentionally submitted Licensor inclusion Work copyright owner individual Legal Entity authorized submit behalf copyright owner. purposes definition, “submitted” means form electronic, verbal, written communication sent Licensor representatives, including limited communication electronic mailing lists, source code control systems, issue tracking systems managed , behalf , Licensor purpose discussing improving Work, excluding communication conspicuously marked otherwise designated writing copyright owner “Contribution.” “Contributor” shall mean Licensor individual Legal Entity behalf Contribution received Licensor subsequently incorporated within Work.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/LICENSE.html","id":"id_2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. 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(Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright [yyyy] [name of copyright owner]  Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at    http://www.apache.org/licenses/LICENSE-2.0  Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"what-is-alpha-diversity","dir":"Articles","previous_headings":"","what":"What is Alpha Diversity?","title":"Alpha Diversity","text":"Alpha diversity measures diversity microbial taxa within single sample community. takes account number different taxa (richness) distribution (evenness). Understanding alpha diversity provides insights complexity structure microbial communities local level.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"why-care-about-alpha-diversity","dir":"Articles","previous_headings":"","what":"Why Care About Alpha Diversity?","title":"Alpha Diversity","text":"Researchers interested alpha diversity several reasons: Community Comparisons: Compare diversity microbial communities across different samples conditions. Health Assessments: Assess health stability microbial communities within specific environments host systems. Ecological Understanding: Gain insights ecological dynamics microbial communities local scale.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"how-is-alpha-diversity-calculated","dir":"Articles","previous_headings":"","what":"How is Alpha Diversity Calculated?","title":"Alpha Diversity","text":"package offers three diversity indices calculation: Shannon, Simpson Evenness.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"shannon-diversity-index","dir":"Articles","previous_headings":"How is Alpha Diversity Calculated?","what":"Shannon Diversity Index","title":"Alpha Diversity","text":"Shannon diversity index measures entropy uncertainty predicting identity randomly chosen taxon within sample. can calculated follows:","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::HMP_WGS) #>  [1] \"WGS 4th level EC metagenome abundance data\"               #>  [2] \"WGS Metagenome enzyme pathway abundance data\"             #>  [3] \"WGS Metagenome enzyme pathway coverage data\"              #>  [4] \"WGS Genus\"                                                #>  [5] \"WGS Species\"                                              #>  [6] \"WGS Family\"                                               #>  [7] \"WGS Order\"                                                #>  [8] \"WGS Phylum\"                                               #>  [9] \"WGS Class\"                                                #> [10] \"WGS Normalized number of taxon-specific sequence matches\" #> [11] \"WGS Kingdom\"  ## grab a collection we like genus <- getCollection(microbiomeData::HMP_WGS, 'WGS Genus')  ## get an alpha diversity ComputeResult alphaDivOutput <- alphaDiv(genus, method = 'shannon') #>  #> 2024-04-24 17:37:00.644513 Received df table with 741 samples and 226 taxa. #>  #> 2024-04-24 17:37:00.669897 shannon alpha diversity computation complete. #>  #> 2024-04-24 17:37:00.685402 Alpha diversity computation completed with parameters method= shannon"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"simpson-diversity-index","dir":"Articles","previous_headings":"How is Alpha Diversity Calculated?","what":"Simpson Diversity Index","title":"Alpha Diversity","text":"Simpson diversity index measures probability two individuals randomly selected sample belong different taxa. can calculated follows:","code":"## get an alpha diversity ComputeResult genus <- getCollection(microbiomeData::HMP_WGS, 'WGS Genus') alphaDivOutput <- alphaDiv(genus, method = 'simpson') #>  #> 2024-04-24 17:37:00.779723 Received df table with 741 samples and 226 taxa. #>  #> 2024-04-24 17:37:00.802822 simpson alpha diversity computation complete. #>  #> 2024-04-24 17:37:00.808237 Alpha diversity computation completed with parameters method= simpson"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"species-evenness","dir":"Articles","previous_headings":"How is Alpha Diversity Calculated?","what":"Species Evenness","title":"Alpha Diversity","text":"Species evenness describes distribution abundances across species sample. Species evenness highest species sample abundance approaches zero relative abundances vary.","code":"## get an alpha diversity ComputeResult genus <- getCollection(microbiomeData::HMP_WGS, 'WGS Genus') alphaDivOutput <- alphaDiv(genus, method = 'evenness') #>  #> 2024-04-24 17:37:00.894878 Received df table with 741 samples and 226 taxa. #>  #> 2024-04-24 17:37:00.913373 evenness alpha diversity computation complete. #>  #> 2024-04-24 17:37:00.916953 Alpha diversity computation completed with parameters method= evenness"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/alphadiv.html","id":"visualizing-alpha-diversity","dir":"Articles","previous_headings":"","what":"Visualizing Alpha Diversity","title":"Alpha Diversity","text":"Alpha Diversity frequently visualized scatter box plots. Creating types plots can done like following:","code":"## choose one or more metadata variables to integrate with the compute result alphaDiv_withMetadata <- getComputeResultWithMetadata(   alphaDivOutput,   microbiomeData::HMP_WGS,   metadataVariables = c('host_body_habitat') )  ## plot the compute result with integrated metadata ggplot(alphaDiv_withMetadata) +   aes(x=alphaDiversity, y=host_body_habitat, fill=host_body_habitat) +   geom_boxplot() +   labs(y= \"Body site\", x = \"Alpha diversity (Shannon)\",         title=\"Alpha diversity by body site\",         caption=paste0(\"produced on \", Sys.time())) +   theme_bw()"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"what-is-beta-diversity","dir":"Articles","previous_headings":"","what":"What is Beta Diversity?","title":"Beta Diversity","text":"Beta diversity measures dissimilarity diversity different microbial communities. context microbiome studies, quantifies microbial compositions vary across samples. Understanding beta diversity allows researchers explore unique features sample identify patterns microbial community structure.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"why-care-about-beta-diversity","dir":"Articles","previous_headings":"","what":"Why Care About Beta Diversity?","title":"Beta Diversity","text":"Researchers interested beta diversity several reasons: Ecological Insights: Beta diversity helps uncover ecological differences microbial communities different environments conditions. Disease Studies: medical research, beta diversity can highlight variations microbial communities associated health disease states. Community Dynamics: Studying beta diversity provides information microbial communities change time response specific factors.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"how-is-beta-diversity-calculated","dir":"Articles","previous_headings":"","what":"How is Beta Diversity Calculated?","title":"Beta Diversity","text":"Beta Diversity can calculated first producing dissimilarity matrix samples applying dimensional reduction technique dissimilarity matrix. package offers flexibility calculating beta diversity providing multiple dissimilarity matrix options:","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"bray-curtis-dissimilarity","dir":"Articles","previous_headings":"How is Beta Diversity Calculated?","what":"Bray-Curtis Dissimilarity","title":"Beta Diversity","text":"Bray-Curtis algorithm measures compositional dissimilarity based presence abundance taxa. calculates normalized absolute differences taxon abundance two samples, providing metric ranges 0 (complete similarity) 1 (complete dissimilarity).","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::HMP_WGS) #>  [1] \"WGS 4th level EC metagenome abundance data\"               #>  [2] \"WGS Metagenome enzyme pathway abundance data\"             #>  [3] \"WGS Metagenome enzyme pathway coverage data\"              #>  [4] \"WGS Genus\"                                                #>  [5] \"WGS Species\"                                              #>  [6] \"WGS Family\"                                               #>  [7] \"WGS Order\"                                                #>  [8] \"WGS Phylum\"                                               #>  [9] \"WGS Class\"                                                #> [10] \"WGS Normalized number of taxon-specific sequence matches\" #> [11] \"WGS Kingdom\"  ## grab a collection we like HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, 'WGS Species')  ## get a betaDiv ComputeResult betaDiv <- betaDiv(HMP_WGS_species, method = \"bray\") #>  #> 2024-04-24 17:37:14.829383 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:37:15.155728 Computed dissimilarity matrix. #>  #> 2024-04-24 17:37:16.089393 Finished ordination step. #>  #> 2024-04-24 17:37:16.11976 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = bray , k = 2 , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"jaccard-dissimilarity","dir":"Articles","previous_headings":"How is Beta Diversity Calculated?","what":"Jaccard Dissimilarity","title":"Beta Diversity","text":"Measures dissimilarity based presence-absence taxa. quantifies proportion taxa shared two samples.","code":"HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, 'WGS Species') betaDiv <- betaDiv(HMP_WGS_species, method = \"jaccard\") #>  #> 2024-04-24 17:37:16.269667 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:37:16.581029 Computed dissimilarity matrix. #>  #> 2024-04-24 17:37:16.769338 Finished ordination step. #>  #> 2024-04-24 17:37:16.780671 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jaccard , k = 2 , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"jensen-shannon-divergence-jsd","dir":"Articles","previous_headings":"How is Beta Diversity Calculated?","what":"Jensen-Shannon Divergence (JSD)","title":"Beta Diversity","text":"Captures dissimilarity considering abundance presence-absence information. symmetric version Kullback-Leibler Divergence, providing measure dissimilarity probability distributions.","code":"HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, 'WGS Species') betaDiv <- betaDiv(HMP_WGS_species, method = \"jsd\") #>  #> 2024-04-24 17:37:16.914771 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:37:23.70449 Computed dissimilarity matrix. #>  #> 2024-04-24 17:37:23.903281 Finished ordination step. #>  #> 2024-04-24 17:37:23.90968 Beta diversity computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = jsd , k = 2 , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"principal-coordinate-analysis-pcoa","dir":"Articles","previous_headings":"How is Beta Diversity Calculated?","what":"Principal Coordinate Analysis (PCoA):","title":"Beta Diversity","text":"PCoA dimensional reduction technique applied dissimilarity matrix, providing visual representation relationships samples lower-dimensional space. transforms dissimilarity matrix set orthogonal axes (principal coordinates) capture maximum variance data. PCoA plot allows researchers visualize spatial arrangement samples, aiding interpretation beta diversity. MicrobiomeDB package performs PCoA part betaDiv method.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"interpreting-pcoa-results","dir":"Articles","previous_headings":"","what":"Interpreting PCoA Results","title":"Beta Diversity","text":"following code produce PCoA plot:  PCoA plot visually represents dissimilarity samples. point plot corresponds sample, position points reflects relationships based beta diversity. ’s interpret PCoA plot:","code":"## choose one or more metadata variables to integrate with the compute result betaDiv_withMetadata <- getComputeResultWithMetadata(   betaDiv,    microbiomeData::HMP_WGS,    metadataVariables = c('host_body_habitat'))  ## plot beta diversity ggplot2::ggplot(betaDiv_withMetadata) +   aes(x=Axis1, y=Axis2, color=host_body_habitat) +   geom_point() +   labs(y= \"Axis 2\", x = \"Axis 1\",         title=\"Beta diversity by body site\",         caption=paste0(\"produced on \", Sys.time())) +   theme_bw()"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"axes-representation","dir":"Articles","previous_headings":"Interpreting PCoA Results","what":"Axes Representation:","title":"Beta Diversity","text":"axes (principal coordinates) PCoA plot represent dimensions maximum variance dissimilarity matrix. distance points plot reflects dissimilarity corresponding samples. axis explains certain percentage total variation data.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"interpreting-axis-direction","dir":"Articles","previous_headings":"Interpreting PCoA Results","what":"Interpreting Axis Direction:","title":"Beta Diversity","text":"direction axes indicates major patterns dissimilarity data. Samples cluster together plot similar , farther apart dissimilar.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"percentage-of-variance","dir":"Articles","previous_headings":"Interpreting PCoA Results","what":"Percentage of Variance:","title":"Beta Diversity","text":"Check percentage variance explained axis. Higher percentages indicate axis captures information dissimilarity samples.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/betadiv.html","id":"biological-interpretation","dir":"Articles","previous_headings":"Interpreting PCoA Results","what":"Biological Interpretation:","title":"Beta Diversity","text":"Interpret biological meaning sample clustering. distinct groups trends data? Color PCoA plot another variable learn patterns!","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"what-is-a-correlation-analysis","dir":"Articles","previous_headings":"","what":"What is a Correlation Analysis?","title":"Correlation","text":"Correlations useful identifying relationships variables. helpful identifying biomarkers functional associations, among things. Biomarkers microbiome data microbial taxa features exhibit significant correlation particular conditions, traits, variables sample metadata. Identifying biomarkers allows researchers uncover associations microbiome external factors, age, disease status, environmental conditions. Biomarkers serve indicators specific biological clinical phenomena within microbial communities. Functional associations microbiome data refer relationships taxonomic relative abundances abundances specific pathways functional features. Understanding associations allows researchers explore taxonomic composition microbial communities influences functional capabilities.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"why-care-about-biomarker-discovery","dir":"Articles","previous_headings":"","what":"Why Care About Biomarker Discovery?","title":"Correlation","text":"Researchers interested biomarker discovery several reasons: Diagnostic Insights: Biomarkers can serve potential diagnostic indicators, helping identify microbial patterns associated specific conditions. Predictive Modeling: Understanding biomarker correlations enables predictive modeling microbial responses external factors. Biological Significance: Biomarkers provide insights biological significance microbial community variations response different conditions.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"why-care-about-functional-associations","dir":"Articles","previous_headings":"","what":"Why Care About Functional Associations?","title":"Correlation","text":"Biological Insights: Explore changes taxonomic composition may impact functional potential microbial communities. Pathway-Level Analysis: Understand specific pathways functional features correlate taxonomic abundance, providing pathway-level insights. Predictive Modeling: Assessing functional associations aids predicting microbial functional responses environmental changes perturbations.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"how-are-correlations-calculated","dir":"Articles","previous_headings":"","what":"How are Correlations Calculated?","title":"Correlation","text":"package employs correlation analysis microbial taxonomic abundances sample metadata abundances pathways functional data using following approach: Users can choose either Spearman Pearson correlation analysis. produce correlation coefficient p-value indicating statistical significance.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"spearman-correlation","dir":"Articles","previous_headings":"How are Correlations Calculated?","what":"Spearman Correlation","title":"Correlation","text":"Use relationship variables monotonic necessarily linear. Suitable non-linear associations.","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::HMP_WGS) #>  [1] \"WGS 4th level EC metagenome abundance data\"               #>  [2] \"WGS Metagenome enzyme pathway abundance data\"             #>  [3] \"WGS Metagenome enzyme pathway coverage data\"              #>  [4] \"WGS Genus\"                                                #>  [5] \"WGS Species\"                                              #>  [6] \"WGS Family\"                                               #>  [7] \"WGS Order\"                                                #>  [8] \"WGS Phylum\"                                               #>  [9] \"WGS Class\"                                                #> [10] \"WGS Normalized number of taxon-specific sequence matches\" #> [11] \"WGS Kingdom\"  ## grab a collection of interest HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, \"WGS Species\", continuousMetadataOnly = TRUE)  ## get a correlation ComputeResult ## this is not necessarily to recommend spearman for metadata.  ## it is simply exemplary. Always look at your data! species_vs_metadata <- correlation(HMP_WGS_species, method = 'spearman')  #>  #> 2024-04-24 17:37:37.301624 Removed 7 records with no data. #>  #> 2024-04-24 17:37:37.331011 Removed 7 records with no data. #>  #> 2024-04-24 17:37:37.367011 Removed 7 records with no data. #>  #> 2024-04-24 17:37:38.706018 Completed correlation with method=spearman. Formatting results. #>  #> 2024-04-24 17:37:38.707003 Received df table with 734 samples and 316 features with values. #>  #> 2024-04-24 17:37:38.711433 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method =  spearman"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"pearson-correlation","dir":"Articles","previous_headings":"How are Correlations Calculated?","what":"Pearson Correlation","title":"Correlation","text":"Use relationship variables linear. Suitable assessing linear associations.","code":"## grab two collections of interest, in this case species level data and pathway abundance data HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, \"WGS Species\") HMP_WGS_pathways <- getCollection(microbiomeData::HMP_WGS, \"WGS Metagenome enzyme pathway abundance data\" )  ## get a correlation ComputeResult ## this is not necessarily to recommend pearson for functional data. ## it is simply exemplary. Always look at your data! pathway_vs_species <- correlation(HMP_WGS_species, HMP_WGS_pathways, method = 'pearson') #>  #> 2024-04-24 17:37:39.633612 Removed 7 records with no data. #>  #> 2024-04-24 17:37:39.670784 Removed 7 records with no data. #>  #> 2024-04-24 17:37:39.823658 Removed 7 records with no data. #>  #> 2024-04-24 17:37:39.834297 Received first df table with 734 samples and 319 features with values. #>  #> 2024-04-24 17:37:39.834609 Received second df table with 741 samples and 371 features with values. #>  #> 2024-04-24 17:37:39.834852 Found 734 samples in common between data1 and data2. Only these samples will be used. #>  #> 2024-04-24 17:37:40.250861 Completed correlation with method=pearson. Formatting results. #>  #> 2024-04-24 17:37:40.256431 Correlation computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method =  pearson"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/correlation.html","id":"interpreting-results","dir":"Articles","previous_headings":"","what":"Interpreting Results","title":"Correlation","text":"Correlation Coefficients: Assess strength direction correlations. Positive coefficients indicate positive correlations, negative coefficients indicate negative correlations. p-values Adjusted p-values: Identify biomarkers statistically significant correlations, considering adjustments multiple testing. can extract metrics sort filter results : can also visualize custom htmlwidgets: Finally, advanced analysis network, can extract igraph object:","code":"## you can extract network metrics  pathway_vs_species.metrics <- as_tibble(   getComputeResult(     pathway_vs_species,     correlationCoefThreshold = 0.8,     pValueThreshold = 0.05   ) )  ## it's also easy to sort and filter these network metrics ## begin by renaming columns colnames(pathway_vs_species.metrics) <- c('species', 'pathway', 'correlationCoef', 'pValue') pathway_vs_species.metrics %>%   filter(species == \"Faecalibacterium prausnitzii\") %>%   filter(correlationCoef > 0.5) %>%   arrange(desc(correlationCoef)) #> # A tibble: 1 × 4 #>   species                      pathway                    correlationCoef pValue #>   <chr>                        <fct>                                <dbl>  <dbl> #> 1 Faecalibacterium prausnitzii PWY-5177: glutaryl-CoA de…           0.825      0 ## now plot the network ## filters can be applied based on correlation coefficient and p-value ## renders an interactive htmlwidget, using a predetermined layout correlationNetwork(   pathway_vs_species,   correlationCoefThreshold = 0.8,   pValueThreshold = 0.05 ) ## if you extract the network as an igraph object, you can get more detailed metrics pathway_vs_species.igraph <- getComputeResult(pathway_vs_species, format = 'igraph') degree <- degree(pathway_vs_species.igraph) edgeBT <- edge_betweenness(pathway_vs_species.igraph) pgRank <- page_rank(pathway_vs_species.igraph) coords <- layout_with_kk(pathway_vs_species.igraph)  #plot(pathway_vs_species.igraph, layout = coords)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/ranked-abundance.html","id":"what-are-relative-abundances","dir":"Articles","previous_headings":"","what":"What are Relative Abundances","title":"Ranked Relative Abundances","text":"Relative abundances refer proportion percentage taxonomic group microbial species within given sample ecosystem. quantifies contribution taxon overall microbial community, providing insights distribution dominance different organisms. Relative abundances typically determined techniques like amplicon sequencing metagenomic analysis, allowing researchers compare prevalence various taxa across different samples conditions. information crucial understanding structure, dynamics, ecological roles microbial communities.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/ranked-abundance.html","id":"why-compare-or-find-taxa-based-on-relative-abundances","dir":"Articles","previous_headings":"","what":"Why Compare or Find Taxa Based on Relative Abundances?","title":"Ranked Relative Abundances","text":"Researchers drawn comparing finding taxa based relative abundances multitude reasons: Ecosystem Dynamics: Assessing relative abundances allows researchers unravel shifts microbial community structures time response environmental changes, offering insights ecosystem dynamics stability. Biological Significance: Identifying taxa significant shifts relative abundances can unveil roles ecosystem functions, providing valuable clues ecological significance potential impacts ecosystem processes. Disease Associations: Comparing taxa based relative abundances can reveal microbial signatures associated various diseases health conditions, paving way potential biomarker discovery diagnostic insights. Taxonomic Profiling: Understanding relative abundances different taxa provides comprehensive snapshot microbial community compositions, aiding taxonomic profiling classification efforts. deciphering ecological shifts uncovering disease markers, comparing finding taxa based relative abundances offers powerful lens researchers can explore intricate world microbial communities.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/ranked-abundance.html","id":"how-to-find-ranked-relative-abundances","dir":"Articles","previous_headings":"","what":"How to Find Ranked Relative Abundances?","title":"Ranked Relative Abundances","text":"package offers convenience function finding taxa ranking relative abundances metric interest. Available metrics max, median, q3 variance.","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::HMP_WGS) #>  [1] \"WGS 4th level EC metagenome abundance data\"               #>  [2] \"WGS Metagenome enzyme pathway abundance data\"             #>  [3] \"WGS Metagenome enzyme pathway coverage data\"              #>  [4] \"WGS Genus\"                                                #>  [5] \"WGS Species\"                                              #>  [6] \"WGS Family\"                                               #>  [7] \"WGS Order\"                                                #>  [8] \"WGS Phylum\"                                               #>  [9] \"WGS Class\"                                                #> [10] \"WGS Normalized number of taxon-specific sequence matches\" #> [11] \"WGS Kingdom\"  ## grab a collection of interest HMP_WGS_species <- getCollection(microbiomeData::HMP_WGS, \"WGS Species\")  ## get a ranked abundance ComputeResult ## top 10 taxa by max relative abundance across all samples rankedAbund <- rankedAbundance(HMP_WGS_species, method = \"max\", cutoff = 10)  #>  #> 2024-04-24 17:37:54.182368 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:37:54.213604 Finished ranking taxa #>  #> 2024-04-24 17:37:54.234347 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = max , cutoff = 10 , naToZero =  TRUE , verbose = TRUE ## top 8 taxa by median relative abundance across all samples rankedAbund <- rankedAbundance(HMP_WGS_species, method = \"median\", cutoff = 8) #>  #> 2024-04-24 17:37:54.955539 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:37:54.976285 Finished ranking taxa #>  #> 2024-04-24 17:37:54.984991 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = median , cutoff = 8 , naToZero =  TRUE , verbose = TRUE ## top 20 taxa by third quartile relative abundance across all samples rankedAbund <- rankedAbundance(HMP_WGS_species, method = \"q3\", cutoff = 20) #>  #> 2024-04-24 17:37:55.011114 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:37:55.118115 Finished ranking taxa #>  #> 2024-04-24 17:37:55.124598 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = q3 , cutoff = 20 , naToZero =  TRUE , verbose = TRUE ## top 10 taxa by greatest variance in relative abundance across all samples rankedAbund <- rankedAbundance(HMP_WGS_species, method = \"variance\", cutoff = 10) #>  #> 2024-04-24 17:37:55.150866 Received df table with 741 samples and 704 taxa. #>  #> 2024-04-24 17:37:55.171238 Finished ranking taxa #>  #> 2024-04-24 17:37:55.176685 Ranked abundance computation completed with parameters recordIdColumn= Metagenomic_sequencing_assay_Id , method = variance , cutoff = 10 , naToZero =  TRUE , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/ranked-abundance.html","id":"visualizing-ranked-relative-abundances","dir":"Articles","previous_headings":"","what":"Visualizing Ranked Relative Abundances","title":"Ranked Relative Abundances","text":"Abundances frequently visualized scatter box plots. Creating types plots can done like following:","code":"## combine ranked abundance result with sample metadata of interest rankedAbund_withMetadata <- getComputeResultWithMetadata(     rankedAbund,      microbiomeData::HMP_WGS,      metadataVariables = c('host_body_habitat'))  ## pivot the dataframe to be able to plot it rankedAbund_withMetadata.pivot <- pivot_longer(rankedAbund_withMetadata, # dataframe to be pivoted                                     cols = 4:13, # column names to be stored as a SINGLE variable                                     names_to = \"taxa\", # name of that new variable (column)                                     values_to = \"abundance\") # name of new variable (column) storing all the values (data)  ## plot the compute result with integrated metadata ggplot2::ggplot(rankedAbund_withMetadata.pivot) +     aes(x=abundance, y=taxa, fill = factor(host_body_habitat)) +     geom_boxplot() +     labs(y= \"Taxon\", x = \"Relative abundance\",         title=\"Relative abudnace of top taxa\",         caption=paste0(\"produced on \", Sys.time())) +     theme_bw()"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/self-correlation.html","id":"what-is-a-correlation-analysis","dir":"Articles","previous_headings":"","what":"What is a Correlation Analysis?","title":"Self Correlation","text":"Correlations useful identifying relationships variables. correlate taxonomic abundance variables , essentially produces microbial network. Producing analyzing networks complicated fact microbiome data inherently compositional. properly accounted , can result lot spurious negative correlations.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/self-correlation.html","id":"why-care-about-microbial-network-analysis","dir":"Articles","previous_headings":"","what":"Why Care About Microbial Network Analysis?","title":"Self Correlation","text":"Scientists delve microbial network analysis large number reasons: Unraveling Complex Interactions: Microbial network analysis unveils intricate relationships microorganisms, shedding light interconnectedness within ecosystems. Diagnostic Potential: Identifying key nodes microbial networks can unveil potential diagnostic markers, offering glimpse microbial dynamics associated various diseases environmental conditions. Insights Functionality: Microbial network analysis elucidates functional roles within microbial communities, offering valuable insights ecological physiological significance. unraveling ecological mysteries informing medical diagnoses, microbial network analysis proves indispensable understanding intricate world microorganisms.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/self-correlation.html","id":"how-are-correlations-calculated","dir":"Articles","previous_headings":"","what":"How are Correlations Calculated?","title":"Self Correlation","text":"package employs SPARCC correlation analysis microbial taxa. SPARCC calculates correlations account compositional nature microbiome data.","code":"## first lets find some interesting data microbiomeData::getCuratedDatasetNames() #>  [1] \"Anopheles_albimanus\"     \"BONUS\"                   #>  [3] \"Bangladesh\"              \"DailyBaby\"               #>  [5] \"DiabImmune\"              \"ECAM\"                    #>  [7] \"EcoCF\"                   \"FARMM\"                   #>  [9] \"GEMS1\"                   \"HMP_V1V3\"                #> [11] \"HMP_V3V5\"                \"HMP_WGS\"                 #> [13] \"Leishmaniasis\"           \"MALED_2yr\"               #> [15] \"MALED_diarrhea\"          \"MORDOR\"                  #> [17] \"Malaysia_helminth\"       \"NICU_NEC\"                #> [19] \"PIH_Uganda\"              \"PretermInfantResistome1\" #> [21] \"PretermInfantResistome2\" \"UgandaMaternal\"  getCollectionNames(microbiomeData::FARMM) #>  [1] \"Metabolomics Mass spectrometry assay\"                     #>  [2] \"WGS 4th level EC metagenome abundance data\"               #>  [3] \"WGS Metagenome enzyme pathway abundance data\"             #>  [4] \"WGS Metagenome enzyme pathway coverage data\"              #>  [5] \"WGS Genus\"                                                #>  [6] \"WGS Species\"                                              #>  [7] \"WGS Family\"                                               #>  [8] \"WGS Order\"                                                #>  [9] \"WGS Phylum\"                                               #> [10] \"WGS Class\"                                                #> [11] \"WGS Normalized number of taxon-specific sequence matches\" #> [12] \"WGS Kingdom\"  ## grab a collection of interest ## these methods can be used with other data types as well farmm_metabolomics <- getCollection(microbiomeData::FARMM, \"Metabolomics Mass spectrometry assay\") #>  #> 2024-04-24 17:38:08.623847 Integer values detected. Converting collection to AbsoluteAbundanceData  ## get a self correlation ComputeResult ## methods spearman and pearson are options here as well, for data known to not be compositional selfCorrelation_metabolomics <- selfCorrelation(farmm_metabolomics, method='spearman') #>  #> 2024-04-24 17:38:09.960696 Completed correlation with method=spearman. Formatting results. #>  #> 2024-04-24 17:38:10.821158 Received df table with 150 samples and 479 features with abundances. #>  #> 2024-04-24 17:38:10.825808 Correlation computation completed with parameters recordIdColumn= Mass_spectrometry_assay_Id , method =  spearman"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/articles/self-correlation.html","id":"interpreting-results","dir":"Articles","previous_headings":"","what":"Interpreting Results","title":"Self Correlation","text":"Correlation Coefficients: Assess strength direction correlations. Positive coefficients indicate positive correlations, negative coefficients indicate negative correlations. p-values Adjusted p-values: Identify biomarkers statistically significant correlations, considering adjustments multiple testing. can extract metrics sort filter results : can also visualize custom htmlwidgets: Finally, advanced analysis network, can extract igraph object:","code":"## you can extract network metrics  selfCorrelation_metabolomics.metrics <- as_tibble(     getComputeResult(         selfCorrelation_metabolomics,         correlationCoefThreshold = 0.5,         pValueThreshold = 0.05     ) )  ## it's also easy to sort and filter these network metrics ## begin by renaming columns colnames(selfCorrelation_metabolomics.metrics) <- c('metabolite1', 'metabolite2', 'correlationCoef', 'pValue') selfCorrelation_metabolomics.metrics %>%     filter(correlationCoef > 0.5) %>%     arrange(desc(correlationCoef)) #> # A tibble: 11,027 × 4 #>    metabolite1                       metabolite2          correlationCoef pValue #>    <fct>                             <fct>                          <dbl>  <dbl> #>  1 C46:3 TAG +NH4:C8-pos: Metabolite C46:3 TAG:C8-pos: M…           0.999      0 #>  2 C44:1 TAG +NH4:C8-pos: Metabolite C44:1 TAG:C8-pos: M…           0.999      0 #>  3 C16:0 LPC:C8-pos: Metabolite      C20:3 LPC:C8-pos: M…           0.999      0 #>  4 C44:2 TAG +NH4:C8-pos: Metabolite C44:2 TAG:C8-pos: M…           0.999      0 #>  5 C46:2 TAG +NH4:C8-pos: Metabolite C46:2 TAG:C8-pos: M…           0.998      0 #>  6 C52:0 TAG +NH4:C8-pos: Metabolite C52:0 TAG:C8-pos: M…           0.997      0 #>  7 C52:1 TAG +NH4:C8-pos: Metabolite C52:1 TAG:C8-pos: M…           0.997      0 #>  8 C50:0 TAG +NH4:C8-pos: Metabolite C50:0 TAG:C8-pos: M…           0.996      0 #>  9 C42:0 TAG +NH4:C8-pos: Metabolite C42:0 TAG:C8-pos: M…           0.995      0 #> 10 C48:3 TAG +NH4:C8-pos: Metabolite C48:3 TAG:C8-pos: M…           0.995      0 #> # ℹ 11,017 more rows ## now plot the network ## filters can be applied based on correlation coefficient and p-value ## renders an interactive htmlwidget, using a predetermined layout correlationNetwork(     selfCorrelation_metabolomics,     correlationCoefThreshold = 0.5,     pValueThreshold = 0.05 ) ## if you extract the network as an igraph object, you can get more detailed metrics selfCorrelation_metabolomics.igraph <- getComputeResult(selfCorrelation_metabolomics, format = 'igraph') degree <- degree(selfCorrelation_metabolomics.igraph) edgeBT <- edge_betweenness(selfCorrelation_metabolomics.igraph) pgRank <- page_rank(selfCorrelation_metabolomics.igraph) coords <- layout_with_kk(selfCorrelation_metabolomics.igraph)  #plot(selfCorrelation_metabolomics.igraph, coords)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Danielle Callan. Author, maintainer.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Callan D (2024). MicrobiomeDB: Curated Data Analysis Tools MicrobiomeDB.org. R package version 1.0.0, https://microbiomedb.github.io/MicrobiomeDB/, https://github.com/microbiomeDB/MicrobiomeDB.","code":"@Manual{,   title = {MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org},   author = {Danielle Callan},   year = {2024},   note = {R package version 1.0.0, https://microbiomedb.github.io/MicrobiomeDB/},   url = {https://github.com/microbiomeDB/MicrobiomeDB}, }"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"microbiomedb","dir":"","previous_headings":"","what":"Curated Data and Analysis Tools from MicrobiomeDB.org","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"R package containing data MicrobiomeDB.org, tools analyzing visualizing .","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"Use R package remotes install MicrobiomeDB. R command prompt:","code":"remotes::install_github('microbiomeDB/MicrobiomeDB')"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"package intended used explore curated datasets MicrobiomeDB.org, well datasets. comes pre-packaged functions used power analysis tools website. also contains functions facilitate easily transforming data custom objects, phyloseq objects, .biom files can upload website. package paired dedicated data package called micribomeData includes number pre-built MbioDataset objects representing curated data MicrobiomeDB.org website. can see names like: return list names data objects installed package. One dataset ‘DiabImmune’, ’ll use following example. MbioDataset objects contain two things metadata collections. Metadata typically include details samples dataset, age person collected . Collections can group variables represent unified biological concept measured consistent comparable range values. example might relative abundances various genera. myCollection, can start using microbiomeComputations package (installed installed one) fun things like: give ComputeResult object, slots data statistics can explore. objects can difficult parse, ’ve added functions help format results usable exciting ways! called getComputeResult getComputeResultWithMetadata return data.tables (sometimes igraph objects) can use like : can take results data.table object use build plots things ggplot2 tool like. Let us know build something interesting, encounter bugs, just wish something easier . ’d love hear !","code":"remotes::install_github('microbiomeDB/microbiomeData') microbiomeData::getCuratedDatasetNames() getCollectionNames(DiabImmune) # will print the names of collections myCollection <- getCollection(DiabImmune, '16S Species') # NOTE: you can also use the `format` argument here to get these as phyloseq objects alphaDivResults <- alphaDiv(myCollection) correlationResults <- correlation(myCollection) differentialAbundanceResults <- differentialAbundance(   myCollection,    \"breastfed_duration_days\", # see getMetadataVariableNames() and getMetadataVariableSummary()   groupA = function(x) {x < 300},   groupB = function(x) {x >= 300},   method = 'Maaslin2') myCorrelationDT <- getComputeResult(correlationResults) myCorrelationGraph <- getComputeResult(correlationResults, format = 'igraph') MicrobiomeDB::correlationNetwork(myCorrelationDT) # will render a network visualization of the results using widgets from our own `corGraph` project  getMetadataVariableNames(DiabImmune) # will print names of metadata variables you can ask for myAlphaDivDT <- getComputeResultWithMetadata(alphaDivResults, DiabImmune, 'host_body_site')"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"Pull requests welcome. major changes, please open issue first discuss like change. Please make sure update tests appropriate.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Curated Data and Analysis Tools from MicrobiomeDB.org","text":"Apache 2.0","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/DESeqDataSetFromCollection.html","id":null,"dir":"Reference","previous_headings":"","what":"DESeqDataSet object from a Collection — DESeqDataSetFromCollection","title":"DESeqDataSet object from a Collection — DESeqDataSetFromCollection","text":"DESeqDataSet subclass RangedSummarizedExperiment, used store input values, intermediate calculations results analysis differential expression.  DESeqDataSet class enforces non-negative integer values \"counts\" matrix stored first element assay list. addition, formula specifies design experiment must provided.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/DESeqDataSetFromCollection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DESeqDataSet object from a Collection — DESeqDataSetFromCollection","text":"","code":"DESeqDataSetFromCollection(data, verbose = c(TRUE, FALSE), ...)  # S4 method for AbsoluteAbundanceData DESeqDataSetFromCollection(data, verbose = c(TRUE, FALSE), ...)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/DESeqDataSetFromCollection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DESeqDataSet object from a Collection — DESeqDataSetFromCollection","text":"data AbsoluteAbundanceData object verbose boolean indicating timed logging desired ... additional arguments passed DESeq2::DESeqDataSetFromMatrix","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/Maaslin2.html","id":null,"dir":"Reference","previous_headings":"","what":"Maaslin2 from a Collection — Maaslin2","title":"Maaslin2 from a Collection — Maaslin2","text":"MaAsLin2 finds associations microbiome meta-omics features complex metadata population-scale epidemiological studies. software includes multiple analysis methods (including support multiple covariates repeated measures) filtering, normalization, transform options customize analysis specific study.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/Maaslin2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Maaslin2 from a Collection — Maaslin2","text":"","code":"Maaslin2(data, verbose = c(TRUE, FALSE), ...)  # S4 method for CollectionWithMetadata Maaslin2(data, verbose = c(TRUE, FALSE), ...)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/Maaslin2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Maaslin2 from a Collection — Maaslin2","text":"data CollectionWithMetadata verbose boolean indicating timed logging desired ... additional arguments pass Maaslin2::Maaslin2","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/Maaslin2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Maaslin2 from a Collection — Maaslin2","text":"","code":"maaslinOutput <- MicrobiomeDB::Maaslin2(        data = getCollection(microbiomeData::DiabImmune, '16S (V4) Genus'),         output = tempfile(\"maaslin\"),        #min_prevalence = 0,        fixed_effects = 'delivery_mode',        analysis_method = \"LM\", # default LM        normalization = \"TSS\", # default TSS        transform = \"LOG\", # default LOG        plot_heatmap = FALSE,        plot_scatter = FALSE) #> [1] \"data.table\" \"data.frame\" #> [1] \"Creating output folder\" #> [1] \"Creating output feature tables folder\" #> [1] \"Creating output fits folder\" #> 2024-04-24 17:16:17.137393 INFO::Writing function arguments to log file #> 2024-04-24 17:16:17.152308 INFO::Verifying options selected are valid #> 2024-04-24 17:16:17.181968 INFO::Determining format of input files #> 2024-04-24 17:16:17.183541 INFO::Input format is data samples as rows and metadata samples as rows #> 2024-04-24 17:16:17.197836 INFO::Formula for fixed effects: expr ~  delivery_mode #> 2024-04-24 17:16:17.198775 INFO::Filter data based on min abundance and min prevalence #> 2024-04-24 17:16:17.199319 INFO::Total samples in data: 3184 #> 2024-04-24 17:16:17.199795 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000 #> 2024-04-24 17:16:17.219658 INFO::Total filtered features: 563 #> 2024-04-24 17:16:17.220761 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97 #> 2024-04-24 17:16:17.228667 INFO::Total filtered features with variance filtering: 0 #> 2024-04-24 17:16:17.229223 INFO::Filtered feature names from variance filtering: #> 2024-04-24 17:16:17.229697 INFO::Running selected normalization method: TSS #> 2024-04-24 17:16:17.288467 INFO::Applying z-score to standardize continuous metadata #> 2024-04-24 17:16:17.296834 INFO::Running selected transform method: LOG #> 2024-04-24 17:16:17.35947 INFO::Running selected analysis method: LM #> 2024-04-24 17:16:17.365472 INFO::Fitting model to feature number 1, Actinomyces #> 2024-04-24 17:16:17.374012 INFO::Fitting model to feature number 2, Agathobacter #> 2024-04-24 17:16:17.378144 INFO::Fitting model to feature number 3, Akkermansia #> 2024-04-24 17:16:17.38224 INFO::Fitting model to feature number 4, Alistipes #> 2024-04-24 17:16:17.386331 INFO::Fitting model to feature number 5, Anaerostipes #> 2024-04-24 17:16:17.390452 INFO::Fitting model to feature number 6, Atopobium #> 2024-04-24 17:16:17.3945 INFO::Fitting model to feature number 7, Bacteroides #> 2024-04-24 17:16:17.398598 INFO::Fitting model to feature number 8, Barnesiella #> 2024-04-24 17:16:17.402634 INFO::Fitting model to feature number 9, Bifidobacterium #> 2024-04-24 17:16:17.406713 INFO::Fitting model to feature number 10, Bilophila #> 2024-04-24 17:16:17.410826 INFO::Fitting model to feature number 11, Blautia #> 2024-04-24 17:16:17.432689 INFO::Fitting model to feature number 12, Butyricicoccus #> 2024-04-24 17:16:17.437162 INFO::Fitting model to feature number 13, CAG.352 #> 2024-04-24 17:16:17.441193 INFO::Fitting model to feature number 14, Campylobacter #> 2024-04-24 17:16:17.445297 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group #> 2024-04-24 17:16:17.449362 INFO::Fitting model to feature number 16, Clostridioides #> 2024-04-24 17:16:17.453418 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 #> 2024-04-24 17:16:17.457496 INFO::Fitting model to feature number 18, Colidextribacter #> 2024-04-24 17:16:17.46159 INFO::Fitting model to feature number 19, Collinsella #> 2024-04-24 17:16:17.465642 INFO::Fitting model to feature number 20, Coprobacillus #> 2024-04-24 17:16:17.46976 INFO::Fitting model to feature number 21, Coprococcus #> 2024-04-24 17:16:17.473836 INFO::Fitting model to feature number 22, DTU089 #> 2024-04-24 17:16:17.477946 INFO::Fitting model to feature number 23, Dialister #> 2024-04-24 17:16:17.482205 INFO::Fitting model to feature number 24, Dorea #> 2024-04-24 17:16:17.486331 INFO::Fitting model to feature number 25, Eggerthella #> 2024-04-24 17:16:17.490447 INFO::Fitting model to feature number 26, Eisenbergiella #> 2024-04-24 17:16:17.494556 INFO::Fitting model to feature number 27, Enterococcus #> 2024-04-24 17:16:17.498703 INFO::Fitting model to feature number 28, Erysipelatoclostridium #> 2024-04-24 17:16:17.502821 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003 #> 2024-04-24 17:16:17.506915 INFO::Fitting model to feature number 30, Escherichia.Shigella #> 2024-04-24 17:16:17.510962 INFO::Fitting model to feature number 31, Faecalibacterium #> 2024-04-24 17:16:17.515036 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group #> 2024-04-24 17:16:17.519112 INFO::Fitting model to feature number 33, Flavonifractor #> 2024-04-24 17:16:17.523153 INFO::Fitting model to feature number 34, Fusicatenibacter #> 2024-04-24 17:16:17.527172 INFO::Fitting model to feature number 35, Fusobacterium #> 2024-04-24 17:16:17.531253 INFO::Fitting model to feature number 36, Gemella #> 2024-04-24 17:16:17.535288 INFO::Fitting model to feature number 37, Granulicatella #> 2024-04-24 17:16:17.539339 INFO::Fitting model to feature number 38, Haemophilus #> 2024-04-24 17:16:17.543461 INFO::Fitting model to feature number 39, Holdemania #> 2024-04-24 17:16:17.547532 INFO::Fitting model to feature number 40, Hungatella #> 2024-04-24 17:16:17.551624 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. #> 2024-04-24 17:16:17.555752 INFO::Fitting model to feature number 42, Intestinibacter #> 2024-04-24 17:16:17.567054 INFO::Fitting model to feature number 43, Intestinimonas #> 2024-04-24 17:16:17.571323 INFO::Fitting model to feature number 44, Klebsiella #> 2024-04-24 17:16:17.575483 INFO::Fitting model to feature number 45, Lachnoclostridium #> 2024-04-24 17:16:17.579586 INFO::Fitting model to feature number 46, Lachnospira #> 2024-04-24 17:16:17.58366 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group #> 2024-04-24 17:16:17.587696 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group #> 2024-04-24 17:16:17.591765 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group #> 2024-04-24 17:16:17.595816 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001 #> 2024-04-24 17:16:17.599863 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004 #> 2024-04-24 17:16:17.603962 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009 #> 2024-04-24 17:16:17.608043 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010 #> 2024-04-24 17:16:17.612105 INFO::Fitting model to feature number 54, Lactobacillus #> 2024-04-24 17:16:17.616189 INFO::Fitting model to feature number 55, Lactococcus #> 2024-04-24 17:16:17.620257 INFO::Fitting model to feature number 56, Mannheimia #> 2024-04-24 17:16:17.624327 INFO::Fitting model to feature number 57, Megasphaera #> 2024-04-24 17:16:17.628387 INFO::Fitting model to feature number 58, Monoglobus #> 2024-04-24 17:16:17.632524 INFO::Fitting model to feature number 59, Neisseria #> 2024-04-24 17:16:17.636647 INFO::Fitting model to feature number 60, Odoribacter #> 2024-04-24 17:16:17.640717 INFO::Fitting model to feature number 61, Oscillibacter #> 2024-04-24 17:16:17.644774 INFO::Fitting model to feature number 62, Oscillospira #> 2024-04-24 17:16:17.64883 INFO::Fitting model to feature number 63, Parabacteroides #> 2024-04-24 17:16:17.652919 INFO::Fitting model to feature number 64, Parasutterella #> 2024-04-24 17:16:17.657008 INFO::Fitting model to feature number 65, Prevotella #> 2024-04-24 17:16:17.661202 INFO::Fitting model to feature number 66, Pseudomonas #> 2024-04-24 17:16:17.665254 INFO::Fitting model to feature number 67, Romboutsia #> 2024-04-24 17:16:17.669317 INFO::Fitting model to feature number 68, Roseburia #> 2024-04-24 17:16:17.673414 INFO::Fitting model to feature number 69, Rothia #> 2024-04-24 17:16:17.677464 INFO::Fitting model to feature number 70, Ruminococcus #> 2024-04-24 17:16:17.681498 INFO::Fitting model to feature number 71, Sellimonas #> 2024-04-24 17:16:17.685598 INFO::Fitting model to feature number 72, Solobacterium #> 2024-04-24 17:16:17.689627 INFO::Fitting model to feature number 73, Staphylococcus #> 2024-04-24 17:16:17.701293 INFO::Fitting model to feature number 74, Streptococcus #> 2024-04-24 17:16:17.705551 INFO::Fitting model to feature number 75, Subdoligranulum #> 2024-04-24 17:16:17.709659 INFO::Fitting model to feature number 76, Sutterella #> 2024-04-24 17:16:17.713776 INFO::Fitting model to feature number 77, Terrisporobacter #> 2024-04-24 17:16:17.717878 INFO::Fitting model to feature number 78, Turicibacter #> 2024-04-24 17:16:17.721924 INFO::Fitting model to feature number 79, Tuzzerella #> 2024-04-24 17:16:17.72599 INFO::Fitting model to feature number 80, Tyzzerella #> 2024-04-24 17:16:17.730034 INFO::Fitting model to feature number 81, UBA1819 #> 2024-04-24 17:16:17.734133 INFO::Fitting model to feature number 82, UCG.002 #> 2024-04-24 17:16:17.738212 INFO::Fitting model to feature number 83, UCG.003 #> 2024-04-24 17:16:17.742338 INFO::Fitting model to feature number 84, UCG.005 #> 2024-04-24 17:16:17.746497 INFO::Fitting model to feature number 85, Veillonella #> 2024-04-24 17:16:17.750615 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group #> 2024-04-24 17:16:17.754696 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group #> 2024-04-24 17:16:17.758765 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group #> 2024-04-24 17:16:17.762878 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group #> 2024-04-24 17:16:17.767056 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group #> 2024-04-24 17:16:17.771185 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group #> 2024-04-24 17:16:17.775296 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group #> 2024-04-24 17:16:17.779359 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group #> 2024-04-24 17:16:17.783436 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group #> 2024-04-24 17:16:17.787523 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group #> 2024-04-24 17:16:17.79159 INFO::Fitting model to feature number 96, unclassified.Chloroplast #> 2024-04-24 17:16:17.795679 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014 #> 2024-04-24 17:16:17.799751 INFO::Fitting model to feature number 98, unclassified.Clostridia #> 2024-04-24 17:16:17.803801 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group #> 2024-04-24 17:16:17.807838 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales #> 2024-04-24 17:16:17.811925 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae #> 2024-04-24 17:16:17.815993 INFO::Fitting model to feature number 102, unclassified.Mitochondria #> 2024-04-24 17:16:17.827484 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae #> 2024-04-24 17:16:17.831639 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus #> 2024-04-24 17:16:17.835698 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales #> 2024-04-24 17:16:17.839779 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae #> 2024-04-24 17:16:17.843884 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group #> 2024-04-24 17:16:17.863447 INFO::Counting total values for each feature #> 2024-04-24 17:16:17.869231 INFO::Writing filtered data to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/features/filtered_data.tsv #> 2024-04-24 17:16:18.014656 INFO::Writing filtered, normalized data to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/features/filtered_data_norm.tsv #> 2024-04-24 17:16:18.16445 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/features/filtered_data_norm_transformed.tsv #> 2024-04-24 17:16:18.437835 INFO::Writing residuals to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/fits/residuals.rds #> 2024-04-24 17:16:18.512103 INFO::Writing fitted values to file /tmp/RtmpfBGTvS/maaslin195842d2cad5/fits/fitted.rds #> 2024-04-24 17:16:18.536584 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin195842d2cad5/all_results.tsv #> 2024-04-24 17:16:18.538183 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin195842d2cad5/significant_results.tsv"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MbioDataset-class.html","id":null,"dir":"Reference","previous_headings":"","what":"MicrobiomeDB Dataset — MbioDataset-class","title":"MicrobiomeDB Dataset — MbioDataset-class","text":"class represents MicrobiomeDB dataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MbioDataset-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a Microbiome Dataset — MbioDataset","title":"Create a Microbiome Dataset — MbioDataset","text":"constructor MbioDataset class. creates MbioDataset containing list Collections SampleMetadata object.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MbioDataset-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a Microbiome Dataset — MbioDataset","text":"","code":"MbioDataset(collections, metadata, ontology)  # S4 method for missing,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,SampleMetadata,character MbioDataset(collections, metadata, ontology)  # S4 method for Collections,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for Collections,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,list,character MbioDataset(collections, metadata, ontology)  # S4 method for Collections,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for Collections,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collections,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collections,character,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,SampleMetadata,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,list,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for Collection,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for Collection,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for Collection,character,character MbioDataset(collections, metadata, ontology)  # S4 method for list,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,SampleMetadata,character MbioDataset(collections, metadata, ontology)  # S4 method for list,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for list,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for list,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,list,character MbioDataset(collections, metadata, ontology)  # S4 method for list,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for list,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for list,character,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,SampleMetadata,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,list,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for data.frame,character,character MbioDataset(collections, metadata, ontology)  # S4 method for character,character,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,character,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,character,character MbioDataset(collections, metadata, ontology)  # S4 method for character,list,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,list,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,list,character MbioDataset(collections, metadata, ontology)  # S4 method for character,missing,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,missing,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,missing,character MbioDataset(collections, metadata, ontology)  # S4 method for character,data.frame,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,data.frame,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,data.frame,character MbioDataset(collections, metadata, ontology)  # S4 method for character,SampleMetadata,missing MbioDataset(collections, metadata, ontology)  # S4 method for character,SampleMetadata,data.frame MbioDataset(collections, metadata, ontology)  # S4 method for character,SampleMetadata,character MbioDataset(collections, metadata, ontology)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MbioDataset-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a Microbiome Dataset — MbioDataset","text":"collections list Collection objects, data.frame containing multiple collections, character vector containing one file path(s) metadata SampleMetadata object, data.frame containing sample metadata, list file path(s) ontology data.frame containing ontology dataset, character vector containing file path data.frame","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MicrobiomeDB-package.html","id":null,"dir":"Reference","previous_headings":"","what":"MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org — MicrobiomeDB-package","title":"MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org — MicrobiomeDB-package","text":"package intended used explore curated datasets MicrobiomeDB.org, well datasets. comes pre-packaged functions used power analysis tools website. also contains functions facilitate easily transforming data custom objects, phyloseq objects, .biom files can upload website.","code":""},{"path":[]},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/MicrobiomeDB-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MicrobiomeDB: Curated Data and Analysis Tools from MicrobiomeDB.org — MicrobiomeDB-package","text":"Maintainer: Danielle Callan dcallan@upenn.edu","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Alpha diversity — alphaDiv","title":"Alpha diversity — alphaDiv","text":"function returns alpha diversity values sample.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alpha diversity — alphaDiv","text":"","code":"alphaDiv(   data,   method = c(\"shannon\", \"simpson\", \"evenness\"),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alpha diversity — alphaDiv","text":"data AbundanceData object method string defining alpha diversity method. Accepted values 'shannon','simpson', 'evenness' verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alpha diversity — alphaDiv","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/alphaDiv-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Alpha diversity — alphaDiv","text":"","code":"alphaDivOutput <- alphaDiv(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = \"shannon\" ) #>  #> 2024-04-24 17:16:19.888041 Received df table with 3184 samples and 673 taxa. #>  #> 2024-04-24 17:16:20.061473 shannon alpha diversity computation complete. #>  #> 2024-04-24 17:16:20.07684 Alpha diversity computation completed with parameters method= shannon"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Beta diversity — betaDiv","title":"Beta diversity — betaDiv","text":"function returns pcoa coordinates calculated beta diversity dissimilarity matrix.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Beta diversity — betaDiv","text":"","code":"betaDiv(   data,   method = c(\"bray\", \"jaccard\", \"jsd\"),   k = 2,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Beta diversity — betaDiv","text":"data AbundanceData object method string defining beta diversity dissimilarity method. Accepted values 'bray','jaccard', 'jsd' k integer determining number pcoa axes return verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Beta diversity — betaDiv","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/betaDiv-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Beta diversity — betaDiv","text":"","code":"betaDivOutput <- betaDiv(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = \"bray\",       k = 2 ) #>  #> 2024-04-24 17:16:21.020579 Received df table with 3184 samples and 673 taxa. #>  #> 2024-04-24 17:16:26.282943 Computed dissimilarity matrix. #>  #> 2024-04-24 17:16:35.655616 Finished ordination step. #>  #> 2024-04-24 17:16:35.665821 Beta diversity computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = bray , k = 2 , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation — correlation","title":"Correlation — correlation","text":"function returns correlation coefficients variables one dataset variables second dataset","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation — correlation","text":"","code":"correlation(   data1,   data2,   method,   format = c(\"ComputeResult\", \"data.table\"),   verbose = c(TRUE, FALSE),   ... )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation — correlation","text":"data1 first dataset. data.table data2 second dataset. data.table method string defining type correlation run. currently supported values specific class data1 data2. format string defining desired format result. currently supported values 'data.table' 'ComputeResult'. verbose boolean indicating timed logging desired ... additional parameters","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation — correlation","text":"data.frame correlation coefficients ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlation-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation — correlation","text":"","code":"diabImmune_genus <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\",       continuousMetadataOnly = TRUE )  correlationDT <- correlation(      diabImmune_genus,       method = 'spearman',       format = 'data.table' ) #>  #> 2024-04-24 17:16:39.709734 Completed correlation with method=spearman. Formatting results. #>  #> 2024-04-24 17:16:39.710918 Received df table with 3184 samples and 138 features with values.  correlationOutput <- correlation(      diabImmune_genus,       method = 'spearman',       format = 'ComputeResult' ) #>  #> 2024-04-24 17:16:43.545779 Completed correlation with method=spearman. Formatting results. #>  #> 2024-04-24 17:16:43.546683 Received df table with 3184 samples and 138 features with values. #>  #> 2024-04-24 17:16:43.548213 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  spearman  alsoCorrelationDT <- getComputeResult(      correlationOutput,       \"data.table\" )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlationNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation Network Visualization — correlationNetwork","title":"Correlation Network Visualization — correlationNetwork","text":"Visualize correlation result network","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlationNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation Network Visualization — correlationNetwork","text":"","code":"correlationNetwork(   object,   correlationCoefThreshold = 0.5,   pValueThreshold = 0.05,   ... )  # S4 method for ComputeResult correlationNetwork(   object,   correlationCoefThreshold = 0.5,   pValueThreshold = 0.05,   ... )  # S4 method for data.frame correlationNetwork(   object,   correlationCoefThreshold = 0.5,   pValueThreshold = 0.05,   bipartiteNetwork = c(FALSE, TRUE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlationNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation Network Visualization — correlationNetwork","text":"object ComputeResult data.frame correlationCoefThreshold threshold filter edges correlation coefficient. Edges correlation coefficients threshold removed. Default .5 pValueThreshold threshold filter edges p-value. Edges p-values threshold removed. Default .05 ... additional arguments bipartiteNetwork network use bipartite unipartite layout? Defaults unipartite.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/correlationNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation Network Visualization — correlationNetwork","text":"","code":"correlationOutput <- MicrobiomeDB::correlation(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\", continuousMetadataOnly = TRUE),       method='spearman',       verbose=FALSE ) correlationNetwork(correlationOutput) ## renders html widget  {\"x\":{\"data\":{\"links\":[{\"source\":\"Coprobacter\",\"target\":\"age_at_type_1_diabetes_diagnosis_days\",\"value\":0.524663091444649,\"pValue\":4.676770082312487e-11},{\"source\":\"unclassified Muribaculaceae\",\"target\":\"age_at_type_1_diabetes_diagnosis_days\",\"value\":0.509019797520334,\"pValue\":2.13462136855469e-10},{\"source\":\"Alistipes\",\"target\":\"age_months\",\"value\":0.5397456630921771,\"pValue\":0},{\"source\":\"Colidextribacter\",\"target\":\"age_months\",\"value\":0.5192217431279649,\"pValue\":0},{\"source\":\"Faecalibacterium\",\"target\":\"age_months\",\"value\":0.5564628845629651,\"pValue\":0},{\"source\":\"Lachnospiraceae NK4A136 group\",\"target\":\"age_months\",\"value\":0.5664616643798602,\"pValue\":0},{\"source\":\"Lachnospiraceae UCG-004\",\"target\":\"age_months\",\"value\":0.5013839365679983,\"pValue\":0},{\"source\":\"Oscillibacter\",\"target\":\"age_months\",\"value\":0.5610703084864889,\"pValue\":0},{\"source\":\"Ruminococcus\",\"target\":\"age_months\",\"value\":0.5464471254786487,\"pValue\":0},{\"source\":\"unclassified Lachnospiraceae\",\"target\":\"age_months\",\"value\":0.5141615087602621,\"pValue\":0}],\"column1NodeIds\":[\"Coprobacter\",\"unclassified Muribaculaceae\",\"Alistipes\",\"Colidextribacter\",\"Faecalibacterium\",\"Lachnospiraceae NK4A136 group\",\"Lachnospiraceae UCG-004\",\"Oscillibacter\",\"Ruminococcus\",\"unclassified Lachnospiraceae\"],\"column2NodeIds\":[\"age_at_type_1_diabetes_diagnosis_days\",\"age_months\"]}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential abundance — differentialAbundance","title":"Differential abundance — differentialAbundance","text":"function returns fold change associated p value differential abundance analysis. useful finding taxa abundance strongly differs two groups samples, finding taxa abundance differs skin saliva samples. function allows one recreate results differential abundance analysis MicrobiomeDB.org. However, recognize function makes assumptions data may valid contexts. better support longitudinal studies metabolomic data, example, please see wrapper/ helper methods Maaslin2 (MicrobiomeDB::Maaslin2) DESeq2 (DESeqDataSetFromCollection).","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential abundance — differentialAbundance","text":"","code":"differentialAbundance(   data,   covariate,   groupA,   groupB,   method = c(\"Maaslin2\", \"DESeq2\"),   verbose = c(TRUE, FALSE) )  # S4 method for CollectionWithMetadata,character,missingOrNULL,missingOrNULL differentialAbundance(   data,   covariate,   groupA,   groupB,   method = c(\"Maaslin2\", \"DESeq2\"),   verbose = c(TRUE, FALSE) )  # S4 method for CollectionWithMetadata,character,function,missingOrNULL differentialAbundance(   data,   covariate,   groupA,   groupB,   method = c(\"Maaslin2\", \"DESeq2\"),   verbose = c(TRUE, FALSE) )  # S4 method for CollectionWithMetadata,character,function,function differentialAbundance(   data,   covariate,   groupA,   groupB,   method = c(\"Maaslin2\", \"DESeq2\"),   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential abundance — differentialAbundance","text":"data AbundanceData object covariate character vector giving name metadata variable interest. variable two values, need provide functions arguments groupA groupB. groupA function takes vector values returns TRUE FALSE value. used assign samples groupA. groupB function takes vector values returns TRUE FALSE value. used assign samples groupB. provided, groupB complement groupA. method string defining differential abundance method. Accepted values 'DESeq2' 'Maaslin2'. Default 'Maaslin2', 'DESeq2' supports counts. verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential abundance — differentialAbundance","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/differentialAbundance-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Differential abundance — differentialAbundance","text":"","code":"## a continuous variable diffAbundOutput <- MicrobiomeDB::differentialAbundance(        getCollection(microbiomeData::DiabImmune, '16S (V4) Genus'),         \"breastfed_duration_days\",         groupA = function(x) {x<300},        groupB = function(x) {x>=300},        method='Maaslin2',         verbose=TRUE ) #>  #> 2024-04-24 17:16:48.600773 Found NAs in specified variable. Removing these records. #>  #> 2024-04-24 17:16:48.704625 Received abundance table with 2533 samples and 673 taxa. #>  #> 2024-04-24 17:16:48.707878 Found 2533 samples with a value for breastfed_duration_days in either groupA or groupB. The calculation will continue with only these samples. #> [1] \"Creating output folder\" #> [1] \"Creating output feature tables folder\" #> [1] \"Creating output fits folder\" #> 2024-04-24 17:16:48.843086 INFO::Writing function arguments to log file #> 2024-04-24 17:16:48.846796 INFO::Verifying options selected are valid #> 2024-04-24 17:16:48.847406 INFO::Determining format of input files #> 2024-04-24 17:16:48.848624 INFO::Input format is data samples as rows and metadata samples as rows #> 2024-04-24 17:16:48.860602 INFO::Formula for fixed effects: expr ~  breastfed_duration_days #> 2024-04-24 17:16:48.861377 INFO::Filter data based on min abundance and min prevalence #> 2024-04-24 17:16:48.861863 INFO::Total samples in data: 2533 #> 2024-04-24 17:16:48.862344 INFO::Min samples required with min abundance for a feature not to be filtered: 253.300000 #> 2024-04-24 17:16:48.878531 INFO::Total filtered features: 521 #> 2024-04-24 17:16:48.879519 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Candidatus.Arthromitus, Candidatus.Obscuribacter, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Faecalicoccus, Faecalitalea, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavobacterium, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Marvinbryantia, Massilia, Megamonas, Merdibacter, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Myxococcus, NK4A214.group, Nakamurella, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phaseolibacter, Phocea, Phyllobacterium, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudoflavonifractor, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tetragenococcus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97 #> 2024-04-24 17:16:48.885978 INFO::Total filtered features with variance filtering: 0 #> 2024-04-24 17:16:48.886525 INFO::Filtered feature names from variance filtering: #> 2024-04-24 17:16:48.887012 INFO::Running selected normalization method: TSS #> 2024-04-24 17:16:48.923679 INFO::Applying z-score to standardize continuous metadata #> 2024-04-24 17:16:48.926611 INFO::Running selected transform method: LOG #> 2024-04-24 17:16:48.975602 INFO::Running selected analysis method: LM #> 2024-04-24 17:16:48.976333 INFO::Fitting model to feature number 1, Actinomyces #> 2024-04-24 17:16:48.980361 INFO::Fitting model to feature number 2, Agathobacter #> 2024-04-24 17:16:48.98392 INFO::Fitting model to feature number 3, Akkermansia #> 2024-04-24 17:16:48.987482 INFO::Fitting model to feature number 4, Alistipes #> 2024-04-24 17:16:48.991061 INFO::Fitting model to feature number 5, Anaerostipes #> 2024-04-24 17:16:48.994589 INFO::Fitting model to feature number 6, Atopobium #> 2024-04-24 17:16:48.998177 INFO::Fitting model to feature number 7, Bacteroides #> 2024-04-24 17:16:49.001764 INFO::Fitting model to feature number 8, Barnesiella #> 2024-04-24 17:16:49.00534 INFO::Fitting model to feature number 9, Bifidobacterium #> 2024-04-24 17:16:49.008974 INFO::Fitting model to feature number 10, Bilophila #> 2024-04-24 17:16:49.012591 INFO::Fitting model to feature number 11, Blautia #> 2024-04-24 17:16:49.016168 INFO::Fitting model to feature number 12, Butyricicoccus #> 2024-04-24 17:16:49.019768 INFO::Fitting model to feature number 13, CAG.352 #> 2024-04-24 17:16:49.023367 INFO::Fitting model to feature number 14, Campylobacter #> 2024-04-24 17:16:49.02695 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group #> 2024-04-24 17:16:49.03051 INFO::Fitting model to feature number 16, Clostridioides #> 2024-04-24 17:16:49.034149 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 #> 2024-04-24 17:16:49.037743 INFO::Fitting model to feature number 18, Colidextribacter #> 2024-04-24 17:16:49.041389 INFO::Fitting model to feature number 19, Collinsella #> 2024-04-24 17:16:49.044945 INFO::Fitting model to feature number 20, Coprobacillus #> 2024-04-24 17:16:49.048523 INFO::Fitting model to feature number 21, Coprococcus #> 2024-04-24 17:16:49.052146 INFO::Fitting model to feature number 22, DTU089 #> 2024-04-24 17:16:49.055731 INFO::Fitting model to feature number 23, Dialister #> 2024-04-24 17:16:49.059315 INFO::Fitting model to feature number 24, Dorea #> 2024-04-24 17:16:49.062861 INFO::Fitting model to feature number 25, Eggerthella #> 2024-04-24 17:16:49.067444 INFO::Fitting model to feature number 26, Eisenbergiella #> 2024-04-24 17:16:49.072906 INFO::Fitting model to feature number 27, Enterococcus #> 2024-04-24 17:16:49.078475 INFO::Fitting model to feature number 28, Erysipelatoclostridium #> 2024-04-24 17:16:49.084011 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003 #> 2024-04-24 17:16:49.08941 INFO::Fitting model to feature number 30, Escherichia.Shigella #> 2024-04-24 17:16:49.092985 INFO::Fitting model to feature number 31, Faecalibacterium #> 2024-04-24 17:16:49.096567 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group #> 2024-04-24 17:16:49.100204 INFO::Fitting model to feature number 33, Flavonifractor #> 2024-04-24 17:16:49.103798 INFO::Fitting model to feature number 34, Fusicatenibacter #> 2024-04-24 17:16:49.107383 INFO::Fitting model to feature number 35, Fusobacterium #> 2024-04-24 17:16:49.110925 INFO::Fitting model to feature number 36, Gemella #> 2024-04-24 17:16:49.114463 INFO::Fitting model to feature number 37, Granulicatella #> 2024-04-24 17:16:49.118025 INFO::Fitting model to feature number 38, Haemophilus #> 2024-04-24 17:16:49.121603 INFO::Fitting model to feature number 39, Holdemania #> 2024-04-24 17:16:49.125136 INFO::Fitting model to feature number 40, Hungatella #> 2024-04-24 17:16:49.128701 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. #> 2024-04-24 17:16:49.132299 INFO::Fitting model to feature number 42, Intestinibacter #> 2024-04-24 17:16:49.135896 INFO::Fitting model to feature number 43, Intestinimonas #> 2024-04-24 17:16:49.139476 INFO::Fitting model to feature number 44, Klebsiella #> 2024-04-24 17:16:49.143127 INFO::Fitting model to feature number 45, Lachnoclostridium #> 2024-04-24 17:16:49.146711 INFO::Fitting model to feature number 46, Lachnospira #> 2024-04-24 17:16:49.150302 INFO::Fitting model to feature number 47, Lachnospiraceae.ND3007.group #> 2024-04-24 17:16:49.153897 INFO::Fitting model to feature number 48, Lachnospiraceae.NK4A136.group #> 2024-04-24 17:16:49.15763 INFO::Fitting model to feature number 49, Lachnospiraceae.UCG.001 #> 2024-04-24 17:16:49.16134 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.004 #> 2024-04-24 17:16:49.164931 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.009 #> 2024-04-24 17:16:49.168539 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.010 #> 2024-04-24 17:16:49.172123 INFO::Fitting model to feature number 53, Lactobacillus #> 2024-04-24 17:16:49.175735 INFO::Fitting model to feature number 54, Lactococcus #> 2024-04-24 17:16:49.17937 INFO::Fitting model to feature number 55, Mannheimia #> 2024-04-24 17:16:49.182969 INFO::Fitting model to feature number 56, Megasphaera #> 2024-04-24 17:16:49.186574 INFO::Fitting model to feature number 57, Monoglobus #> 2024-04-24 17:16:49.190192 INFO::Fitting model to feature number 58, Neisseria #> 2024-04-24 17:16:49.193823 INFO::Fitting model to feature number 59, Odoribacter #> 2024-04-24 17:16:49.197427 INFO::Fitting model to feature number 60, Oscillibacter #> 2024-04-24 17:16:49.20107 INFO::Fitting model to feature number 61, Oscillospira #> 2024-04-24 17:16:49.204689 INFO::Fitting model to feature number 62, Parabacteroides #> 2024-04-24 17:16:49.208342 INFO::Fitting model to feature number 63, Parasutterella #> 2024-04-24 17:16:49.211993 INFO::Fitting model to feature number 64, Phascolarctobacterium #> 2024-04-24 17:16:49.215601 INFO::Fitting model to feature number 65, Prevotella #> 2024-04-24 17:16:49.219189 INFO::Fitting model to feature number 66, Pseudomonas #> 2024-04-24 17:16:49.22276 INFO::Fitting model to feature number 67, Romboutsia #> 2024-04-24 17:16:49.226463 INFO::Fitting model to feature number 68, Roseburia #> 2024-04-24 17:16:49.23005 INFO::Fitting model to feature number 69, Rothia #> 2024-04-24 17:16:49.23365 INFO::Fitting model to feature number 70, Ruminococcus #> 2024-04-24 17:16:49.2373 INFO::Fitting model to feature number 71, Sellimonas #> 2024-04-24 17:16:49.240968 INFO::Fitting model to feature number 72, Solobacterium #> 2024-04-24 17:16:49.244585 INFO::Fitting model to feature number 73, Staphylococcus #> 2024-04-24 17:16:49.248228 INFO::Fitting model to feature number 74, Streptococcus #> 2024-04-24 17:16:49.251845 INFO::Fitting model to feature number 75, Subdoligranulum #> 2024-04-24 17:16:49.255519 INFO::Fitting model to feature number 76, Sutterella #> 2024-04-24 17:16:49.259158 INFO::Fitting model to feature number 77, Terrisporobacter #> 2024-04-24 17:16:49.262745 INFO::Fitting model to feature number 78, Turicibacter #> 2024-04-24 17:16:49.266374 INFO::Fitting model to feature number 79, Tuzzerella #> 2024-04-24 17:16:49.269949 INFO::Fitting model to feature number 80, Tyzzerella #> 2024-04-24 17:16:49.273539 INFO::Fitting model to feature number 81, UBA1819 #> 2024-04-24 17:16:49.277157 INFO::Fitting model to feature number 82, UCG.002 #> 2024-04-24 17:16:49.280774 INFO::Fitting model to feature number 83, UCG.003 #> 2024-04-24 17:16:49.284424 INFO::Fitting model to feature number 84, UCG.005 #> 2024-04-24 17:16:49.288046 INFO::Fitting model to feature number 85, Veillonella #> 2024-04-24 17:16:49.291635 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group #> 2024-04-24 17:16:49.295258 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group #> 2024-04-24 17:16:49.298843 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group #> 2024-04-24 17:16:49.302456 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group #> 2024-04-24 17:16:49.306091 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group #> 2024-04-24 17:16:49.309665 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group #> 2024-04-24 17:16:49.313267 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group #> 2024-04-24 17:16:49.316923 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group #> 2024-04-24 17:16:49.320577 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group #> 2024-04-24 17:16:49.324228 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group #> 2024-04-24 17:16:49.327848 INFO::Fitting model to feature number 96, unclassified.Chloroplast #> 2024-04-24 17:16:49.33145 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014 #> 2024-04-24 17:16:49.335068 INFO::Fitting model to feature number 98, unclassified.Clostridia #> 2024-04-24 17:16:49.338648 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group #> 2024-04-24 17:16:49.342247 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales #> 2024-04-24 17:16:49.345847 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae #> 2024-04-24 17:16:49.349469 INFO::Fitting model to feature number 102, unclassified.Mitochondria #> 2024-04-24 17:16:49.353108 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae #> 2024-04-24 17:16:49.356689 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus #> 2024-04-24 17:16:49.360342 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales #> 2024-04-24 17:16:49.363909 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae #> 2024-04-24 17:16:49.367611 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group #> 2024-04-24 17:16:49.383164 INFO::Counting total values for each feature #> 2024-04-24 17:16:49.388217 INFO::Writing filtered data to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/features/filtered_data.tsv #> 2024-04-24 17:16:49.504738 INFO::Writing filtered, normalized data to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/features/filtered_data_norm.tsv #> 2024-04-24 17:16:49.624761 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/features/filtered_data_norm_transformed.tsv #> 2024-04-24 17:16:49.839021 INFO::Writing residuals to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/fits/residuals.rds #> 2024-04-24 17:16:49.893575 INFO::Writing fitted values to file /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/fits/fitted.rds #> 2024-04-24 17:16:49.912584 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/all_results.tsv #> 2024-04-24 17:16:49.91421 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin19587ef8aa0d/significant_results.tsv #>  #> 2024-04-24 17:16:49.916079 Completed method=Maaslin2. Formatting results. #>  #> 2024-04-24 17:16:49.919326 Differential abundance computation completed with parameters recordIdColumn =  16S_rRNA_(V4)_assay_Id , comparatorColName =  breastfed_duration_days , method =  Maaslin2 , groupA = groupA , groupB =  groupB  ## a categorical variable with 3 values, one of which we exclude diffAbundOutput <- MicrobiomeDB::differentialAbundance(        getCollection(microbiomeData::DiabImmune, '16S (V4) Genus'),         \"country\",         groupA = function(x) {x==\"Russia\"},        groupB = function(x) {x==\"Finland\"},        method='Maaslin2',         verbose=FALSE ) #> [1] \"Creating output folder\" #> [1] \"Creating output feature tables folder\" #> [1] \"Creating output fits folder\" #> 2024-04-24 17:16:50.196045 INFO::Writing function arguments to log file #> 2024-04-24 17:16:50.199926 INFO::Verifying options selected are valid #> 2024-04-24 17:16:50.200479 INFO::Determining format of input files #> 2024-04-24 17:16:50.201769 INFO::Input format is data samples as rows and metadata samples as rows #> 2024-04-24 17:16:50.214262 INFO::Formula for fixed effects: expr ~  country #> 2024-04-24 17:16:50.21509 INFO::Filter data based on min abundance and min prevalence #> 2024-04-24 17:16:50.215583 INFO::Total samples in data: 2692 #> 2024-04-24 17:16:50.216047 INFO::Min samples required with min abundance for a feature not to be filtered: 269.200000 #> 2024-04-24 17:16:50.232627 INFO::Total filtered features: 521 #> 2024-04-24 17:16:50.23363 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asticcacaulis, Aureimonas, Bacillus, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FCS020.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Marinilactibacillus, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylobacillus, Methylobacterium.Methylorubrum, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, Paenibacillus, Paeniclostridium, Paludicola, Papillibacter, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Piscinibacter, Planifilum, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinivibrio, Sulfurospirillum, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gastranaerophilales, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97 #> 2024-04-24 17:16:50.240345 INFO::Total filtered features with variance filtering: 0 #> 2024-04-24 17:16:50.240901 INFO::Filtered feature names from variance filtering: #> 2024-04-24 17:16:50.241369 INFO::Running selected normalization method: TSS #> 2024-04-24 17:16:50.292056 INFO::Applying z-score to standardize continuous metadata #> 2024-04-24 17:16:50.295007 INFO::Running selected transform method: LOG #> 2024-04-24 17:16:50.347621 INFO::Running selected analysis method: LM #> 2024-04-24 17:16:50.348336 INFO::Fitting model to feature number 1, Actinomyces #> 2024-04-24 17:16:50.352555 INFO::Fitting model to feature number 2, Agathobacter #> 2024-04-24 17:16:50.356368 INFO::Fitting model to feature number 3, Akkermansia #> 2024-04-24 17:16:50.36011 INFO::Fitting model to feature number 4, Alistipes #> 2024-04-24 17:16:50.363925 INFO::Fitting model to feature number 5, Anaerostipes #> 2024-04-24 17:16:50.367708 INFO::Fitting model to feature number 6, Atopobium #> 2024-04-24 17:16:50.371444 INFO::Fitting model to feature number 7, Bacteroides #> 2024-04-24 17:16:50.375173 INFO::Fitting model to feature number 8, Barnesiella #> 2024-04-24 17:16:50.378835 INFO::Fitting model to feature number 9, Bifidobacterium #> 2024-04-24 17:16:50.38256 INFO::Fitting model to feature number 10, Bilophila #> 2024-04-24 17:16:50.386305 INFO::Fitting model to feature number 11, Blautia #> 2024-04-24 17:16:50.389993 INFO::Fitting model to feature number 12, Butyricicoccus #> 2024-04-24 17:16:50.39375 INFO::Fitting model to feature number 13, CAG.352 #> 2024-04-24 17:16:50.397455 INFO::Fitting model to feature number 14, Campylobacter #> 2024-04-24 17:16:50.40119 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group #> 2024-04-24 17:16:50.404904 INFO::Fitting model to feature number 16, Clostridioides #> 2024-04-24 17:16:50.408609 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 #> 2024-04-24 17:16:50.412314 INFO::Fitting model to feature number 18, Colidextribacter #> 2024-04-24 17:16:50.416275 INFO::Fitting model to feature number 19, Collinsella #> 2024-04-24 17:16:50.420022 INFO::Fitting model to feature number 20, Coprobacillus #> 2024-04-24 17:16:50.423736 INFO::Fitting model to feature number 21, Coprococcus #> 2024-04-24 17:16:50.427498 INFO::Fitting model to feature number 22, Corynebacterium #> 2024-04-24 17:16:50.431297 INFO::Fitting model to feature number 23, DTU089 #> 2024-04-24 17:16:50.435004 INFO::Fitting model to feature number 24, Dialister #> 2024-04-24 17:16:50.438678 INFO::Fitting model to feature number 25, Dorea #> 2024-04-24 17:16:50.442431 INFO::Fitting model to feature number 26, Eggerthella #> 2024-04-24 17:16:50.446229 INFO::Fitting model to feature number 27, Eisenbergiella #> 2024-04-24 17:16:50.450008 INFO::Fitting model to feature number 28, Enterococcus #> 2024-04-24 17:16:50.453808 INFO::Fitting model to feature number 29, Erysipelatoclostridium #> 2024-04-24 17:16:50.457582 INFO::Fitting model to feature number 30, Erysipelotrichaceae.UCG.003 #> 2024-04-24 17:16:50.461339 INFO::Fitting model to feature number 31, Escherichia.Shigella #> 2024-04-24 17:16:50.465102 INFO::Fitting model to feature number 32, Faecalibacterium #> 2024-04-24 17:16:50.468873 INFO::Fitting model to feature number 33, Family.XIII.AD3011.group #> 2024-04-24 17:16:50.472607 INFO::Fitting model to feature number 34, Flavonifractor #> 2024-04-24 17:16:50.476376 INFO::Fitting model to feature number 35, Fusicatenibacter #> 2024-04-24 17:16:50.480095 INFO::Fitting model to feature number 36, Fusobacterium #> 2024-04-24 17:16:50.483825 INFO::Fitting model to feature number 37, Gemella #> 2024-04-24 17:16:50.487579 INFO::Fitting model to feature number 38, Gordonibacter #> 2024-04-24 17:16:50.491306 INFO::Fitting model to feature number 39, Granulicatella #> 2024-04-24 17:16:50.49501 INFO::Fitting model to feature number 40, Haemophilus #> 2024-04-24 17:16:50.498741 INFO::Fitting model to feature number 41, Holdemania #> 2024-04-24 17:16:50.502461 INFO::Fitting model to feature number 42, Hungatella #> 2024-04-24 17:16:50.506173 INFO::Fitting model to feature number 43, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. #> 2024-04-24 17:16:50.509959 INFO::Fitting model to feature number 44, Intestinibacter #> 2024-04-24 17:16:50.51371 INFO::Fitting model to feature number 45, Intestinimonas #> 2024-04-24 17:16:50.517435 INFO::Fitting model to feature number 46, Klebsiella #> 2024-04-24 17:16:50.521145 INFO::Fitting model to feature number 47, Lachnoclostridium #> 2024-04-24 17:16:50.524839 INFO::Fitting model to feature number 48, Lachnospira #> 2024-04-24 17:16:50.528552 INFO::Fitting model to feature number 49, Lachnospiraceae.ND3007.group #> 2024-04-24 17:16:50.53229 INFO::Fitting model to feature number 50, Lachnospiraceae.NK4A136.group #> 2024-04-24 17:16:50.536035 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.001 #> 2024-04-24 17:16:50.539745 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.004 #> 2024-04-24 17:16:50.543442 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.009 #> 2024-04-24 17:16:50.547173 INFO::Fitting model to feature number 54, Lachnospiraceae.UCG.010 #> 2024-04-24 17:16:50.550853 INFO::Fitting model to feature number 55, Lactobacillus #> 2024-04-24 17:16:50.554646 INFO::Fitting model to feature number 56, Lactococcus #> 2024-04-24 17:16:50.558405 INFO::Fitting model to feature number 57, Mannheimia #> 2024-04-24 17:16:50.562241 INFO::Fitting model to feature number 58, Megasphaera #> 2024-04-24 17:16:50.565961 INFO::Fitting model to feature number 59, Monoglobus #> 2024-04-24 17:16:50.569868 INFO::Fitting model to feature number 60, Neisseria #> 2024-04-24 17:16:50.57365 INFO::Fitting model to feature number 61, Odoribacter #> 2024-04-24 17:16:50.577368 INFO::Fitting model to feature number 62, Oscillibacter #> 2024-04-24 17:16:50.581139 INFO::Fitting model to feature number 63, Oscillospira #> 2024-04-24 17:16:50.584899 INFO::Fitting model to feature number 64, Parabacteroides #> 2024-04-24 17:16:50.588673 INFO::Fitting model to feature number 65, Parasutterella #> 2024-04-24 17:16:50.592399 INFO::Fitting model to feature number 66, Prevotella #> 2024-04-24 17:16:50.596152 INFO::Fitting model to feature number 67, Pseudomonas #> 2024-04-24 17:16:50.599874 INFO::Fitting model to feature number 68, Romboutsia #> 2024-04-24 17:16:50.603612 INFO::Fitting model to feature number 69, Roseburia #> 2024-04-24 17:16:50.607336 INFO::Fitting model to feature number 70, Rothia #> 2024-04-24 17:16:50.611045 INFO::Fitting model to feature number 71, Ruminococcus #> 2024-04-24 17:16:50.614707 INFO::Fitting model to feature number 72, Sellimonas #> 2024-04-24 17:16:50.618438 INFO::Fitting model to feature number 73, Solobacterium #> 2024-04-24 17:16:50.622171 INFO::Fitting model to feature number 74, Staphylococcus #> 2024-04-24 17:16:50.625948 INFO::Fitting model to feature number 75, Streptococcus #> 2024-04-24 17:16:50.629743 INFO::Fitting model to feature number 76, Subdoligranulum #> 2024-04-24 17:16:50.633482 INFO::Fitting model to feature number 77, Sutterella #> 2024-04-24 17:16:50.637209 INFO::Fitting model to feature number 78, Terrisporobacter #> 2024-04-24 17:16:50.640958 INFO::Fitting model to feature number 79, Turicibacter #> 2024-04-24 17:16:50.644702 INFO::Fitting model to feature number 80, Tuzzerella #> 2024-04-24 17:16:50.648438 INFO::Fitting model to feature number 81, Tyzzerella #> 2024-04-24 17:16:50.652151 INFO::Fitting model to feature number 82, UBA1819 #> 2024-04-24 17:16:50.655933 INFO::Fitting model to feature number 83, UCG.002 #> 2024-04-24 17:16:50.659814 INFO::Fitting model to feature number 84, UCG.003 #> 2024-04-24 17:16:50.663595 INFO::Fitting model to feature number 85, UCG.005 #> 2024-04-24 17:16:50.667338 INFO::Fitting model to feature number 86, Veillonella #> 2024-04-24 17:16:50.671224 INFO::Fitting model to feature number 87, X.Clostridium..innocuum.group #> 2024-04-24 17:16:50.674993 INFO::Fitting model to feature number 88, X.Eubacterium..eligens.group #> 2024-04-24 17:16:50.678745 INFO::Fitting model to feature number 89, X.Eubacterium..fissicatena.group #> 2024-04-24 17:16:50.68253 INFO::Fitting model to feature number 90, X.Eubacterium..hallii.group #> 2024-04-24 17:16:50.686319 INFO::Fitting model to feature number 91, X.Eubacterium..siraeum.group #> 2024-04-24 17:16:50.690114 INFO::Fitting model to feature number 92, X.Eubacterium..ventriosum.group #> 2024-04-24 17:16:50.693877 INFO::Fitting model to feature number 93, X.Eubacterium..xylanophilum.group #> 2024-04-24 17:16:50.697619 INFO::Fitting model to feature number 94, X.Ruminococcus..gauvreauii.group #> 2024-04-24 17:16:50.701468 INFO::Fitting model to feature number 95, X.Ruminococcus..gnavus.group #> 2024-04-24 17:16:50.705246 INFO::Fitting model to feature number 96, X.Ruminococcus..torques.group #> 2024-04-24 17:16:50.709061 INFO::Fitting model to feature number 97, unclassified.Chloroplast #> 2024-04-24 17:16:50.712789 INFO::Fitting model to feature number 98, unclassified.Clostridia.UCG.014 #> 2024-04-24 17:16:50.716518 INFO::Fitting model to feature number 99, unclassified.Clostridia #> 2024-04-24 17:16:50.720244 INFO::Fitting model to feature number 100, unclassified.Clostridia.vadinBB60.group #> 2024-04-24 17:16:50.723988 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae #> 2024-04-24 17:16:50.727733 INFO::Fitting model to feature number 102, unclassified.Mitochondria #> 2024-04-24 17:16:50.731469 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae #> 2024-04-24 17:16:50.73519 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus #> 2024-04-24 17:16:50.738885 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales #> 2024-04-24 17:16:50.742623 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae #> 2024-04-24 17:16:50.746359 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group #> 2024-04-24 17:16:50.761322 INFO::Counting total values for each feature #> 2024-04-24 17:16:50.766469 INFO::Writing filtered data to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/features/filtered_data.tsv #> 2024-04-24 17:16:50.889727 INFO::Writing filtered, normalized data to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/features/filtered_data_norm.tsv #> 2024-04-24 17:16:51.018245 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/features/filtered_data_norm_transformed.tsv #> 2024-04-24 17:16:51.258202 INFO::Writing residuals to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/fits/residuals.rds #> 2024-04-24 17:16:51.318386 INFO::Writing fitted values to file /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/fits/fitted.rds #> 2024-04-24 17:16:51.33811 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/all_results.tsv #> 2024-04-24 17:16:51.339837 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin1958a4cfeb5/significant_results.tsv  ## a categorical variable with 2 values diffAbundOutput <- MicrobiomeDB::differentialAbundance(        getCollection(microbiomeData::DiabImmune, '16S (V4) Genus'),        \"delivery_mode\",        method='Maaslin2',         verbose=FALSE )  #> [1] \"Creating output folder\" #> [1] \"Creating output feature tables folder\" #> [1] \"Creating output fits folder\" #> 2024-04-24 17:16:51.641871 INFO::Writing function arguments to log file #> 2024-04-24 17:16:51.6457 INFO::Verifying options selected are valid #> 2024-04-24 17:16:51.646238 INFO::Determining format of input files #> 2024-04-24 17:16:51.647745 INFO::Input format is data samples as rows and metadata samples as rows #> 2024-04-24 17:16:51.662126 INFO::Formula for fixed effects: expr ~  delivery_mode #> 2024-04-24 17:16:51.662966 INFO::Filter data based on min abundance and min prevalence #> 2024-04-24 17:16:51.663476 INFO::Total samples in data: 3184 #> 2024-04-24 17:16:51.663964 INFO::Min samples required with min abundance for a feature not to be filtered: 318.400000 #> 2024-04-24 17:16:51.683603 INFO::Total filtered features: 563 #> 2024-04-24 17:16:51.684458 INFO::Filtered feature names from abundance and prevalence filtering: X28.4, Abiotrophia, Acetanaerobacterium, Acetobacter, Achromobacter, Acidaminococcus, Acidibacter, Acidiphilium, Acidipropionibacterium, Acidocella, Acidovorax, Acinetobacter, Actinobacillus, Actinobaculum, Actinotignum, Adlercreutzia, Aerococcus, Aeromonas, Afipia, Aggregatibacter, Alcaligenes, Alicycliphilus, Allisonella, Allobaculum, Alloprevotella, Allorhizobium.Neorhizobium.Pararhizobium.Rhizobium, Alloscardovia, Amaricoccus, Amnibacterium, Anaerobium, Anaerocolumna, Anaerofilum, Anaerofustis, Anaeroglobus, Anaeromyxobacter, Anaeroplasma, Anaerosporobacter, Anaerosporomusa, Anaerostignum, Anaerotruncus, Angelakisella, Angustibacter, Anoxybacillus, Aquabacterium, Aquamonas, Arcanobacterium, Arcticibacter, Asaccharospora, Asaia, Asinibacterium, Asteroleplasma, Asticcacaulis, Aureimonas, Azospira, Bacillus, Bacteriovorax, Bdellovibrio, Belnapia, Bergeyella, Blastomonas, Bordetella, Bosea, Brachybacterium, Bradyrhizobium, Brevibacterium, Brevundimonas, Brucella, Bulleidia, Burkholderia.Caballeronia.Paraburkholderia, Buttiauxella, Butyricimonas, CAG.56, CAG.873, CHKCI001, CHKCI002, CL500.29.marine.group, Caloribacterium, Candidatus.Arthromitus, Candidatus.Metachlamydia, Candidatus.Obscuribacter, Candidatus.Phytoplasma, Candidatus.Soleaferrea, Candidatus.Stoquefichus, Capnocytophaga, Caproiciproducens, Cardiobacterium, Carnobacterium, Caryophanon, Castellaniella, Catabacter, Catenibacillus, Catenibacterium, Catenisphaera, Catonella, Caulobacter, Cellulomonas, Cellulosilyticum, Cellvibrio, Centipeda, Cetobacterium, Christensenella, Chryseobacterium, Chryseomicrobium, Chungangia, Citrobacter, Clavibacter, Cloacibacillus, Cloacibacterium, Clostridium.sensu.stricto.12, Clostridium.sensu.stricto.13, Clostridium.sensu.stricto.15, Clostridium.sensu.stricto.18, Clostridium.sensu.stricto.2, Clostridium.sensu.stricto.3, Clostridium.sensu.stricto.4, Clostridium.sensu.stricto.6, Comamonas, Conexibacter, Conservatibacter, Coprobacter, Coriobacteriaceae.UCG.002, Corynebacterium, Cosenzaea, Criibacterium, Cryptobacterium, Curvibacter, Cutibacterium, Cytophaga, DNF00809, DSSD61, Dechloromonas, Defluviicoccus, Defluviitaleaceae.UCG.011, Delftia, Denitrobacterium, Dermabacter, Desemzia, Desulfovibrio, Devosia, Diaphorobacter, Dickeya, Dielma, Dietzia, Dinghuibacter, Diplosphaera, Dolosigranulum, Duganella, Dysgonomonas, Edaphobaculum, Eikenella, Empedobacter, Endobacter, Enhydrobacter, Enterobacter, Enterorhabdus, Enteroscipio, Epulopiscium, Erwinia, Erysipelotrichaceae.UCG.006, Eubacterium, Exiguobacterium, Extensimonas, F0058, F0332, FD2005, Facklamia, Faecalicoccus, Faecalitalea, Falsochrobactrum, Family.XIII.UCG.001, Fictibacillus, Flaviflexus, Flavihumibacter, Flavobacterium, Floricoccus, Fluviicola, Fournierella, Fretibacterium, Frisingicoccus, Fructobacillus, GCA.900066575, GCA.900066755, Galbibacter, Garciella, Gemmata, Geobacillus, Gluconobacter, Glutamicibacter, Gordonia, Gordonibacter, Gulbenkiania, Hafnia.Obesumbacterium, Halomonas, Haoranjiania, Harryflintia, Helicobacter, Hephaestia, Herbaspirillum, Herbinix, Holdemanella, Howardella, Hydrocarboniphaga, Hydrogenophilus, Hymenobacter, Iamia, Ignavigranum, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis., Incertae.Sedis..EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis., Janthinobacterium, Jeotgalicoccus, Johnsonella, Kingella, Knoellia, Kocuria, Kosakonia, Lachnoanaerobaculum, Lachnobacterium, Lachnospiraceae.AC2044.group, Lachnospiraceae.FE2018.group, Lachnospiraceae.NC2004.group, Lachnospiraceae.UCG.002, Lachnospiraceae.UCG.003, Lachnospiraceae.UCG.008, Lachnospiraceae.XPB1014.group, Lachnotalea, Lactonifactor, Lautropia, Lawsonella, Legionella, Leptotrichia, Leuconostoc, Libanicoccus, Luteimonas, Luteolibacter, Macellibacteroides, Macrococcus, Mailhella, Marinilactibacillus, Marmoricola, Martelella, Marvinbryantia, Massilia, Megamonas, Merdibacter, Mesorhizobium, Methanobrevibacter, Methylibium, Methylobacillus, Methylobacterium.Methylorubrum, Methylorosula, Methylotenera, Micrococcus, Mitsuokella, Mobiluncus, Mogibacterium, Moheibacter, Mongoliitalea, Moraxella, Morganella, Moryella, Mucilaginibacter, Muribaculum, Murimonas, Mycobacterium, Mycoplasma, Myxococcus, NK4A214.group, Nakamurella, Nannocystis, Necropsobacter, Negativibacillus, Negativicoccus, Neochlamydia, Neomegalonema, Neorhizobium, Neoscardovia, Nesterenkonia, Nocardioides, Nocardiopsis, Novosphingobium, Oceanivirga, Oceanobacillus, Ochrobactrum, Olsenella, Oribacterium, Ottowia, Oxalobacter, Oxobacter, P3OB.42, Paenibacillus, Paeniclostridium, Paenisporosarcina, Paludicola, Papillibacter, Paraclostridium, Paracoccus, Paramesorhizobium, Paraprevotella, Parapusillimonas, Parascardovia, Parvibacter, Pasteurella, Paucibacter, Pediococcus, Pedobacter, Peptoclostridium, Peptococcus, Peptostreptococcus, Perlucidibaca, Phascolarctobacterium, Phaseolibacter, Phocea, Phoenicibacter, Phyllobacterium, Piscinibacter, Planifilum, Plesiomonas, Plot4.2H12, Pluralibacter, Polaromonas, Porphyromonas, Prevotellaceae.NK3B31.group, Prevotellaceae.UCG.001, Propionibacterium, Prosthecobacter, Proteus, Providencia, Pseudacidovorax, Pseudaminobacter, Pseudocitrobacter, Pseudoflavonifractor, Pseudoglutamicibacter, Pseudoramibacter, Pseudoxanthomonas, Psychrobacter, Pygmaiobacter, Pyramidobacter, Qipengyuania, Ralstonia, Raoultella, Raoultibacter, Reyranella, Rhizorhapis, Rhodanobacter, Rhodobacter, Rhodococcus, Rikenella, Rikenellaceae.RC9.gut.group, Rivicola, Robinsoniella, Rodentibacter, Roseisolibacter, Rubellimicrobium, Rummeliibacillus, S5.A14a, SH.PL14, Saccharothrix, Salinimicrobium, Salinisphaera, Salipaludibacillus, Salmonella, Sanguibacteroides, Sarcina, Scardovia, Sedimentibacter, Segetibacter, Selenomonas, Senegalimassilia, Serratia, Shimwellia, Shuttleworthia, Slackia, Sneathia, Solibacillus, Sphingoaurantiacus, Sphingobacterium, Sphingobium, Sphingomonas, Sphingopyxis, Sporolactobacillus, Stenotrophomonas, Stomatobaculum, Streptobacillus, Succinatimonas, Succiniclasticum, Succinivibrio, Sulfurospirillum, Synergistes, TM7x, Tannerella, Tatumella, Tepidimonas, Tepidiphilus, Tetragenococcus, Thermus, Timonella, Tolumonas, Trabulsiella, Tropheryma, Trueperella, UC5.1.2E3, UCG.004, UCG.007, UCG.008, UCG.009, Ureibacillus, Varibaculum, Variovorax, Verticiella, Victivallis, Vulcaniibacterium, Weissella, Xanthomonas, Yersinia, Yokenella, Zoogloea, X.Bacteroides..pectinophilus.group, X.Eubacterium..brachy.group, X.Eubacterium..nodatum.group, X.Eubacterium..oxidoreducens.group, X.Eubacterium..ruminantium.group, unclassified.0319.6G20, unclassified.67.14, unclassified.A0839, unclassified.Acetobacteraceae, unclassified.Acidaminococcaceae, unclassified.Actinobacteria, unclassified.Actinomycetaceae, unclassified.Aeromonadales, unclassified.Anaerococcus, unclassified.Anaerosalibacter, unclassified.Anaerovoracaceae, unclassified.Armatimonadales, unclassified.Atopobiaceae, unclassified.Bacillaceae, unclassified.Bacillales, unclassified.Bacilli, unclassified.Bacteroidales, unclassified.Bacteroidia, unclassified.Barnesiellaceae, unclassified.Bifidobacteriaceae, unclassified.Burkholderiales, unclassified.Butyricicoccaceae, unclassified.Caloramatoraceae, unclassified.Carnobacteriaceae, unclassified.Caulobacteraceae, unclassified.Christensenellaceae, unclassified.Chroococcidiopsaceae, unclassified.Clostridiaceae, unclassified.Clostridiales, unclassified.Comamonadaceae, unclassified.Coriobacteriales.Incertae.Sedis, unclassified.Coriobacteriales, unclassified.Corynebacteriaceae, unclassified.Desulfovibrionaceae, unclassified.Devosiaceae, unclassified.Diplorickettsiaceae, unclassified.Eggerthellaceae, unclassified.Enterobacterales, unclassified.Enterobacteriaceae, unclassified.Enterococcaceae, unclassified.Erwiniaceae, unclassified.Erysipelatoclostridiaceae, unclassified.Erysipelotrichaceae, unclassified.Erysipelotrichales, unclassified.Ethanoligenenaceae, unclassified.Eubacteriaceae, unclassified.Ezakiella, unclassified.Fastidiosipila, unclassified.Fenollaria, unclassified.Fimbriimonadaceae, unclassified.Finegoldia, unclassified.Firmicutes, unclassified.Flavobacteriaceae, unclassified.Flavobacteriales, unclassified.Fusobacteriaceae, unclassified.Gaiellales, unclassified.Gallicola, unclassified.Gammaproteobacteria, unclassified.Gemmataceae, unclassified.Hungateiclostridiaceae, unclassified.Hydrogenoanaerobacterium, unclassified.Izemoplasmatales, unclassified.JI49D030, unclassified.KD3.93, unclassified.Kapabacteriales, unclassified.Lachnospirales, unclassified.Lactobacillales, unclassified.Leuconostocaceae, unclassified.Lineage.IV, unclassified.MAT.CR.H4.C10, unclassified.Methylococcaceae, unclassified.Micavibrionales, unclassified.Microbacteriaceae, unclassified.Micrococcaceae, unclassified.Micrococcales, unclassified.Moraxellaceae, unclassified.Murdochiella, unclassified.Muribaculaceae, unclassified.NS9.marine.group, unclassified.Neisseriaceae, unclassified.OLB14, unclassified.Opitutales, unclassified.Oscillospirales, unclassified.Oxalobacteraceae, unclassified.P5D1.392, unclassified.PLTA13, unclassified.Paenibacillaceae, unclassified.Paracaedibacteraceae, unclassified.Parachlamydiaceae, unclassified.Parvimonas, unclassified.Pasteurellaceae, unclassified.Peptococcaceae, unclassified.Peptostreptococcaceae, unclassified.Peptostreptococcales.Tissierellales, unclassified.Planctomycetales, unclassified.Planococcaceae, unclassified.Prevotellaceae, unclassified.Promicromonosporaceae, unclassified.Propionibacteriaceae, unclassified.Proteobacteria, unclassified.Pseudomonadaceae, unclassified.Puniceicoccaceae, unclassified.RF39, unclassified.Rhizobiaceae, unclassified.Rhizobiales.Incertae.Sedis, unclassified.Rhizobiales, unclassified.Rhodobacteraceae, unclassified.Rhodocyclaceae, unclassified.Rickettsiales, unclassified.Rikenellaceae, unclassified.Ruminiclostridium, unclassified.ST.12K33, unclassified.Saccharimonadales, unclassified.Sandaracinaceae, unclassified.Selenomonadaceae, unclassified.Simkaniaceae, unclassified.Solimonadaceae, unclassified.Sphingobacteriales, unclassified.Sphingomonadaceae, unclassified.Staphylococcaceae, unclassified.Streptococcaceae, unclassified.Succinivibrionaceae, unclassified.Sutterellaceae, unclassified.TRA3.20, unclassified.Tannerellaceae, unclassified.Tepidimicrobium, unclassified.UCG.010, unclassified.UCG.011, unclassified.Veillonellaceae, unclassified.Veillonellales.Selenomonadales, unclassified.Vermiphilaceae, unclassified.Verrucomicrobiales, unclassified.Verrucomicrobiota, unclassified.Victivallaceae, unclassified.W5053, unclassified.WPS.2, unclassified.Weeksellaceae, unclassified.Xanthobacteraceae, unclassified.Yersiniaceae, unclassified..Clostridium..methylpentosum.group, unclassified.vadinBE97 #> 2024-04-24 17:16:51.691984 INFO::Total filtered features with variance filtering: 0 #> 2024-04-24 17:16:51.692518 INFO::Filtered feature names from variance filtering: #> 2024-04-24 17:16:51.692974 INFO::Running selected normalization method: TSS #> 2024-04-24 17:16:51.741262 INFO::Applying z-score to standardize continuous metadata #> 2024-04-24 17:16:51.744238 INFO::Running selected transform method: LOG #> 2024-04-24 17:16:51.807753 INFO::Running selected analysis method: LM #> 2024-04-24 17:16:51.808467 INFO::Fitting model to feature number 1, Actinomyces #> 2024-04-24 17:16:51.813009 INFO::Fitting model to feature number 2, Agathobacter #> 2024-04-24 17:16:51.817101 INFO::Fitting model to feature number 3, Akkermansia #> 2024-04-24 17:16:51.821279 INFO::Fitting model to feature number 4, Alistipes #> 2024-04-24 17:16:51.825387 INFO::Fitting model to feature number 5, Anaerostipes #> 2024-04-24 17:16:51.829515 INFO::Fitting model to feature number 6, Atopobium #> 2024-04-24 17:16:51.833546 INFO::Fitting model to feature number 7, Bacteroides #> 2024-04-24 17:16:51.837641 INFO::Fitting model to feature number 8, Barnesiella #> 2024-04-24 17:16:51.841688 INFO::Fitting model to feature number 9, Bifidobacterium #> 2024-04-24 17:16:51.84576 INFO::Fitting model to feature number 10, Bilophila #> 2024-04-24 17:16:51.849827 INFO::Fitting model to feature number 11, Blautia #> 2024-04-24 17:16:51.853912 INFO::Fitting model to feature number 12, Butyricicoccus #> 2024-04-24 17:16:51.857984 INFO::Fitting model to feature number 13, CAG.352 #> 2024-04-24 17:16:51.862052 INFO::Fitting model to feature number 14, Campylobacter #> 2024-04-24 17:16:51.866104 INFO::Fitting model to feature number 15, Christensenellaceae.R.7.group #> 2024-04-24 17:16:51.870146 INFO::Fitting model to feature number 16, Clostridioides #> 2024-04-24 17:16:51.874193 INFO::Fitting model to feature number 17, Clostridium.sensu.stricto.1 #> 2024-04-24 17:16:51.878295 INFO::Fitting model to feature number 18, Colidextribacter #> 2024-04-24 17:16:51.882366 INFO::Fitting model to feature number 19, Collinsella #> 2024-04-24 17:16:51.886409 INFO::Fitting model to feature number 20, Coprobacillus #> 2024-04-24 17:16:51.890463 INFO::Fitting model to feature number 21, Coprococcus #> 2024-04-24 17:16:51.894513 INFO::Fitting model to feature number 22, DTU089 #> 2024-04-24 17:16:51.898586 INFO::Fitting model to feature number 23, Dialister #> 2024-04-24 17:16:51.902681 INFO::Fitting model to feature number 24, Dorea #> 2024-04-24 17:16:51.906735 INFO::Fitting model to feature number 25, Eggerthella #> 2024-04-24 17:16:51.910797 INFO::Fitting model to feature number 26, Eisenbergiella #> 2024-04-24 17:16:51.914993 INFO::Fitting model to feature number 27, Enterococcus #> 2024-04-24 17:16:51.91906 INFO::Fitting model to feature number 28, Erysipelatoclostridium #> 2024-04-24 17:16:51.92312 INFO::Fitting model to feature number 29, Erysipelotrichaceae.UCG.003 #> 2024-04-24 17:16:51.927198 INFO::Fitting model to feature number 30, Escherichia.Shigella #> 2024-04-24 17:16:51.931323 INFO::Fitting model to feature number 31, Faecalibacterium #> 2024-04-24 17:16:51.935394 INFO::Fitting model to feature number 32, Family.XIII.AD3011.group #> 2024-04-24 17:16:51.939488 INFO::Fitting model to feature number 33, Flavonifractor #> 2024-04-24 17:16:51.943558 INFO::Fitting model to feature number 34, Fusicatenibacter #> 2024-04-24 17:16:51.947632 INFO::Fitting model to feature number 35, Fusobacterium #> 2024-04-24 17:16:51.951736 INFO::Fitting model to feature number 36, Gemella #> 2024-04-24 17:16:51.955823 INFO::Fitting model to feature number 37, Granulicatella #> 2024-04-24 17:16:51.959917 INFO::Fitting model to feature number 38, Haemophilus #> 2024-04-24 17:16:51.964061 INFO::Fitting model to feature number 39, Holdemania #> 2024-04-24 17:16:51.96823 INFO::Fitting model to feature number 40, Hungatella #> 2024-04-24 17:16:51.97232 INFO::Fitting model to feature number 41, Incertae.Sedis..EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis. #> 2024-04-24 17:16:51.976407 INFO::Fitting model to feature number 42, Intestinibacter #> 2024-04-24 17:16:51.980541 INFO::Fitting model to feature number 43, Intestinimonas #> 2024-04-24 17:16:51.984639 INFO::Fitting model to feature number 44, Klebsiella #> 2024-04-24 17:16:51.988772 INFO::Fitting model to feature number 45, Lachnoclostridium #> 2024-04-24 17:16:51.992852 INFO::Fitting model to feature number 46, Lachnospira #> 2024-04-24 17:16:52.00783 INFO::Fitting model to feature number 47, Lachnospiraceae.FCS020.group #> 2024-04-24 17:16:52.012055 INFO::Fitting model to feature number 48, Lachnospiraceae.ND3007.group #> 2024-04-24 17:16:52.016165 INFO::Fitting model to feature number 49, Lachnospiraceae.NK4A136.group #> 2024-04-24 17:16:52.020285 INFO::Fitting model to feature number 50, Lachnospiraceae.UCG.001 #> 2024-04-24 17:16:52.024375 INFO::Fitting model to feature number 51, Lachnospiraceae.UCG.004 #> 2024-04-24 17:16:52.028476 INFO::Fitting model to feature number 52, Lachnospiraceae.UCG.009 #> 2024-04-24 17:16:52.032567 INFO::Fitting model to feature number 53, Lachnospiraceae.UCG.010 #> 2024-04-24 17:16:52.036638 INFO::Fitting model to feature number 54, Lactobacillus #> 2024-04-24 17:16:52.040771 INFO::Fitting model to feature number 55, Lactococcus #> 2024-04-24 17:16:52.044824 INFO::Fitting model to feature number 56, Mannheimia #> 2024-04-24 17:16:52.048883 INFO::Fitting model to feature number 57, Megasphaera #> 2024-04-24 17:16:52.052965 INFO::Fitting model to feature number 58, Monoglobus #> 2024-04-24 17:16:52.057095 INFO::Fitting model to feature number 59, Neisseria #> 2024-04-24 17:16:52.061193 INFO::Fitting model to feature number 60, Odoribacter #> 2024-04-24 17:16:52.065239 INFO::Fitting model to feature number 61, Oscillibacter #> 2024-04-24 17:16:52.069337 INFO::Fitting model to feature number 62, Oscillospira #> 2024-04-24 17:16:52.073477 INFO::Fitting model to feature number 63, Parabacteroides #> 2024-04-24 17:16:52.077561 INFO::Fitting model to feature number 64, Parasutterella #> 2024-04-24 17:16:52.081631 INFO::Fitting model to feature number 65, Prevotella #> 2024-04-24 17:16:52.085779 INFO::Fitting model to feature number 66, Pseudomonas #> 2024-04-24 17:16:52.089899 INFO::Fitting model to feature number 67, Romboutsia #> 2024-04-24 17:16:52.093973 INFO::Fitting model to feature number 68, Roseburia #> 2024-04-24 17:16:52.098027 INFO::Fitting model to feature number 69, Rothia #> 2024-04-24 17:16:52.102139 INFO::Fitting model to feature number 70, Ruminococcus #> 2024-04-24 17:16:52.106226 INFO::Fitting model to feature number 71, Sellimonas #> 2024-04-24 17:16:52.110327 INFO::Fitting model to feature number 72, Solobacterium #> 2024-04-24 17:16:52.114395 INFO::Fitting model to feature number 73, Staphylococcus #> 2024-04-24 17:16:52.118479 INFO::Fitting model to feature number 74, Streptococcus #> 2024-04-24 17:16:52.122612 INFO::Fitting model to feature number 75, Subdoligranulum #> 2024-04-24 17:16:52.126734 INFO::Fitting model to feature number 76, Sutterella #> 2024-04-24 17:16:52.130818 INFO::Fitting model to feature number 77, Terrisporobacter #> 2024-04-24 17:16:52.135185 INFO::Fitting model to feature number 78, Turicibacter #> 2024-04-24 17:16:52.139626 INFO::Fitting model to feature number 79, Tuzzerella #> 2024-04-24 17:16:52.143763 INFO::Fitting model to feature number 80, Tyzzerella #> 2024-04-24 17:16:52.147933 INFO::Fitting model to feature number 81, UBA1819 #> 2024-04-24 17:16:52.152114 INFO::Fitting model to feature number 82, UCG.002 #> 2024-04-24 17:16:52.156343 INFO::Fitting model to feature number 83, UCG.003 #> 2024-04-24 17:16:52.16053 INFO::Fitting model to feature number 84, UCG.005 #> 2024-04-24 17:16:52.164685 INFO::Fitting model to feature number 85, Veillonella #> 2024-04-24 17:16:52.168866 INFO::Fitting model to feature number 86, X.Clostridium..innocuum.group #> 2024-04-24 17:16:52.172972 INFO::Fitting model to feature number 87, X.Eubacterium..eligens.group #> 2024-04-24 17:16:52.177117 INFO::Fitting model to feature number 88, X.Eubacterium..fissicatena.group #> 2024-04-24 17:16:52.181239 INFO::Fitting model to feature number 89, X.Eubacterium..hallii.group #> 2024-04-24 17:16:52.185343 INFO::Fitting model to feature number 90, X.Eubacterium..siraeum.group #> 2024-04-24 17:16:52.189446 INFO::Fitting model to feature number 91, X.Eubacterium..ventriosum.group #> 2024-04-24 17:16:52.193608 INFO::Fitting model to feature number 92, X.Eubacterium..xylanophilum.group #> 2024-04-24 17:16:52.197704 INFO::Fitting model to feature number 93, X.Ruminococcus..gauvreauii.group #> 2024-04-24 17:16:52.201757 INFO::Fitting model to feature number 94, X.Ruminococcus..gnavus.group #> 2024-04-24 17:16:52.205876 INFO::Fitting model to feature number 95, X.Ruminococcus..torques.group #> 2024-04-24 17:16:52.209989 INFO::Fitting model to feature number 96, unclassified.Chloroplast #> 2024-04-24 17:16:52.214132 INFO::Fitting model to feature number 97, unclassified.Clostridia.UCG.014 #> 2024-04-24 17:16:52.218226 INFO::Fitting model to feature number 98, unclassified.Clostridia #> 2024-04-24 17:16:52.222431 INFO::Fitting model to feature number 99, unclassified.Clostridia.vadinBB60.group #> 2024-04-24 17:16:52.226542 INFO::Fitting model to feature number 100, unclassified.Gastranaerophilales #> 2024-04-24 17:16:52.230672 INFO::Fitting model to feature number 101, unclassified.Lachnospiraceae #> 2024-04-24 17:16:52.234797 INFO::Fitting model to feature number 102, unclassified.Mitochondria #> 2024-04-24 17:16:52.238919 INFO::Fitting model to feature number 103, unclassified.Oscillospiraceae #> 2024-04-24 17:16:52.243027 INFO::Fitting model to feature number 104, unclassified.Peptoniphilus #> 2024-04-24 17:16:52.247104 INFO::Fitting model to feature number 105, unclassified.Rhodospirillales #> 2024-04-24 17:16:52.251336 INFO::Fitting model to feature number 106, unclassified.Ruminococcaceae #> 2024-04-24 17:16:52.255428 INFO::Fitting model to feature number 107, unclassified..Eubacterium..coprostanoligenes.group #> 2024-04-24 17:16:52.271535 INFO::Counting total values for each feature #> 2024-04-24 17:16:52.276874 INFO::Writing filtered data to file /tmp/RtmpfBGTvS/maaslin195822b50425/features/filtered_data.tsv #> 2024-04-24 17:16:52.421668 INFO::Writing filtered, normalized data to file /tmp/RtmpfBGTvS/maaslin195822b50425/features/filtered_data_norm.tsv #> 2024-04-24 17:16:52.619771 INFO::Writing filtered, normalized, transformed data to file /tmp/RtmpfBGTvS/maaslin195822b50425/features/filtered_data_norm_transformed.tsv #> 2024-04-24 17:16:52.892076 INFO::Writing residuals to file /tmp/RtmpfBGTvS/maaslin195822b50425/fits/residuals.rds #> 2024-04-24 17:16:52.962332 INFO::Writing fitted values to file /tmp/RtmpfBGTvS/maaslin195822b50425/fits/fitted.rds #> 2024-04-24 17:16:52.986202 INFO::Writing all results to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin195822b50425/all_results.tsv #> 2024-04-24 17:16:52.987827 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): /tmp/RtmpfBGTvS/maaslin195822b50425/significant_results.tsv"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Collection — getCollection","title":"Get Microbiome Dataset Collection — getCollection","text":"Get collection Microbiome Dataset. collection returned AbundanceData, phyloseq, Collection object.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Collection — getCollection","text":"","code":"getCollection(   object,   collectionName,   format = c(\"AbundanceData\", \"phyloseq\", \"Collection\"),   continuousMetadataOnly = c(FALSE, TRUE) )  # S4 method for MbioDataset getCollection(   object,   collectionName = character(0),   format = c(\"AbundanceData\", \"phyloseq\", \"Collection\"),   continuousMetadataOnly = c(FALSE, TRUE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Collection — getCollection","text":"object Microbiome Dataset collectionName name collection return format format collection return. Currently supported options \"AbundanceData\", \"phyloseq\" \"Collection\". continuousMetadataOnly TRUE, continuous metadata returned. FALSE, metadata returned.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Collection — getCollection","text":"AbundanceData, phyloseq, Collection object representing collection associated study metadata","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollection.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Collection — getCollection","text":"","code":"genus <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\" )  genus_phyloseq <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\",       format = \"phyloseq\" )  ## to pass to correlation method, we want only continuous metadata genus_continuous <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\",       continuousMetadataOnly = TRUE )   ## with no metadata genus_collection <- getCollection(      microbiomeData::DiabImmune,       \"16S (V4) Genus\",       format = \"Collection\" )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Names of Collections — getCollectionNames,MbioDataset-method","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"Get names collections MbioDataset object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getCollectionNames(object)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"object MbioDataset","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"character vector collection names","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionNames-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Names of Collections — getCollectionNames,MbioDataset-method","text":"","code":"getCollectionNames(microbiomeData::DiabImmune) #>  [1] \"16S (V4) Order\"                                           #>  [2] \"16S (V4) Genus\"                                           #>  [3] \"16S (V4) Family\"                                          #>  [4] \"16S (V4) Species\"                                         #>  [5] \"16S (V4) Class\"                                           #>  [6] \"16S (V4) Phylum\"                                          #>  [7] \"16S (V4) Kingdom\"                                         #>  [8] \"WGS 4th level EC metagenome abundance data\"               #>  [9] \"WGS Metagenome enzyme pathway abundance data\"             #> [10] \"WGS Metagenome enzyme pathway coverage data\"              #> [11] \"WGS Genus\"                                                #> [12] \"WGS Species\"                                              #> [13] \"WGS Family\"                                               #> [14] \"WGS Order\"                                                #> [15] \"WGS Phylum\"                                               #> [16] \"WGS Class\"                                                #> [17] \"WGS Kingdom\"                                              #> [18] \"WGS Normalized number of taxon-specific sequence matches\""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"Get variable names collection Microbiome Dataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getCollectionVariableNames(object, collectionName)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"object Microbiome Dataset collectionName name collection return variable names ","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"character vector variable names requested collection","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getCollectionVariableNames-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Collection Variable Names — getCollectionVariableNames,MbioDataset-method","text":"","code":"variableNames <- getCollectionVariableNames(microbiomeData::DiabImmune, \"16S (V4) Genus\")"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Compute Result — getComputeResult","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"Get compute result Microbiome Dataset particular format. formats may supported compute results.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"","code":"getComputeResult(object, format = c(\"data.table\"), ...)  # S4 method for ComputeResult getComputeResult(object, format = c(\"data.table\", \"igraph\"), ...)  # S4 method for CorrelationResult getComputeResult(   object,   format = c(\"data.table\", \"igraph\"),   correlationCoefThreshold = 0.5,   pValueThreshold = 0.05 )  # S4 method for DifferentialAbundanceResult getComputeResult(object, format = c(\"data.table\"))"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"object Microbiome Dataset format format compute result. Currently \"data.table\" \"igraph\" supported. ... additional arguments passed getComputeResult method subclasses ComputeResult correlationCoefThreshold threshold filter edges correlation coefficient. Edges correlation coefficients threshold removed. Default .5 pValueThreshold threshold filter edges p-value. Edges p-values threshold removed. Default .05","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"compute result specified format","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResult.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Compute Result — getComputeResult","text":"","code":"correlationOutput <- MicrobiomeDB::selfCorrelation(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method='spearman',       verbose=FALSE ) #>  #> 2024-04-24 17:16:54.012372 Removed 1 records with no data. #>  #> 2024-04-24 17:16:54.019006 Removed 1 records with no data. correlationDT <- getComputeResult(correlationOutput, \"data.table\") correlationIGraph <- getComputeResult(correlationOutput, \"igraph\")"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"Get compute result Microbiome Dataset particular format metadata.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"","code":"getComputeResultWithMetadata(   object,   dataset,   format = c(\"data.table\"),   metadataVariables = NULL )  # S4 method for ComputeResult,MbioDataset getComputeResultWithMetadata(   object,   dataset = NULL,   format = c(\"data.table\"),   metadataVariables = NULL )  # S4 method for ComputeResult,Collection getComputeResultWithMetadata(   object,   dataset = NULL,   format = c(\"data.table\"),   metadataVariables = NULL )  # S4 method for ComputeResult,AbundanceData getComputeResultWithMetadata(   object,   dataset = NULL,   format = c(\"data.table\"),   metadataVariables = NULL )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"object Microbiome Dataset dataset MbioDataset, AbundanceData Collection object compute result obtained. format format want compute result . Currently \"data.table\" supported. metadataVariables metadata variables include compute result. NULL, metadata variables included.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"compute result specified format","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getComputeResultWithMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Compute Result With Metadata — getComputeResultWithMetadata","text":"","code":"alphaDivOutput <- MicrobiomeDB::alphaDiv(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method='shannon',       verbose=FALSE )  alphaDivDT <- getComputeResultWithMetadata(      alphaDivOutput,       microbiomeData::DiabImmune,       metadataVariables = c('country', 'delivery_mode') )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"Get names metadata variables MbioDataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getMetadataVariableNames(object)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"object MbioDataset","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"character vector metadata variable names","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableNames-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Variable Names of Metadata — getMetadataVariableNames,MbioDataset-method","text":"","code":"getMetadataVariableNames(microbiomeData::DiabImmune) #>  [1] \"Participant_Id\"                                       #>  [2] \"Participant_repeated_measure_Id\"                      #>  [3] \"age_1st_animal_milk_or_solids_given_days\"             #>  [4] \"age_1st_given_apple_months\"                           #>  [5] \"age_1st_given_banana_months\"                          #>  [6] \"age_1st_given_barley_months\"                          #>  [7] \"age_1st_given_beef_months\"                            #>  [8] \"age_1st_given_berries_months\"                         #>  [9] \"age_1st_given_cabbs_months\"                           #> [10] \"age_1st_given_carrot_months\"                          #> [11] \"age_1st_given_corn_months\"                            #> [12] \"age_1st_given_cowsmilk_months\"                        #> [13] \"age_1st_given_egg_months\"                             #> [14] \"age_1st_given_fish_months\"                            #> [15] \"age_1st_given_milk_products_months\"                   #> [16] \"age_1st_given_oat_months\"                             #> [17] \"age_1st_given_pear_months\"                            #> [18] \"age_1st_given_peas_months\"                            #> [19] \"age_1st_given_plum_months\"                            #> [20] \"age_1st_given_pork_months\"                            #> [21] \"age_1st_given_potato_months\"                          #> [22] \"age_1st_given_poultry_months\"                         #> [23] \"age_1st_given_rice_months\"                            #> [24] \"age_1st_given_rye_months\"                             #> [25] \"age_1st_given_sweet_potato_months\"                    #> [26] \"age_1st_given_tomato_months\"                          #> [27] \"age_1st_given_wheat_months\"                           #> [28] \"age_at_anthropometry_days\"                            #> [29] \"age_at_two_autoantibodies_positive_days\"              #> [30] \"age_at_type_1_diabetes_diagnosis_days\"                #> [31] \"antibiotics_before_delivery_by_maternal_report\"       #> [32] \"bmi_minus_for_minus_age_z_minus_score\"                #> [33] \"breastfed_duration_days\"                              #> [34] \"country\"                                              #> [35] \"delivery_mode\"                                        #> [36] \"diet_in_first_three_days\"                             #> [37] \"exclusive_breastfed_duration_days\"                    #> [38] \"gestational_diabetes_by_maternal_report\"              #> [39] \"glutamic_acid_decarboxylase_autoantibodies\"           #> [40] \"hla_risk_by_hla_haplotyping\"                          #> [41] \"height_minus_for_minus_age_z_minus_score\"             #> [42] \"insulin_autoantibodies\"                               #> [43] \"insulinoma_minus_associated_protein_2_autoantibodies\" #> [44] \"islet_cell_autoantibodies\"                            #> [45] \"linear_growth_during_1st_year_cm\"                     #> [46] \"maternal_age_at_birth_months\"                         #> [47] \"mean_linear_growth_during_1st_3_years\"                #> [48] \"mean_weight_gain_during_1st_3_years\"                  #> [49] \"sex\"                                                  #> [50] \"study_group\"                                          #> [51] \"type_1_diabetes_diagnosed\"                            #> [52] \"urban_or_rural_site\"                                  #> [53] \"weight_gain_during_1st_year_kg\"                       #> [54] \"weight_minus_for_minus_age_z_minus_score\"             #> [55] \"zinc_transporter_8_autoantibodies\"                    #> [56] \"age_months\"                                           #> [57] \"Sample_Id\"                                            #> [58] \"habitat\"                                              #> [59] \"host_body_habitat\"                                    #> [60] \"host_body_product\"                                    #> [61] \"host_body_site\"                                       #> [62] \"sample_type\""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"Get summary requested metadata variable MbioDataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getMetadataVariableSummary(object, variable)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"object MbioDataset variable character vector representing name metadata variable summarize","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"table summarizing values requested metadata variable","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getMetadataVariableSummary-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Summary of Metadata Variables — getMetadataVariableSummary,MbioDataset-method","text":"","code":"getMetadataVariableSummary(microbiomeData::DiabImmune, \"age_months\") #>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.  #>    0.00    8.00   15.00   15.62   22.00   38.00  getMetadataVariableSummary(microbiomeData::DiabImmune, \"sex\") #> Female   Male  #>   1475   1874  getMetadataVariableSummary(microbiomeData::DiabImmune, \"country\") #> Estonia Finland  Russia  #>     555    2142     652"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"Returns data.table sample metadata","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getSampleMetadata(   object,   asCopy = c(TRUE, FALSE),   includeIds = c(TRUE, FALSE),   metadataVariables = NULL )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"object MbioDataset asCopy boolean indicating whether return data copy reference includeIds boolean indicating whether include recordIdColumn ancestorIdColumns metadataVariables metadata variables include sample metadata. NULL, metadata variables included.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"data.table sample metadata","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadata-MbioDataset-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get data.table of sample metadata from MbioDataset — getSampleMetadata,MbioDataset-method","text":"","code":"getSampleMetadata(microbiomeData::DiabImmune) #>         Participant_Id Participant_repeated_measure_Id #>                 <char>                          <char> #>    1: E000823 (Source)              E000823_1 (Source) #>    2: E000823 (Source)             E000823_10 (Source) #>    3: E000823 (Source)             E000823_12 (Source) #>    4: E000823 (Source)             E000823_13 (Source) #>    5: E000823 (Source)             E000823_15 (Source) #>   ---                                                  #> 3345: T029922 (Source)             T029922_14 (Source) #> 3346: T029922 (Source)             T029922_16 (Source) #> 3347: T029922 (Source)             T029922_19 (Source) #> 3348: T029922 (Source)             T029922_22 (Source) #> 3349: T029922 (Source)              T029922_7 (Source) #>       age_1st_animal_milk_or_solids_given_days age_1st_given_apple_months #>                                          <num>                      <num> #>    1:                                        5                          6 #>    2:                                        5                          6 #>    3:                                        5                          6 #>    4:                                        5                          6 #>    5:                                        5                          6 #>   ---                                                                     #> 3345:                                        4                          4 #> 3346:                                        4                          4 #> 3347:                                        4                          4 #> 3348:                                        4                          4 #> 3349:                                        4                          4 #>       age_1st_given_banana_months age_1st_given_barley_months #>                             <num>                       <num> #>    1:                           6                          11 #>    2:                           6                          11 #>    3:                           6                          11 #>    4:                           6                          11 #>    5:                           6                          11 #>   ---                                                         #> 3345:                           4                          10 #> 3346:                           4                          10 #> 3347:                           4                          10 #> 3348:                           4                          10 #> 3349:                           4                          10 #>       age_1st_given_beef_months age_1st_given_berries_months #>                           <num>                        <num> #>    1:                       6.0                          6.0 #>    2:                       6.0                          6.0 #>    3:                       6.0                          6.0 #>    4:                       6.0                          6.0 #>    5:                       6.0                          6.0 #>   ---                                                        #> 3345:                       5.5                          7.5 #> 3346:                       5.5                          7.5 #> 3347:                       5.5                          7.5 #> 3348:                       5.5                          7.5 #> 3349:                       5.5                          7.5 #>       age_1st_given_cabbs_months age_1st_given_carrot_months #>                            <num>                       <num> #>    1:                          7                           5 #>    2:                          7                           5 #>    3:                          7                           5 #>    4:                          7                           5 #>    5:                          7                           5 #>   ---                                                        #> 3345:                          5                           4 #> 3346:                          5                           4 #> 3347:                          5                           4 #> 3348:                          5                           4 #> 3349:                          5                           4 #>       age_1st_given_corn_months age_1st_given_cowsmilk_months #>                           <num>                         <num> #>    1:                         6                          12.0 #>    2:                         6                          12.0 #>    3:                         6                          12.0 #>    4:                         6                          12.0 #>    5:                         6                          12.0 #>   ---                                                         #> 3345:                         5                           8.5 #> 3346:                         5                           8.5 #> 3347:                         5                           8.5 #> 3348:                         5                           8.5 #> 3349:                         5                           8.5 #>       age_1st_given_egg_months age_1st_given_fish_months #>                          <num>                     <num> #>    1:                        8                         7 #>    2:                        8                         7 #>    3:                        8                         7 #>    4:                        8                         7 #>    5:                        8                         7 #>   ---                                                    #> 3345:                       11                         6 #> 3346:                       11                         6 #> 3347:                       11                         6 #> 3348:                       11                         6 #> 3349:                       11                         6 #>       age_1st_given_milk_products_months age_1st_given_oat_months #>                                    <num>                    <num> #>    1:                                 10                        5 #>    2:                                 10                        5 #>    3:                                 10                        5 #>    4:                                 10                        5 #>    5:                                 10                        5 #>   ---                                                             #> 3345:                                  7                        5 #> 3346:                                  7                        5 #> 3347:                                  7                        5 #> 3348:                                  7                        5 #> 3349:                                  7                        5 #>       age_1st_given_pear_months age_1st_given_peas_months #>                           <num>                     <num> #>    1:                      10.0                       6.5 #>    2:                      10.0                       6.5 #>    3:                      10.0                       6.5 #>    4:                      10.0                       6.5 #>    5:                      10.0                       6.5 #>   ---                                                     #> 3345:                       4.5                       5.0 #> 3346:                       4.5                       5.0 #> 3347:                       4.5                       5.0 #> 3348:                       4.5                       5.0 #> 3349:                       4.5                       5.0 #>       age_1st_given_plum_months age_1st_given_pork_months #>                           <num>                     <num> #>    1:                       5.0                         7 #>    2:                       5.0                         7 #>    3:                       5.0                         7 #>    4:                       5.0                         7 #>    5:                       5.0                         7 #>   ---                                                     #> 3345:                       4.5                         8 #> 3346:                       4.5                         8 #> 3347:                       4.5                         8 #> 3348:                       4.5                         8 #> 3349:                       4.5                         8 #>       age_1st_given_potato_months age_1st_given_poultry_months #>                             <num>                        <num> #>    1:                           5                            6 #>    2:                           5                            6 #>    3:                           5                            6 #>    4:                           5                            6 #>    5:                           5                            6 #>   ---                                                          #> 3345:                           5                            5 #> 3346:                           5                            5 #> 3347:                           5                            5 #> 3348:                           5                            5 #> 3349:                           5                            5 #>       age_1st_given_rice_months age_1st_given_rye_months #>                           <num>                    <num> #>    1:                       5.0                     11.0 #>    2:                       5.0                     11.0 #>    3:                       5.0                     11.0 #>    4:                       5.0                     11.0 #>    5:                       5.0                     11.0 #>   ---                                                    #> 3345:                       4.5                      7.5 #> 3346:                       4.5                      7.5 #> 3347:                       4.5                      7.5 #> 3348:                       4.5                      7.5 #> 3349:                       4.5                      7.5 #>       age_1st_given_sweet_potato_months age_1st_given_tomato_months #>                                   <num>                       <num> #>    1:                                NA                           9 #>    2:                                NA                           9 #>    3:                                NA                           9 #>    4:                                NA                           9 #>    5:                                NA                           9 #>   ---                                                               #> 3345:                                NA                           6 #> 3346:                                NA                           6 #> 3347:                                NA                           6 #> 3348:                                NA                           6 #> 3349:                                NA                           6 #>       age_1st_given_wheat_months age_at_anthropometry_days #>                            <num>                     <int> #>    1:                         12                      1110 #>    2:                         12                      1110 #>    3:                         12                      1110 #>    4:                         12                      1110 #>    5:                         12                      1110 #>   ---                                                      #> 3345:                          6                      1123 #> 3346:                          6                      1123 #> 3347:                          6                      1123 #> 3348:                          6                      1123 #> 3349:                          6                      1123 #>       age_at_two_autoantibodies_positive_days #>                                         <int> #>    1:                                      NA #>    2:                                      NA #>    3:                                      NA #>    4:                                      NA #>    5:                                      NA #>   ---                                         #> 3345:                                      NA #> 3346:                                      NA #> 3347:                                      NA #> 3348:                                      NA #> 3349:                                      NA #>       age_at_type_1_diabetes_diagnosis_days #>                                       <int> #>    1:                                    NA #>    2:                                    NA #>    3:                                    NA #>    4:                                    NA #>    5:                                    NA #>   ---                                       #> 3345:                                    NA #> 3346:                                    NA #> 3347:                                    NA #> 3348:                                    NA #> 3349:                                    NA #>       antibiotics_before_delivery_by_maternal_report #>                                               <char> #>    1:                                             No #>    2:                                             No #>    3:                                             No #>    4:                                             No #>    5:                                             No #>   ---                                                #> 3345:                                                #> 3346:                                                #> 3347:                                                #> 3348:                                                #> 3349:                                                #>       bmi_minus_for_minus_age_z_minus_score breastfed_duration_days country #>                                       <num>                   <int>  <char> #>    1:                                  1.62                     397 Finland #>    2:                                  1.62                     397 Finland #>    3:                                  1.62                     397 Finland #>    4:                                  1.62                     397 Finland #>    5:                                  1.62                     397 Finland #>   ---                                                                       #> 3345:                                  0.63                      83 Estonia #> 3346:                                  0.63                      83 Estonia #> 3347:                                  0.63                      83 Estonia #> 3348:                                  0.63                      83 Estonia #> 3349:                                  0.63                      83 Estonia #>       delivery_mode diet_in_first_three_days exclusive_breastfed_duration_days #>              <char>                   <char>                             <int> #>    1:       Vaginal     Mother's breast milk                               150 #>    2:       Vaginal     Mother's breast milk                               150 #>    3:       Vaginal     Mother's breast milk                               150 #>    4:       Vaginal     Mother's breast milk                               150 #>    5:       Vaginal     Mother's breast milk                               150 #>   ---                                                                          #> 3345:      Cesarean     Mother's breast milk                                 1 #> 3346:      Cesarean     Mother's breast milk                                 1 #> 3347:      Cesarean     Mother's breast milk                                 1 #> 3348:      Cesarean     Mother's breast milk                                 1 #> 3349:      Cesarean     Mother's breast milk                                 1 #>       gestational_diabetes_by_maternal_report #>                                        <char> #>    1:                                      No #>    2:                                      No #>    3:                                      No #>    4:                                      No #>    5:                                      No #>   ---                                         #> 3345:                                      No #> 3346:                                      No #> 3347:                                      No #> 3348:                                      No #> 3349:                                      No #>       glutamic_acid_decarboxylase_autoantibodies hla_risk_by_hla_haplotyping #>                                           <char>                       <int> #>    1:                                         No                           2 #>    2:                                         No                           2 #>    3:                                         No                           2 #>    4:                                         No                           2 #>    5:                                         No                           2 #>   ---                                                                        #> 3345:                                         No                           3 #> 3346:                                         No                           3 #> 3347:                                         No                           3 #> 3348:                                         No                           3 #> 3349:                                         No                           3 #>       height_minus_for_minus_age_z_minus_score insulin_autoantibodies #>                                          <num>                 <char> #>    1:                                     1.46                     No #>    2:                                     1.46                     No #>    3:                                     1.46                     No #>    4:                                     1.46                     No #>    5:                                     1.46                     No #>   ---                                                                 #> 3345:                                    -0.25                     No #> 3346:                                    -0.25                     No #> 3347:                                    -0.25                     No #> 3348:                                    -0.25                     No #> 3349:                                    -0.25                     No #>       insulinoma_minus_associated_protein_2_autoantibodies #>                                                     <char> #>    1:                                                   No #>    2:                                                   No #>    3:                                                   No #>    4:                                                   No #>    5:                                                   No #>   ---                                                      #> 3345:                                                   No #> 3346:                                                   No #> 3347:                                                   No #> 3348:                                                   No #> 3349:                                                   No #>       islet_cell_autoantibodies linear_growth_during_1st_year_cm #>                          <char>                            <num> #>    1:                        No                         29.83651 #>    2:                        No                         29.83651 #>    3:                        No                         29.83651 #>    4:                        No                         29.83651 #>    5:                        No                         29.83651 #>   ---                                                            #> 3345:                        No                         31.48248 #> 3346:                        No                         31.48248 #> 3347:                        No                         31.48248 #> 3348:                        No                         31.48248 #> 3349:                        No                         31.48248 #>       maternal_age_at_birth_months mean_linear_growth_during_1st_3_years #>                              <num>                                 <num> #>    1:                     35.75342                              16.77027 #>    2:                     35.75342                              16.77027 #>    3:                     35.75342                              16.77027 #>    4:                     35.75342                              16.77027 #>    5:                     35.75342                              16.77027 #>   ---                                                                    #> 3345:                     36.23288                              16.47863 #> 3346:                     36.23288                              16.47863 #> 3347:                     36.23288                              16.47863 #> 3348:                     36.23288                              16.47863 #> 3349:                     36.23288                              16.47863 #>       mean_weight_gain_during_1st_3_years    sex                    study_group #>                                     <num> <char>                         <char> #>    1:                            4.876532   Male             Antibiotics cohort #>    2:                            4.876532   Male             Antibiotics cohort #>    3:                            4.876532   Male             Antibiotics cohort #>    4:                            4.876532   Male             Antibiotics cohort #>    5:                            4.876532   Male             Antibiotics cohort #>   ---                                                                           #> 3345:                            4.059528   Male Three country cohort (Karelia) #> 3346:                            4.059528   Male Three country cohort (Karelia) #> 3347:                            4.059528   Male Three country cohort (Karelia) #> 3348:                            4.059528   Male Three country cohort (Karelia) #> 3349:                            4.059528   Male Three country cohort (Karelia) #>       type_1_diabetes_diagnosed urban_or_rural_site #>                          <char>              <char> #>    1:                        No               Rural #>    2:                        No               Rural #>    3:                        No               Rural #>    4:                        No               Rural #>    5:                        No               Rural #>   ---                                               #> 3345:                        No               Urban #> 3346:                        No               Urban #> 3347:                        No               Urban #> 3348:                        No               Urban #> 3349:                        No               Urban #>       weight_gain_during_1st_year_kg weight_minus_for_minus_age_z_minus_score #>                                <num>                                    <num> #>    1:                       7.886785                                     2.06 #>    2:                       7.886785                                     2.06 #>    3:                       7.886785                                     2.06 #>    4:                       7.886785                                     2.06 #>    5:                       7.886785                                     2.06 #>   ---                                                                         #> 3345:                       8.942992                                     0.29 #> 3346:                       8.942992                                     0.29 #> 3347:                       8.942992                                     0.29 #> 3348:                       8.942992                                     0.29 #> 3349:                       8.942992                                     0.29 #>       zinc_transporter_8_autoantibodies age_months Sample_Id habitat #>                                  <char>      <int>     <int>  <char> #>    1:                                No          1   3000150   Human #>    2:                                No         10   3102722   Human #>    3:                                No         12   3106237   Human #>    4:                                No         13   3106238   Human #>    5:                                No         15   3106239   Human #>   ---                                                                #> 3345:                                No         14   3117645   Human #> 3346:                                No         16   3117647   Human #> 3347:                                No         19   3119973   Human #> 3348:                                No         22   3119976   Human #> 3349:                                No          7   3116926   Human #>       host_body_habitat host_body_product host_body_site sample_type #>                  <char>            <char>         <char>      <char> #>    1:             Colon             Feces          Colon       Stool #>    2:             Colon             Feces          Colon       Stool #>    3:             Colon             Feces          Colon       Stool #>    4:             Colon             Feces          Colon       Stool #>    5:             Colon             Feces          Colon       Stool #>   ---                                                                #> 3345:             Colon             Feces          Colon       Stool #> 3346:             Colon             Feces          Colon       Stool #> 3347:             Colon             Feces          Colon       Stool #> 3348:             Colon             Feces          Colon       Stool #> 3349:             Colon             Feces          Colon       Stool getSampleMetadata(microbiomeData::DiabImmune, metadataVariables = c(\"age_months\", \"sex\")) #>       Sample_Id   Participant_Id Participant_repeated_measure_Id age_months #>           <int>           <char>                          <char>      <int> #>    1:   3000150 E000823 (Source)              E000823_1 (Source)          1 #>    2:   3102722 E000823 (Source)             E000823_10 (Source)         10 #>    3:   3106237 E000823 (Source)             E000823_12 (Source)         12 #>    4:   3106238 E000823 (Source)             E000823_13 (Source)         13 #>    5:   3106239 E000823 (Source)             E000823_15 (Source)         15 #>   ---                                                                       #> 3345:   3117645 T029922 (Source)             T029922_14 (Source)         14 #> 3346:   3117647 T029922 (Source)             T029922_16 (Source)         16 #> 3347:   3119973 T029922 (Source)             T029922_19 (Source)         19 #> 3348:   3119976 T029922 (Source)             T029922_22 (Source)         22 #> 3349:   3116926 T029922 (Source)              T029922_7 (Source)          7 #>          sex #>       <char> #>    1:   Male #>    2:   Male #>    3:   Male #>    4:   Male #>    5:   Male #>   ---        #> 3345:   Male #> 3346:   Male #> 3347:   Male #> 3348:   Male #> 3349:   Male"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadataIdColumns-MbioDataset-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","title":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","text":"Get names record ancestor id columns sample metadata MbioDataset object.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadataIdColumns-MbioDataset-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","text":"","code":"# S4 method for MbioDataset getSampleMetadataIdColumns(object)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadataIdColumns-MbioDataset-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","text":"object MbioDataset","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getSampleMetadataIdColumns-MbioDataset-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Sample Metadata Id Column Names — getSampleMetadataIdColumns,MbioDataset-method","text":"character vector id column names","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Microbiome Dataset Variables — getVariables","title":"Get Microbiome Dataset Variables — getVariables","text":"Get variables Microbiome Dataset names. requested variables belong collection metadata. returned data.table contain requested variables columns appropriate identifiers. one requested variables returned, warning printed.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Microbiome Dataset Variables — getVariables","text":"","code":"getVariables(object, variables)  # S4 method for MbioDataset getVariables(object, variables)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Microbiome Dataset Variables — getVariables","text":"object Microbiome Dataset variables names variables return. named list names collection names values variable names collection. case metadata variables, name \"metadata\".","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Microbiome Dataset Variables — getVariables","text":"data.table requested variables","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/getVariables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Microbiome Dataset Variables — getVariables","text":"","code":"getCollectionVariableNames(microbiomeData::DiabImmune, \"16S (V4) Genus\") #>   [1] \"28-4\"                                                                                                                       #>   [2] \"Abiotrophia\"                                                                                                                #>   [3] \"Acetanaerobacterium\"                                                                                                        #>   [4] \"Acetobacter\"                                                                                                                #>   [5] \"Achromobacter\"                                                                                                              #>   [6] \"Acidaminococcus\"                                                                                                            #>   [7] \"Acidibacter\"                                                                                                                #>   [8] \"Acidiphilium\"                                                                                                               #>   [9] \"Acidipropionibacterium\"                                                                                                     #>  [10] \"Acidocella\"                                                                                                                 #>  [11] \"Acidovorax\"                                                                                                                 #>  [12] \"Acinetobacter\"                                                                                                              #>  [13] \"Actinobacillus\"                                                                                                             #>  [14] \"Actinobaculum\"                                                                                                              #>  [15] \"Actinomyces\"                                                                                                                #>  [16] \"Actinotignum\"                                                                                                               #>  [17] \"Adlercreutzia\"                                                                                                              #>  [18] \"Aerococcus\"                                                                                                                 #>  [19] \"Aeromonas\"                                                                                                                  #>  [20] \"Afipia\"                                                                                                                     #>  [21] \"Agathobacter\"                                                                                                               #>  [22] \"Aggregatibacter\"                                                                                                            #>  [23] \"Akkermansia\"                                                                                                                #>  [24] \"Alcaligenes\"                                                                                                                #>  [25] \"Alicycliphilus\"                                                                                                             #>  [26] \"Alistipes\"                                                                                                                  #>  [27] \"Allisonella\"                                                                                                                #>  [28] \"Allobaculum\"                                                                                                                #>  [29] \"Alloprevotella\"                                                                                                             #>  [30] \"Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium\"                                                                         #>  [31] \"Alloscardovia\"                                                                                                              #>  [32] \"Amaricoccus\"                                                                                                                #>  [33] \"Amnibacterium\"                                                                                                              #>  [34] \"Anaerobium\"                                                                                                                 #>  [35] \"Anaerocolumna\"                                                                                                              #>  [36] \"Anaerofilum\"                                                                                                                #>  [37] \"Anaerofustis\"                                                                                                               #>  [38] \"Anaeroglobus\"                                                                                                               #>  [39] \"Anaeromyxobacter\"                                                                                                           #>  [40] \"Anaeroplasma\"                                                                                                               #>  [41] \"Anaerosporobacter\"                                                                                                          #>  [42] \"Anaerosporomusa\"                                                                                                            #>  [43] \"Anaerostignum\"                                                                                                              #>  [44] \"Anaerostipes\"                                                                                                               #>  [45] \"Anaerotruncus\"                                                                                                              #>  [46] \"Angelakisella\"                                                                                                              #>  [47] \"Angustibacter\"                                                                                                              #>  [48] \"Anoxybacillus\"                                                                                                              #>  [49] \"Aquabacterium\"                                                                                                              #>  [50] \"Aquamonas\"                                                                                                                  #>  [51] \"Arcanobacterium\"                                                                                                            #>  [52] \"Arcticibacter\"                                                                                                              #>  [53] \"Asaccharospora\"                                                                                                             #>  [54] \"Asaia\"                                                                                                                      #>  [55] \"Asinibacterium\"                                                                                                             #>  [56] \"Asteroleplasma\"                                                                                                             #>  [57] \"Asticcacaulis\"                                                                                                              #>  [58] \"Atopobium\"                                                                                                                  #>  [59] \"Aureimonas\"                                                                                                                 #>  [60] \"Azospira\"                                                                                                                   #>  [61] \"Bacillus\"                                                                                                                   #>  [62] \"Bacteriovorax\"                                                                                                              #>  [63] \"Bacteroides\"                                                                                                                #>  [64] \"Barnesiella\"                                                                                                                #>  [65] \"Bdellovibrio\"                                                                                                               #>  [66] \"Belnapia\"                                                                                                                   #>  [67] \"Bergeyella\"                                                                                                                 #>  [68] \"Bifidobacterium\"                                                                                                            #>  [69] \"Bilophila\"                                                                                                                  #>  [70] \"Blastomonas\"                                                                                                                #>  [71] \"Blautia\"                                                                                                                    #>  [72] \"Bordetella\"                                                                                                                 #>  [73] \"Bosea\"                                                                                                                      #>  [74] \"Brachybacterium\"                                                                                                            #>  [75] \"Bradyrhizobium\"                                                                                                             #>  [76] \"Brevibacterium\"                                                                                                             #>  [77] \"Brevundimonas\"                                                                                                              #>  [78] \"Brucella\"                                                                                                                   #>  [79] \"Bulleidia\"                                                                                                                  #>  [80] \"Burkholderia-Caballeronia-Paraburkholderia\"                                                                                 #>  [81] \"Buttiauxella\"                                                                                                               #>  [82] \"Butyricicoccus\"                                                                                                             #>  [83] \"Butyricimonas\"                                                                                                              #>  [84] \"CAG-352\"                                                                                                                    #>  [85] \"CAG-56\"                                                                                                                     #>  [86] \"CAG-873\"                                                                                                                    #>  [87] \"CHKCI001\"                                                                                                                   #>  [88] \"CHKCI002\"                                                                                                                   #>  [89] \"CL500-29 marine group\"                                                                                                      #>  [90] \"Caloribacterium\"                                                                                                            #>  [91] \"Campylobacter\"                                                                                                              #>  [92] \"Candidatus Arthromitus\"                                                                                                     #>  [93] \"Candidatus Metachlamydia\"                                                                                                   #>  [94] \"Candidatus Obscuribacter\"                                                                                                   #>  [95] \"Candidatus Phytoplasma\"                                                                                                     #>  [96] \"Candidatus Soleaferrea\"                                                                                                     #>  [97] \"Candidatus Stoquefichus\"                                                                                                    #>  [98] \"Capnocytophaga\"                                                                                                             #>  [99] \"Caproiciproducens\"                                                                                                          #> [100] \"Cardiobacterium\"                                                                                                            #> [101] \"Carnobacterium\"                                                                                                             #> [102] \"Caryophanon\"                                                                                                                #> [103] \"Castellaniella\"                                                                                                             #> [104] \"Catabacter\"                                                                                                                 #> [105] \"Catenibacillus\"                                                                                                             #> [106] \"Catenibacterium\"                                                                                                            #> [107] \"Catenisphaera\"                                                                                                              #> [108] \"Catonella\"                                                                                                                  #> [109] \"Caulobacter\"                                                                                                                #> [110] \"Cellulomonas\"                                                                                                               #> [111] \"Cellulosilyticum\"                                                                                                           #> [112] \"Cellvibrio\"                                                                                                                 #> [113] \"Centipeda\"                                                                                                                  #> [114] \"Cetobacterium\"                                                                                                              #> [115] \"Christensenella\"                                                                                                            #> [116] \"Christensenellaceae R-7 group\"                                                                                              #> [117] \"Chryseobacterium\"                                                                                                           #> [118] \"Chryseomicrobium\"                                                                                                           #> [119] \"Chungangia\"                                                                                                                 #> [120] \"Citrobacter\"                                                                                                                #> [121] \"Clavibacter\"                                                                                                                #> [122] \"Cloacibacillus\"                                                                                                             #> [123] \"Cloacibacterium\"                                                                                                            #> [124] \"Clostridioides\"                                                                                                             #> [125] \"Clostridium sensu stricto 1\"                                                                                                #> [126] \"Clostridium sensu stricto 12\"                                                                                               #> [127] \"Clostridium sensu stricto 13\"                                                                                               #> [128] \"Clostridium sensu stricto 15\"                                                                                               #> [129] \"Clostridium sensu stricto 18\"                                                                                               #> [130] \"Clostridium sensu stricto 2\"                                                                                                #> [131] \"Clostridium sensu stricto 3\"                                                                                                #> [132] \"Clostridium sensu stricto 4\"                                                                                                #> [133] \"Clostridium sensu stricto 6\"                                                                                                #> [134] \"Colidextribacter\"                                                                                                           #> [135] \"Collinsella\"                                                                                                                #> [136] \"Comamonas\"                                                                                                                  #> [137] \"Conexibacter\"                                                                                                               #> [138] \"Conservatibacter\"                                                                                                           #> [139] \"Coprobacillus\"                                                                                                              #> [140] \"Coprobacter\"                                                                                                                #> [141] \"Coprococcus\"                                                                                                                #> [142] \"Coriobacteriaceae UCG-002\"                                                                                                  #> [143] \"Corynebacterium\"                                                                                                            #> [144] \"Cosenzaea\"                                                                                                                  #> [145] \"Criibacterium\"                                                                                                              #> [146] \"Cryptobacterium\"                                                                                                            #> [147] \"Curvibacter\"                                                                                                                #> [148] \"Cutibacterium\"                                                                                                              #> [149] \"Cytophaga\"                                                                                                                  #> [150] \"DNF00809\"                                                                                                                   #> [151] \"DSSD61\"                                                                                                                     #> [152] \"DTU089\"                                                                                                                     #> [153] \"Dechloromonas\"                                                                                                              #> [154] \"Defluviicoccus\"                                                                                                             #> [155] \"Defluviitaleaceae UCG-011\"                                                                                                  #> [156] \"Delftia\"                                                                                                                    #> [157] \"Denitrobacterium\"                                                                                                           #> [158] \"Dermabacter\"                                                                                                                #> [159] \"Desemzia\"                                                                                                                   #> [160] \"Desulfovibrio\"                                                                                                              #> [161] \"Devosia\"                                                                                                                    #> [162] \"Dialister\"                                                                                                                  #> [163] \"Diaphorobacter\"                                                                                                             #> [164] \"Dickeya\"                                                                                                                    #> [165] \"Dielma\"                                                                                                                     #> [166] \"Dietzia\"                                                                                                                    #> [167] \"Dinghuibacter\"                                                                                                              #> [168] \"Diplosphaera\"                                                                                                               #> [169] \"Dolosigranulum\"                                                                                                             #> [170] \"Dorea\"                                                                                                                      #> [171] \"Duganella\"                                                                                                                  #> [172] \"Dysgonomonas\"                                                                                                               #> [173] \"Edaphobaculum\"                                                                                                              #> [174] \"Eggerthella\"                                                                                                                #> [175] \"Eikenella\"                                                                                                                  #> [176] \"Eisenbergiella\"                                                                                                             #> [177] \"Empedobacter\"                                                                                                               #> [178] \"Endobacter\"                                                                                                                 #> [179] \"Enhydrobacter\"                                                                                                              #> [180] \"Enterobacter\"                                                                                                               #> [181] \"Enterococcus\"                                                                                                               #> [182] \"Enterorhabdus\"                                                                                                              #> [183] \"Enteroscipio\"                                                                                                               #> [184] \"Epulopiscium\"                                                                                                               #> [185] \"Erwinia\"                                                                                                                    #> [186] \"Erysipelatoclostridium\"                                                                                                     #> [187] \"Erysipelotrichaceae UCG-003\"                                                                                                #> [188] \"Erysipelotrichaceae UCG-006\"                                                                                                #> [189] \"Escherichia/Shigella\"                                                                                                       #> [190] \"Eubacterium\"                                                                                                                #> [191] \"Exiguobacterium\"                                                                                                            #> [192] \"Extensimonas\"                                                                                                               #> [193] \"F0058\"                                                                                                                      #> [194] \"F0332\"                                                                                                                      #> [195] \"FD2005\"                                                                                                                     #> [196] \"Facklamia\"                                                                                                                  #> [197] \"Faecalibacterium\"                                                                                                           #> [198] \"Faecalicoccus\"                                                                                                              #> [199] \"Faecalitalea\"                                                                                                               #> [200] \"Falsochrobactrum\"                                                                                                           #> [201] \"Family XIII AD3011 group\"                                                                                                   #> [202] \"Family XIII UCG-001\"                                                                                                        #> [203] \"Fictibacillus\"                                                                                                              #> [204] \"Flaviflexus\"                                                                                                                #> [205] \"Flavihumibacter\"                                                                                                            #> [206] \"Flavobacterium\"                                                                                                             #> [207] \"Flavonifractor\"                                                                                                             #> [208] \"Floricoccus\"                                                                                                                #> [209] \"Fluviicola\"                                                                                                                 #> [210] \"Fournierella\"                                                                                                               #> [211] \"Fretibacterium\"                                                                                                             #> [212] \"Frisingicoccus\"                                                                                                             #> [213] \"Fructobacillus\"                                                                                                             #> [214] \"Fusicatenibacter\"                                                                                                           #> [215] \"Fusobacterium\"                                                                                                              #> [216] \"GCA-900066575\"                                                                                                              #> [217] \"GCA-900066755\"                                                                                                              #> [218] \"Galbibacter\"                                                                                                                #> [219] \"Garciella\"                                                                                                                  #> [220] \"Gemella\"                                                                                                                    #> [221] \"Gemmata\"                                                                                                                    #> [222] \"Geobacillus\"                                                                                                                #> [223] \"Gluconobacter\"                                                                                                              #> [224] \"Glutamicibacter\"                                                                                                            #> [225] \"Gordonia\"                                                                                                                   #> [226] \"Gordonibacter\"                                                                                                              #> [227] \"Granulicatella\"                                                                                                             #> [228] \"Gulbenkiania\"                                                                                                               #> [229] \"Haemophilus\"                                                                                                                #> [230] \"Hafnia-Obesumbacterium\"                                                                                                     #> [231] \"Halomonas\"                                                                                                                  #> [232] \"Haoranjiania\"                                                                                                               #> [233] \"Harryflintia\"                                                                                                               #> [234] \"Helicobacter\"                                                                                                               #> [235] \"Hephaestia\"                                                                                                                 #> [236] \"Herbaspirillum\"                                                                                                             #> [237] \"Herbinix\"                                                                                                                   #> [238] \"Holdemanella\"                                                                                                               #> [239] \"Holdemania\"                                                                                                                 #> [240] \"Howardella\"                                                                                                                 #> [241] \"Hungatella\"                                                                                                                 #> [242] \"Hydrocarboniphaga\"                                                                                                          #> [243] \"Hydrogenophilus\"                                                                                                            #> [244] \"Hymenobacter\"                                                                                                               #> [245] \"Iamia\"                                                                                                                      #> [246] \"Ignavigranum\"                                                                                                               #> [247] \"Incertae Sedis [EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Lachnospirales_Lachnospiraceae_Incertae_Sedis]\"               #> [248] \"Incertae Sedis [EUPATH_0009256_Bacteria_Firmicutes_Clostridia_Oscillospirales_Ruminococcaceae_Incertae_Sedis]\"              #> [249] \"Incertae Sedis [EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Erwiniaceae_Incertae_Sedis]\"    #> [250] \"Incertae Sedis [EUPATH_0009256_Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacterales_Morganellaceae_Incertae_Sedis]\" #> [251] \"Intestinibacter\"                                                                                                            #> [252] \"Intestinimonas\"                                                                                                             #> [253] \"Janthinobacterium\"                                                                                                          #> [254] \"Jeotgalicoccus\"                                                                                                             #> [255] \"Johnsonella\"                                                                                                                #> [256] \"Kingella\"                                                                                                                   #> [257] \"Klebsiella\"                                                                                                                 #> [258] \"Knoellia\"                                                                                                                   #> [259] \"Kocuria\"                                                                                                                    #> [260] \"Kosakonia\"                                                                                                                  #> [261] \"Lachnoanaerobaculum\"                                                                                                        #> [262] \"Lachnobacterium\"                                                                                                            #> [263] \"Lachnoclostridium\"                                                                                                          #> [264] \"Lachnospira\"                                                                                                                #> [265] \"Lachnospiraceae AC2044 group\"                                                                                               #> [266] \"Lachnospiraceae FCS020 group\"                                                                                               #> [267] \"Lachnospiraceae FE2018 group\"                                                                                               #> [268] \"Lachnospiraceae NC2004 group\"                                                                                               #> [269] \"Lachnospiraceae ND3007 group\"                                                                                               #> [270] \"Lachnospiraceae NK4A136 group\"                                                                                              #> [271] \"Lachnospiraceae UCG-001\"                                                                                                    #> [272] \"Lachnospiraceae UCG-002\"                                                                                                    #> [273] \"Lachnospiraceae UCG-003\"                                                                                                    #> [274] \"Lachnospiraceae UCG-004\"                                                                                                    #> [275] \"Lachnospiraceae UCG-008\"                                                                                                    #> [276] \"Lachnospiraceae UCG-009\"                                                                                                    #> [277] \"Lachnospiraceae UCG-010\"                                                                                                    #> [278] \"Lachnospiraceae XPB1014 group\"                                                                                              #> [279] \"Lachnotalea\"                                                                                                                #> [280] \"Lactobacillus\"                                                                                                              #> [281] \"Lactococcus\"                                                                                                                #> [282] \"Lactonifactor\"                                                                                                              #> [283] \"Lautropia\"                                                                                                                  #> [284] \"Lawsonella\"                                                                                                                 #> [285] \"Legionella\"                                                                                                                 #> [286] \"Leptotrichia\"                                                                                                               #> [287] \"Leuconostoc\"                                                                                                                #> [288] \"Libanicoccus\"                                                                                                               #> [289] \"Luteimonas\"                                                                                                                 #> [290] \"Luteolibacter\"                                                                                                              #> [291] \"Macellibacteroides\"                                                                                                         #> [292] \"Macrococcus\"                                                                                                                #> [293] \"Mailhella\"                                                                                                                  #> [294] \"Mannheimia\"                                                                                                                 #> [295] \"Marinilactibacillus\"                                                                                                        #> [296] \"Marmoricola\"                                                                                                                #> [297] \"Martelella\"                                                                                                                 #> [298] \"Marvinbryantia\"                                                                                                             #> [299] \"Massilia\"                                                                                                                   #> [300] \"Megamonas\"                                                                                                                  #> [301] \"Megasphaera\"                                                                                                                #> [302] \"Merdibacter\"                                                                                                                #> [303] \"Mesorhizobium\"                                                                                                              #> [304] \"Methanobrevibacter\"                                                                                                         #> [305] \"Methylibium\"                                                                                                                #> [306] \"Methylobacillus\"                                                                                                            #> [307] \"Methylobacterium-Methylorubrum\"                                                                                             #> [308] \"Methylorosula\"                                                                                                              #> [309] \"Methylotenera\"                                                                                                              #> [310] \"Micrococcus\"                                                                                                                #> [311] \"Mitsuokella\"                                                                                                                #> [312] \"Mobiluncus\"                                                                                                                 #> [313] \"Mogibacterium\"                                                                                                              #> [314] \"Moheibacter\"                                                                                                                #> [315] \"Mongoliitalea\"                                                                                                              #> [316] \"Monoglobus\"                                                                                                                 #> [317] \"Moraxella\"                                                                                                                  #> [318] \"Morganella\"                                                                                                                 #> [319] \"Moryella\"                                                                                                                   #> [320] \"Mucilaginibacter\"                                                                                                           #> [321] \"Muribaculum\"                                                                                                                #> [322] \"Murimonas\"                                                                                                                  #> [323] \"Mycobacterium\"                                                                                                              #> [324] \"Mycoplasma\"                                                                                                                 #> [325] \"Myxococcus\"                                                                                                                 #> [326] \"NK4A214 group\"                                                                                                              #> [327] \"Nakamurella\"                                                                                                                #> [328] \"Nannocystis\"                                                                                                                #> [329] \"Necropsobacter\"                                                                                                             #> [330] \"Negativibacillus\"                                                                                                           #> [331] \"Negativicoccus\"                                                                                                             #> [332] \"Neisseria\"                                                                                                                  #> [333] \"Neochlamydia\"                                                                                                               #> [334] \"Neomegalonema\"                                                                                                              #> [335] \"Neorhizobium\"                                                                                                               #> [336] \"Neoscardovia\"                                                                                                               #> [337] \"Nesterenkonia\"                                                                                                              #> [338] \"Nocardioides\"                                                                                                               #> [339] \"Nocardiopsis\"                                                                                                               #> [340] \"Novosphingobium\"                                                                                                            #> [341] \"Oceanivirga\"                                                                                                                #> [342] \"Oceanobacillus\"                                                                                                             #> [343] \"Ochrobactrum\"                                                                                                               #> [344] \"Odoribacter\"                                                                                                                #> [345] \"Olsenella\"                                                                                                                  #> [346] \"Oribacterium\"                                                                                                               #> [347] \"Oscillibacter\"                                                                                                              #> [348] \"Oscillospira\"                                                                                                               #> [349] \"Ottowia\"                                                                                                                    #> [350] \"Oxalobacter\"                                                                                                                #> [351] \"Oxobacter\"                                                                                                                  #> [352] \"P3OB-42\"                                                                                                                    #> [353] \"Paenibacillus\"                                                                                                              #> [354] \"Paeniclostridium\"                                                                                                           #> [355] \"Paenisporosarcina\"                                                                                                          #> [356] \"Paludicola\"                                                                                                                 #> [357] \"Papillibacter\"                                                                                                              #> [358] \"Parabacteroides\"                                                                                                            #> [359] \"Paraclostridium\"                                                                                                            #> [360] \"Paracoccus\"                                                                                                                 #> [361] \"Paramesorhizobium\"                                                                                                          #> [362] \"Paraprevotella\"                                                                                                             #> [363] \"Parapusillimonas\"                                                                                                           #> [364] \"Parascardovia\"                                                                                                              #> [365] \"Parasutterella\"                                                                                                             #> [366] \"Parvibacter\"                                                                                                                #> [367] \"Pasteurella\"                                                                                                                #> [368] \"Paucibacter\"                                                                                                                #> [369] \"Pediococcus\"                                                                                                                #> [370] \"Pedobacter\"                                                                                                                 #> [371] \"Peptoclostridium\"                                                                                                           #> [372] \"Peptococcus\"                                                                                                                #> [373] \"Peptostreptococcus\"                                                                                                         #> [374] \"Perlucidibaca\"                                                                                                              #> [375] \"Phascolarctobacterium\"                                                                                                      #> [376] \"Phaseolibacter\"                                                                                                             #> [377] \"Phocea\"                                                                                                                     #> [378] \"Phoenicibacter\"                                                                                                             #> [379] \"Phyllobacterium\"                                                                                                            #> [380] \"Piscinibacter\"                                                                                                              #> [381] \"Planifilum\"                                                                                                                 #> [382] \"Plesiomonas\"                                                                                                                #> [383] \"Plot4-2H12\"                                                                                                                 #> [384] \"Pluralibacter\"                                                                                                              #> [385] \"Polaromonas\"                                                                                                                #> [386] \"Porphyromonas\"                                                                                                              #> [387] \"Prevotella\"                                                                                                                 #> [388] \"Prevotellaceae NK3B31 group\"                                                                                                #> [389] \"Prevotellaceae UCG-001\"                                                                                                     #> [390] \"Propionibacterium\"                                                                                                          #> [391] \"Prosthecobacter\"                                                                                                            #> [392] \"Proteus\"                                                                                                                    #> [393] \"Providencia\"                                                                                                                #> [394] \"Pseudacidovorax\"                                                                                                            #> [395] \"Pseudaminobacter\"                                                                                                           #> [396] \"Pseudocitrobacter\"                                                                                                          #> [397] \"Pseudoflavonifractor\"                                                                                                       #> [398] \"Pseudoglutamicibacter\"                                                                                                      #> [399] \"Pseudomonas\"                                                                                                                #> [400] \"Pseudoramibacter\"                                                                                                           #> [401] \"Pseudoxanthomonas\"                                                                                                          #> [402] \"Psychrobacter\"                                                                                                              #> [403] \"Pygmaiobacter\"                                                                                                              #> [404] \"Pyramidobacter\"                                                                                                             #> [405] \"Qipengyuania\"                                                                                                               #> [406] \"Ralstonia\"                                                                                                                  #> [407] \"Raoultella\"                                                                                                                 #> [408] \"Raoultibacter\"                                                                                                              #> [409] \"Reyranella\"                                                                                                                 #> [410] \"Rhizorhapis\"                                                                                                                #> [411] \"Rhodanobacter\"                                                                                                              #> [412] \"Rhodobacter\"                                                                                                                #> [413] \"Rhodococcus\"                                                                                                                #> [414] \"Rikenella\"                                                                                                                  #> [415] \"Rikenellaceae RC9 gut group\"                                                                                                #> [416] \"Rivicola\"                                                                                                                   #> [417] \"Robinsoniella\"                                                                                                              #> [418] \"Rodentibacter\"                                                                                                              #> [419] \"Romboutsia\"                                                                                                                 #> [420] \"Roseburia\"                                                                                                                  #> [421] \"Roseisolibacter\"                                                                                                            #> [422] \"Rothia\"                                                                                                                     #> [423] \"Rubellimicrobium\"                                                                                                           #> [424] \"Ruminococcus\"                                                                                                               #> [425] \"Rummeliibacillus\"                                                                                                           #> [426] \"S5-A14a\"                                                                                                                    #> [427] \"SH-PL14\"                                                                                                                    #> [428] \"Saccharothrix\"                                                                                                              #> [429] \"Salinimicrobium\"                                                                                                            #> [430] \"Salinisphaera\"                                                                                                              #> [431] \"Salipaludibacillus\"                                                                                                         #> [432] \"Salmonella\"                                                                                                                 #> [433] \"Sanguibacteroides\"                                                                                                          #> [434] \"Sarcina\"                                                                                                                    #> [435] \"Scardovia\"                                                                                                                  #> [436] \"Sedimentibacter\"                                                                                                            #> [437] \"Segetibacter\"                                                                                                               #> [438] \"Selenomonas\"                                                                                                                #> [439] \"Sellimonas\"                                                                                                                 #> [440] \"Senegalimassilia\"                                                                                                           #> [441] \"Serratia\"                                                                                                                   #> [442] \"Shimwellia\"                                                                                                                 #> [443] \"Shuttleworthia\"                                                                                                             #> [444] \"Slackia\"                                                                                                                    #> [445] \"Sneathia\"                                                                                                                   #> [446] \"Solibacillus\"                                                                                                               #> [447] \"Solobacterium\"                                                                                                              #> [448] \"Sphingoaurantiacus\"                                                                                                         #> [449] \"Sphingobacterium\"                                                                                                           #> [450] \"Sphingobium\"                                                                                                                #> [451] \"Sphingomonas\"                                                                                                               #> [452] \"Sphingopyxis\"                                                                                                               #> [453] \"Sporolactobacillus\"                                                                                                         #> [454] \"Staphylococcus\"                                                                                                             #> [455] \"Stenotrophomonas\"                                                                                                           #> [456] \"Stomatobaculum\"                                                                                                             #> [457] \"Streptobacillus\"                                                                                                            #> [458] \"Streptococcus\"                                                                                                              #> [459] \"Subdoligranulum\"                                                                                                            #> [460] \"Succinatimonas\"                                                                                                             #> [461] \"Succiniclasticum\"                                                                                                           #> [462] \"Succinivibrio\"                                                                                                              #> [463] \"Sulfurospirillum\"                                                                                                           #> [464] \"Sutterella\"                                                                                                                 #> [465] \"Synergistes\"                                                                                                                #> [466] \"TM7x\"                                                                                                                       #> [467] \"Tannerella\"                                                                                                                 #> [468] \"Tatumella\"                                                                                                                  #> [469] \"Tepidimonas\"                                                                                                                #> [470] \"Tepidiphilus\"                                                                                                               #> [471] \"Terrisporobacter\"                                                                                                           #> [472] \"Tetragenococcus\"                                                                                                            #> [473] \"Thermus\"                                                                                                                    #> [474] \"Timonella\"                                                                                                                  #> [475] \"Tolumonas\"                                                                                                                  #> [476] \"Trabulsiella\"                                                                                                               #> [477] \"Tropheryma\"                                                                                                                 #> [478] \"Trueperella\"                                                                                                                #> [479] \"Turicibacter\"                                                                                                               #> [480] \"Tuzzerella\"                                                                                                                 #> [481] \"Tyzzerella\"                                                                                                                 #> [482] \"UBA1819\"                                                                                                                    #> [483] \"UC5-1-2E3\"                                                                                                                  #> [484] \"UCG-002\"                                                                                                                    #> [485] \"UCG-003\"                                                                                                                    #> [486] \"UCG-004\"                                                                                                                    #> [487] \"UCG-005\"                                                                                                                    #> [488] \"UCG-007\"                                                                                                                    #> [489] \"UCG-008\"                                                                                                                    #> [490] \"UCG-009\"                                                                                                                    #> [491] \"Ureibacillus\"                                                                                                               #> [492] \"Varibaculum\"                                                                                                                #> [493] \"Variovorax\"                                                                                                                 #> [494] \"Veillonella\"                                                                                                                #> [495] \"Verticiella\"                                                                                                                #> [496] \"Victivallis\"                                                                                                                #> [497] \"Vulcaniibacterium\"                                                                                                          #> [498] \"Weissella\"                                                                                                                  #> [499] \"Xanthomonas\"                                                                                                                #> [500] \"Yersinia\"                                                                                                                   #> [501] \"Yokenella\"                                                                                                                  #> [502] \"Zoogloea\"                                                                                                                   #> [503] \"[Bacteroides] pectinophilus group\"                                                                                          #> [504] \"[Clostridium] innocuum group\"                                                                                               #> [505] \"[Eubacterium] brachy group\"                                                                                                 #> [506] \"[Eubacterium] eligens group\"                                                                                                #> [507] \"[Eubacterium] fissicatena group\"                                                                                            #> [508] \"[Eubacterium] hallii group\"                                                                                                 #> [509] \"[Eubacterium] nodatum group\"                                                                                                #> [510] \"[Eubacterium] oxidoreducens group\"                                                                                          #> [511] \"[Eubacterium] ruminantium group\"                                                                                            #> [512] \"[Eubacterium] siraeum group\"                                                                                                #> [513] \"[Eubacterium] ventriosum group\"                                                                                             #> [514] \"[Eubacterium] xylanophilum group\"                                                                                           #> [515] \"[Ruminococcus] gauvreauii group\"                                                                                            #> [516] \"[Ruminococcus] gnavus group\"                                                                                                #> [517] \"[Ruminococcus] torques group\"                                                                                               #> [518] \"unclassified 0319-6G20\"                                                                                                     #> [519] \"unclassified 67-14\"                                                                                                         #> [520] \"unclassified A0839\"                                                                                                         #> [521] \"unclassified Acetobacteraceae\"                                                                                              #> [522] \"unclassified Acidaminococcaceae\"                                                                                            #> [523] \"unclassified Actinobacteria\"                                                                                                #> [524] \"unclassified Actinomycetaceae\"                                                                                              #> [525] \"unclassified Aeromonadales\"                                                                                                 #> [526] \"unclassified Anaerococcus\"                                                                                                  #> [527] \"unclassified Anaerosalibacter\"                                                                                              #> [528] \"unclassified Anaerovoracaceae\"                                                                                              #> [529] \"unclassified Armatimonadales\"                                                                                               #> [530] \"unclassified Atopobiaceae\"                                                                                                  #> [531] \"unclassified Bacillaceae\"                                                                                                   #> [532] \"unclassified Bacillales\"                                                                                                    #> [533] \"unclassified Bacilli\"                                                                                                       #> [534] \"unclassified Bacteroidales\"                                                                                                 #> [535] \"unclassified Bacteroidia\"                                                                                                   #> [536] \"unclassified Barnesiellaceae\"                                                                                               #> [537] \"unclassified Bifidobacteriaceae\"                                                                                            #> [538] \"unclassified Burkholderiales\"                                                                                               #> [539] \"unclassified Butyricicoccaceae\"                                                                                             #> [540] \"unclassified Caloramatoraceae\"                                                                                              #> [541] \"unclassified Carnobacteriaceae\"                                                                                             #> [542] \"unclassified Caulobacteraceae\"                                                                                              #> [543] \"unclassified Chloroplast\"                                                                                                   #> [544] \"unclassified Christensenellaceae\"                                                                                           #> [545] \"unclassified Chroococcidiopsaceae\"                                                                                          #> [546] \"unclassified Clostridia UCG-014\"                                                                                            #> [547] \"unclassified Clostridia\"                                                                                                    #> [548] \"unclassified Clostridia vadinBB60 group\"                                                                                    #> [549] \"unclassified Clostridiaceae\"                                                                                                #> [550] \"unclassified Clostridiales\"                                                                                                 #> [551] \"unclassified Comamonadaceae\"                                                                                                #> [552] \"unclassified Coriobacteriales Incertae Sedis\"                                                                               #> [553] \"unclassified Coriobacteriales\"                                                                                              #> [554] \"unclassified Corynebacteriaceae\"                                                                                            #> [555] \"unclassified Desulfovibrionaceae\"                                                                                           #> [556] \"unclassified Devosiaceae\"                                                                                                   #> [557] \"unclassified Diplorickettsiaceae\"                                                                                           #> [558] \"unclassified Eggerthellaceae\"                                                                                               #> [559] \"unclassified Enterobacterales\"                                                                                              #> [560] \"unclassified Enterobacteriaceae\"                                                                                            #> [561] \"unclassified Enterococcaceae\"                                                                                               #> [562] \"unclassified Erwiniaceae\"                                                                                                   #> [563] \"unclassified Erysipelatoclostridiaceae\"                                                                                     #> [564] \"unclassified Erysipelotrichaceae\"                                                                                           #> [565] \"unclassified Erysipelotrichales\"                                                                                            #> [566] \"unclassified Ethanoligenenaceae\"                                                                                            #> [567] \"unclassified Eubacteriaceae\"                                                                                                #> [568] \"unclassified Ezakiella\"                                                                                                     #> [569] \"unclassified Fastidiosipila\"                                                                                                #> [570] \"unclassified Fenollaria\"                                                                                                    #> [571] \"unclassified Fimbriimonadaceae\"                                                                                             #> [572] \"unclassified Finegoldia\"                                                                                                    #> [573] \"unclassified Firmicutes\"                                                                                                    #> [574] \"unclassified Flavobacteriaceae\"                                                                                             #> [575] \"unclassified Flavobacteriales\"                                                                                              #> [576] \"unclassified Fusobacteriaceae\"                                                                                              #> [577] \"unclassified Gaiellales\"                                                                                                    #> [578] \"unclassified Gallicola\"                                                                                                     #> [579] \"unclassified Gammaproteobacteria\"                                                                                           #> [580] \"unclassified Gastranaerophilales\"                                                                                           #> [581] \"unclassified Gemmataceae\"                                                                                                   #> [582] \"unclassified Hungateiclostridiaceae\"                                                                                        #> [583] \"unclassified Hydrogenoanaerobacterium\"                                                                                      #> [584] \"unclassified Izemoplasmatales\"                                                                                              #> [585] \"unclassified JI49D030\"                                                                                                      #> [586] \"unclassified KD3-93\"                                                                                                        #> [587] \"unclassified Kapabacteriales\"                                                                                               #> [588] \"unclassified Lachnospiraceae\"                                                                                               #> [589] \"unclassified Lachnospirales\"                                                                                                #> [590] \"unclassified Lactobacillales\"                                                                                               #> [591] \"unclassified Leuconostocaceae\"                                                                                              #> [592] \"unclassified Lineage IV\"                                                                                                    #> [593] \"unclassified MAT-CR-H4-C10\"                                                                                                 #> [594] \"unclassified Methylococcaceae\"                                                                                              #> [595] \"unclassified Micavibrionales\"                                                                                               #> [596] \"unclassified Microbacteriaceae\"                                                                                             #> [597] \"unclassified Micrococcaceae\"                                                                                                #> [598] \"unclassified Micrococcales\"                                                                                                 #> [599] \"unclassified Mitochondria\"                                                                                                  #> [600] \"unclassified Moraxellaceae\"                                                                                                 #> [601] \"unclassified Murdochiella\"                                                                                                  #> [602] \"unclassified Muribaculaceae\"                                                                                                #> [603] \"unclassified NS9 marine group\"                                                                                              #> [604] \"unclassified Neisseriaceae\"                                                                                                 #> [605] \"unclassified OLB14\"                                                                                                         #> [606] \"unclassified Opitutales\"                                                                                                    #> [607] \"unclassified Oscillospiraceae\"                                                                                              #> [608] \"unclassified Oscillospirales\"                                                                                               #> [609] \"unclassified Oxalobacteraceae\"                                                                                              #> [610] \"unclassified P5D1-392\"                                                                                                      #> [611] \"unclassified PLTA13\"                                                                                                        #> [612] \"unclassified Paenibacillaceae\"                                                                                              #> [613] \"unclassified Paracaedibacteraceae\"                                                                                          #> [614] \"unclassified Parachlamydiaceae\"                                                                                             #> [615] \"unclassified Parvimonas\"                                                                                                    #> [616] \"unclassified Pasteurellaceae\"                                                                                               #> [617] \"unclassified Peptococcaceae\"                                                                                                #> [618] \"unclassified Peptoniphilus\"                                                                                                 #> [619] \"unclassified Peptostreptococcaceae\"                                                                                         #> [620] \"unclassified Peptostreptococcales-Tissierellales\"                                                                           #> [621] \"unclassified Planctomycetales\"                                                                                              #> [622] \"unclassified Planococcaceae\"                                                                                                #> [623] \"unclassified Prevotellaceae\"                                                                                                #> [624] \"unclassified Promicromonosporaceae\"                                                                                         #> [625] \"unclassified Propionibacteriaceae\"                                                                                          #> [626] \"unclassified Proteobacteria\"                                                                                                #> [627] \"unclassified Pseudomonadaceae\"                                                                                              #> [628] \"unclassified Puniceicoccaceae\"                                                                                              #> [629] \"unclassified RF39\"                                                                                                          #> [630] \"unclassified Rhizobiaceae\"                                                                                                  #> [631] \"unclassified Rhizobiales Incertae Sedis\"                                                                                    #> [632] \"unclassified Rhizobiales\"                                                                                                   #> [633] \"unclassified Rhodobacteraceae\"                                                                                              #> [634] \"unclassified Rhodocyclaceae\"                                                                                                #> [635] \"unclassified Rhodospirillales\"                                                                                              #> [636] \"unclassified Rickettsiales\"                                                                                                 #> [637] \"unclassified Rikenellaceae\"                                                                                                 #> [638] \"unclassified Ruminiclostridium\"                                                                                             #> [639] \"unclassified Ruminococcaceae\"                                                                                               #> [640] \"unclassified ST-12K33\"                                                                                                      #> [641] \"unclassified Saccharimonadales\"                                                                                             #> [642] \"unclassified Sandaracinaceae\"                                                                                               #> [643] \"unclassified Selenomonadaceae\"                                                                                              #> [644] \"unclassified Simkaniaceae\"                                                                                                  #> [645] \"unclassified Solimonadaceae\"                                                                                                #> [646] \"unclassified Sphingobacteriales\"                                                                                            #> [647] \"unclassified Sphingomonadaceae\"                                                                                             #> [648] \"unclassified Staphylococcaceae\"                                                                                             #> [649] \"unclassified Streptococcaceae\"                                                                                              #> [650] \"unclassified Succinivibrionaceae\"                                                                                           #> [651] \"unclassified Sutterellaceae\"                                                                                                #> [652] \"unclassified TRA3-20\"                                                                                                       #> [653] \"unclassified Tannerellaceae\"                                                                                                #> [654] \"unclassified Tepidimicrobium\"                                                                                               #> [655] \"unclassified UCG-010\"                                                                                                       #> [656] \"unclassified UCG-011\"                                                                                                       #> [657] \"unclassified Veillonellaceae\"                                                                                               #> [658] \"unclassified Veillonellales-Selenomonadales\"                                                                                #> [659] \"unclassified Vermiphilaceae\"                                                                                                #> [660] \"unclassified Verrucomicrobiales\"                                                                                            #> [661] \"unclassified Verrucomicrobiota\"                                                                                             #> [662] \"unclassified Victivallaceae\"                                                                                                #> [663] \"unclassified W5053\"                                                                                                         #> [664] \"unclassified WPS-2\"                                                                                                         #> [665] \"unclassified Weeksellaceae\"                                                                                                 #> [666] \"unclassified Xanthobacteraceae\"                                                                                             #> [667] \"unclassified Yersiniaceae\"                                                                                                  #> [668] \"unclassified [Clostridium] methylpentosum group\"                                                                            #> [669] \"unclassified [Eubacterium] coprostanoligenes group\"                                                                         #> [670] \"unclassified vadinBE97\"                                                                                                     getMetadataVariableNames(microbiomeData::DiabImmune) #>  [1] \"Participant_Id\"                                       #>  [2] \"Participant_repeated_measure_Id\"                      #>  [3] \"age_1st_animal_milk_or_solids_given_days\"             #>  [4] \"age_1st_given_apple_months\"                           #>  [5] \"age_1st_given_banana_months\"                          #>  [6] \"age_1st_given_barley_months\"                          #>  [7] \"age_1st_given_beef_months\"                            #>  [8] \"age_1st_given_berries_months\"                         #>  [9] \"age_1st_given_cabbs_months\"                           #> [10] \"age_1st_given_carrot_months\"                          #> [11] \"age_1st_given_corn_months\"                            #> [12] \"age_1st_given_cowsmilk_months\"                        #> [13] \"age_1st_given_egg_months\"                             #> [14] \"age_1st_given_fish_months\"                            #> [15] \"age_1st_given_milk_products_months\"                   #> [16] \"age_1st_given_oat_months\"                             #> [17] \"age_1st_given_pear_months\"                            #> [18] \"age_1st_given_peas_months\"                            #> [19] \"age_1st_given_plum_months\"                            #> [20] \"age_1st_given_pork_months\"                            #> [21] \"age_1st_given_potato_months\"                          #> [22] \"age_1st_given_poultry_months\"                         #> [23] \"age_1st_given_rice_months\"                            #> [24] \"age_1st_given_rye_months\"                             #> [25] \"age_1st_given_sweet_potato_months\"                    #> [26] \"age_1st_given_tomato_months\"                          #> [27] \"age_1st_given_wheat_months\"                           #> [28] \"age_at_anthropometry_days\"                            #> [29] \"age_at_two_autoantibodies_positive_days\"              #> [30] \"age_at_type_1_diabetes_diagnosis_days\"                #> [31] \"antibiotics_before_delivery_by_maternal_report\"       #> [32] \"bmi_minus_for_minus_age_z_minus_score\"                #> [33] \"breastfed_duration_days\"                              #> [34] \"country\"                                              #> [35] \"delivery_mode\"                                        #> [36] \"diet_in_first_three_days\"                             #> [37] \"exclusive_breastfed_duration_days\"                    #> [38] \"gestational_diabetes_by_maternal_report\"              #> [39] \"glutamic_acid_decarboxylase_autoantibodies\"           #> [40] \"hla_risk_by_hla_haplotyping\"                          #> [41] \"height_minus_for_minus_age_z_minus_score\"             #> [42] \"insulin_autoantibodies\"                               #> [43] \"insulinoma_minus_associated_protein_2_autoantibodies\" #> [44] \"islet_cell_autoantibodies\"                            #> [45] \"linear_growth_during_1st_year_cm\"                     #> [46] \"maternal_age_at_birth_months\"                         #> [47] \"mean_linear_growth_during_1st_3_years\"                #> [48] \"mean_weight_gain_during_1st_3_years\"                  #> [49] \"sex\"                                                  #> [50] \"study_group\"                                          #> [51] \"type_1_diabetes_diagnosed\"                            #> [52] \"urban_or_rural_site\"                                  #> [53] \"weight_gain_during_1st_year_kg\"                       #> [54] \"weight_minus_for_minus_age_z_minus_score\"             #> [55] \"zinc_transporter_8_autoantibodies\"                    #> [56] \"age_months\"                                           #> [57] \"Sample_Id\"                                            #> [58] \"habitat\"                                              #> [59] \"host_body_habitat\"                                    #> [60] \"host_body_product\"                                    #> [61] \"host_body_site\"                                       #> [62] \"sample_type\"                                          variablesDT <- getVariables(      microbiomeData::DiabImmune,       list(\"metadata\" = c(\"age_months\", \"sex\"),           \"16S (V4) Genus\" = \"Bacteroides\",            \"WGS Metagenome enzyme pathway abundance data\" = \"ANAGLYCOLYSIS-PWY: glycolysis III (from glucose)\"      ) ) #>  #> 2024-04-24 17:16:55.430157 Removed 300 records with no data."},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Ranked abundance — rankedAbundance","title":"Ranked abundance — rankedAbundance","text":"function returns abundances, ranked selected ranking function","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ranked abundance — rankedAbundance","text":"","code":"rankedAbundance(   data,   method = c(\"median\", \"max\", \"q3\", \"variance\"),   cutoff = 10,   verbose = c(TRUE, FALSE) )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ranked abundance — rankedAbundance","text":"data AbundanceData object method string defining ranking strategy order taxa. Accepted values 'median','max','q3','variance'. Note taxa return value 0 given method included results. cutoff integer indicating maximium number taxa kept ranking. verbose boolean indicating timed logging desired","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ranked abundance — rankedAbundance","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/rankedAbundance-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Ranked abundance — rankedAbundance","text":"","code":"rankedAbundOutput <- rankedAbundance(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = \"median\" ) #>  #> 2024-04-24 17:16:55.798224 Received df table with 3184 samples and 673 taxa. #>  #> 2024-04-24 17:16:55.884543 Finished ranking taxa #>  #> 2024-04-24 17:16:55.894467 Ranked abundance computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method = median , cutoff = 10 , naToZero =  TRUE , verbose = TRUE"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Self Correlation — selfCorrelation","title":"Self Correlation — selfCorrelation","text":"function returns correlation coefficients variables one AbundanceData object . generally serves convenience wrapper around veupathUtils::correlation, exception additionally supports sparcc.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Self Correlation — selfCorrelation","text":"","code":"selfCorrelation(   data,   method = c(\"spearman\", \"pearson\", \"sparcc\"),   format = c(\"ComputeResult\", \"data.table\"),   verbose = c(TRUE, FALSE),   ... )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Self Correlation — selfCorrelation","text":"data AbundanceData object method string defining type correlation run. currently supported values 'spearman','pearson' 'sparcc' format string defining desired format result. currently supported values 'data.table' 'ComputeResult'. verbose boolean indicating timed logging desired ... additional parameters","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Self Correlation — selfCorrelation","text":"ComputeResult object","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/selfCorrelation-methods.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Self Correlation — selfCorrelation","text":"","code":"correlationDT <- selfCorrelation(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = 'sparcc',       format = 'data.table' ) #>  #> 2024-04-24 17:16:56.16955 Removed 1 records with no data. #>  #> 2024-04-24 17:16:56.176495 Removed 1 records with no data. #>  #> 2024-04-24 17:16:56.182957 Removed 1 records with no data. #>  #> 2024-04-24 17:26:52.297835 Completed correlation with method=sparcc. Formatting results. #>  #> 2024-04-24 17:26:52.298797 Received df table with 3183 samples and 21 features with abundances.  correlationOutput <- selfCorrelation(      getCollection(microbiomeData::DiabImmune, \"16S (V4) Genus\"),       method = 'sparcc',       format = 'ComputeResult' ) #>  #> 2024-04-24 17:26:52.428313 Removed 1 records with no data. #>  #> 2024-04-24 17:26:52.435343 Removed 1 records with no data. #>  #> 2024-04-24 17:26:52.441997 Removed 1 records with no data. #>  #> 2024-04-24 17:36:47.871937 Completed correlation with method=sparcc. Formatting results. #>  #> 2024-04-24 17:36:47.873227 Received df table with 3183 samples and 21 features with abundances. #>  #> 2024-04-24 17:36:47.874464 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  sparcc  alsoCorrelationDT <- getComputeResult(      correlationOutput,       \"data.table\" )"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Microbiome Dataset Collection Name — updateCollectionName","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"Update name collection Microbiome Dataset.","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"","code":"updateCollectionName(object, oldName, newName)  # S4 method for MbioDataset updateCollectionName(object, oldName, newName)"},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"object Microbiome Dataset oldName name collection update newName new name collection","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"Microbiome Dataset updated collection name","code":""},{"path":"https://microbiomedb.github.io/MicrobiomeDB/reference/updateCollectionName.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Microbiome Dataset Collection Name — updateCollectionName","text":"","code":"myCopyOfDiabImmune <- microbiomeData::DiabImmune myCopyOfDiabImmune <- updateCollectionName(myCopyOfDiabImmune, \"16S (V4) Genus\", \"16S Genus\")"}]