diff --git a/articles/attributes.html b/articles/attributes.html index 32329bc1..cd69b3fd 100644 --- a/articles/attributes.html +++ b/articles/attributes.html @@ -106,14 +106,14 @@

Data about Attributes and Sources

Attributes

Ontology terms can be searched at OSLv3 and OSLv4.

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Sources

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Session info @@ -128,7 +128,7 @@

Session info#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-01-17 +#> date 2024-01-19 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -140,7 +140,7 @@

Session info#> blob 1.2.4 2023-03-17 [1] RSPM (R 4.3.0) #> bold 1.3.0 2023-05-02 [1] RSPM (R 4.3.0) #> bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) -#> bugphyzz * 0.0.1.4 2024-01-17 [1] local +#> bugphyzz * 0.0.1.4 2024-01-19 [1] local #> cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) #> cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) #> codetools 0.2-19 2023-02-01 [2] CRAN (R 4.3.2) @@ -204,7 +204,7 @@

Session info#> utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) #> uuid 1.2-0 2024-01-14 [1] RSPM (R 4.3.0) #> vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) -#> withr 2.5.2 2023-10-30 [1] RSPM (R 4.3.0) +#> withr 3.0.0 2024-01-16 [1] RSPM (R 4.3.0) #> xfun 0.41 2023-11-01 [1] RSPM (R 4.3.0) #> xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0) #> yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) diff --git a/articles/bugphyzz.html b/articles/bugphyzz.html index 829de5e0..5e9d7a9c 100644 --- a/articles/bugphyzz.html +++ b/articles/bugphyzz.html @@ -121,34 +121,34 @@

Import bugphyzz#> Registered S3 method overwritten by 'httr': #> method from #> print.cache_info hoardr -#> Using data downloaded on 2024-01-17 06:37:00. +#> Using data downloaded on 2024-01-19 01:29:48. #> Importing binary data... -#> Using data downloaded on 2024-01-17 06:37:15. +#> Using data downloaded on 2024-01-19 01:30:00. #> Importing numeric data... -#> Using data downloaded on 2024-01-17 06:37:19. +#> Using data downloaded on 2024-01-19 01:30:02. head(map(bp, head)) #> $aerophilicity -#> NCBI_ID Taxon_name Rank Attribute Attribute_value Evidence Frequency -#> 1 3021684 Dryocola genus aerophilicity aerobic asr rarely -#> 2 3021684 Dryocola genus aerophilicity anaerobic asr rarely -#> 3 3016631 Silvania genus aerophilicity aerobic asr rarely -#> 4 3016631 Silvania genus aerophilicity anaerobic asr rarely -#> 5 1330547 Kosakonia genus aerophilicity aerobic asr usually -#> 6 1330547 Kosakonia genus aerophilicity anaerobic asr rarely -#> Score Attribute_source Confidence_in_curation Attribute_type -#> 1 1.057546e-06 <NA> <NA> multistate-intersection -#> 2 1.057546e-06 <NA> <NA> multistate-intersection -#> 3 1.057546e-06 <NA> <NA> multistate-intersection -#> 4 1.057546e-06 <NA> <NA> multistate-intersection -#> 5 9.979367e-01 <NA> <NA> multistate-intersection -#> 6 1.254967e-06 <NA> <NA> multistate-intersection -#> Validation -#> 1 0.73 -#> 2 0.88 -#> 3 0.73 -#> 4 0.88 -#> 5 0.73 -#> 6 0.88 +#> NCBI_ID Taxon_name Rank Attribute Attribute_value +#> 1 1330547 Kosakonia genus aerophilicity aerobic +#> 2 1822002 Enterobacillus genus aerophilicity aerobic +#> 3 2653932 Citrobacter telavivensis species aerophilicity aerobic +#> 4 1903434 Atlantibacter genus aerophilicity aerobic +#> 5 39824 Klebsiella granulomatis species aerophilicity aerobic +#> 6 2489010 Klebsiella africana species aerophilicity aerobic +#> Evidence Frequency Score Attribute_source Confidence_in_curation +#> 1 asr usually 0.9979367 <NA> <NA> +#> 2 asr usually 0.9999572 <NA> <NA> +#> 3 asr usually 0.9868172 <NA> <NA> +#> 4 asr usually 0.9999087 <NA> <NA> +#> 5 asr usually 0.9443181 <NA> <NA> +#> 6 asr usually 0.9552053 <NA> <NA> +#> Attribute_type Validation +#> 1 multistate-intersection 0.73 +#> 2 multistate-intersection 0.73 +#> 3 multistate-intersection 0.73 +#> 4 multistate-intersection 0.73 +#> 5 multistate-intersection 0.73 +#> 6 multistate-intersection 0.73 #> #> $`antimicrobial resistance` #> NCBI_ID Taxon_name Rank @@ -181,73 +181,80 @@

Import bugphyzz#> 6 NA #> #> $arrangement -#> NCBI_ID Taxon_name Rank Attribute Attribute_value Evidence Frequency -#> 1 48381 Thermothrix genus arrangement filamentous asr rarely -#> 2 816 Bacteroides genus arrangement filamentous asr rarely -#> 3 192992 Thermoleophilum genus arrangement filamentous asr rarely -#> 4 1883 Streptomyces genus arrangement filamentous asr rarely -#> 5 187 Aquaspirillum genus arrangement filamentous asr rarely -#> 6 476278 Thiohalospira genus arrangement filamentous asr rarely -#> Score Attribute_source Confidence_in_curation Attribute_type -#> 1 4.808186e-05 <NA> <NA> multistate-intersection -#> 2 3.536734e-07 <NA> <NA> multistate-intersection -#> 3 8.213199e-07 <NA> <NA> multistate-intersection -#> 4 8.213199e-07 <NA> <NA> multistate-intersection -#> 5 8.398390e-06 <NA> <NA> multistate-intersection -#> 6 2.928950e-06 <NA> <NA> multistate-intersection -#> Validation -#> 1 0.68 -#> 2 0.68 -#> 3 0.68 -#> 4 0.68 -#> 5 0.68 -#> 6 0.68 +#> NCBI_ID Taxon_name Rank Attribute Attribute_value Evidence +#> 1 37332 Nocardia seriolae species arrangement filamentous asr +#> 2 257281 Nocardia concava species arrangement filamentous asr +#> 3 1821 Nocardia sp. species arrangement filamentous asr +#> 4 2382165 Nocardia yunnanensis species arrangement filamentous asr +#> 5 2802282 Nocardia acididurans species arrangement filamentous asr +#> 6 2755382 Nocardia huaxiensis species arrangement filamentous asr +#> Frequency Score Attribute_source Confidence_in_curation +#> 1 sometimes 0.7203474 <NA> <NA> +#> 2 sometimes 0.7376650 <NA> <NA> +#> 3 sometimes 0.7279077 <NA> <NA> +#> 4 sometimes 0.7338991 <NA> <NA> +#> 5 sometimes 0.7783409 <NA> <NA> +#> 6 sometimes 0.7909908 <NA> <NA> +#> Attribute_type Validation +#> 1 multistate-intersection 0.68 +#> 2 multistate-intersection 0.68 +#> 3 multistate-intersection 0.68 +#> 4 multistate-intersection 0.68 +#> 5 multistate-intersection 0.68 +#> 6 multistate-intersection 0.68 #> #> $`biosafety level` -#> NCBI_ID Taxon_name Rank Attribute Attribute_value Evidence -#> 1 48381 Thermothrix genus biosafety level biosafety level 1 asr -#> 2 48381 Thermothrix genus biosafety level biosafety level 2 asr -#> 3 816 Bacteroides genus biosafety level biosafety level 1 asr -#> 4 816 Bacteroides genus biosafety level biosafety level 2 asr -#> 5 237 Flavobacterium genus biosafety level biosafety level 1 asr -#> 6 237 Flavobacterium genus biosafety level biosafety level 2 asr -#> Frequency Score Attribute_source Confidence_in_curation -#> 1 usually 9.999567e-01 <NA> <NA> -#> 2 rarely 2.166935e-05 <NA> <NA> -#> 3 usually 9.999968e-01 <NA> <NA> -#> 4 rarely 1.600572e-06 <NA> <NA> -#> 5 usually 9.999968e-01 <NA> <NA> -#> 6 rarely 1.600572e-06 <NA> <NA> +#> NCBI_ID Taxon_name Rank Attribute Attribute_value Evidence +#> 1 48381 Thermothrix genus biosafety level biosafety level 1 asr +#> 2 816 Bacteroides genus biosafety level biosafety level 1 asr +#> 3 237 Flavobacterium genus biosafety level biosafety level 1 asr +#> 4 192992 Thermoleophilum genus biosafety level biosafety level 1 asr +#> 5 1883 Streptomyces genus biosafety level biosafety level 1 asr +#> 6 187 Aquaspirillum genus biosafety level biosafety level 1 asr +#> Frequency Score Attribute_source Confidence_in_curation +#> 1 usually 0.9999567 <NA> <NA> +#> 2 usually 0.9999968 <NA> <NA> +#> 3 usually 0.9999968 <NA> <NA> +#> 4 usually 0.9999966 <NA> <NA> +#> 5 usually 0.9999966 <NA> <NA> +#> 6 usually 0.9999708 <NA> <NA> #> Attribute_type Validation #> 1 multistate-intersection 0.56 -#> 2 multistate-intersection 0.54 +#> 2 multistate-intersection 0.56 #> 3 multistate-intersection 0.56 -#> 4 multistate-intersection 0.54 +#> 4 multistate-intersection 0.56 #> 5 multistate-intersection 0.56 -#> 6 multistate-intersection 0.54 +#> 6 multistate-intersection 0.56 #> -#> $`COGEM pathogenicity rating` -#> NCBI_ID Taxon_name Rank Attribute -#> 1 48381 Thermothrix genus COGEM pathogenicity rating -#> 2 48381 Thermothrix genus COGEM pathogenicity rating -#> 3 48381 Thermothrix genus COGEM pathogenicity rating -#> 4 816 Bacteroides genus COGEM pathogenicity rating -#> 5 816 Bacteroides genus COGEM pathogenicity rating -#> 6 816 Bacteroides genus COGEM pathogenicity rating -#> Attribute_value Evidence Frequency Score Attribute_source -#> 1 COGEM pathogenicity rating 1 asr sometimes 0.819344139 <NA> -#> 2 COGEM pathogenicity rating 2 asr rarely 0.161404509 <NA> -#> 3 COGEM pathogenicity rating 3 asr rarely 0.019251352 <NA> -#> 4 COGEM pathogenicity rating 1 asr sometimes 0.809856918 <NA> -#> 5 COGEM pathogenicity rating 2 asr rarely 0.187502106 <NA> -#> 6 COGEM pathogenicity rating 3 asr rarely 0.002640976 <NA> -#> Confidence_in_curation Attribute_type Validation -#> 1 <NA> multistate-intersection 0.74 -#> 2 <NA> multistate-intersection 0.76 -#> 3 <NA> multistate-intersection 0.72 -#> 4 <NA> multistate-intersection 0.74 -#> 5 <NA> multistate-intersection 0.76 -#> 6 <NA> multistate-intersection 0.72 +#> $`cogem pathogenicity rating` +#> NCBI_ID Taxon_name Rank +#> 1 100053 Leptospira alexanderi species +#> 2 1003110 Micromonospora maris species +#> 3 100901 Wolbachia endosymbiont of Onchocerca ochengi species +#> 4 1015 Bergeyella zoohelcum species +#> 5 1017 Capnocytophaga gingivalis species +#> 6 1018 Capnocytophaga ochracea species +#> Attribute Attribute_value Evidence Frequency +#> 1 cogem pathogenicity rating COGEM pathogenicity rating 2 nas always +#> 2 cogem pathogenicity rating COGEM pathogenicity rating 1 nas always +#> 3 cogem pathogenicity rating COGEM pathogenicity rating 1 nas always +#> 4 cogem pathogenicity rating COGEM pathogenicity rating 2 nas always +#> 5 cogem pathogenicity rating COGEM pathogenicity rating 2 nas always +#> 6 cogem pathogenicity rating COGEM pathogenicity rating 2 nas always +#> Score Attribute_source Confidence_in_curation Attribute_type +#> 1 1 The Microbe Directory low multistate-intersection +#> 2 1 The Microbe Directory low multistate-intersection +#> 3 1 The Microbe Directory low multistate-intersection +#> 4 1 The Microbe Directory low multistate-intersection +#> 5 1 The Microbe Directory low multistate-intersection +#> 6 1 The Microbe Directory low multistate-intersection +#> Validation +#> 1 NA +#> 2 NA +#> 3 NA +#> 4 NA +#> 5 NA +#> 6 NA #> #> $`disease association` #> NCBI_ID Taxon_name Rank Attribute @@ -280,7 +287,7 @@

Explore wich attribute grou #> [2] "antimicrobial resistance" #> [3] "arrangement" #> [4] "biosafety level" -#> [5] "COGEM pathogenicity rating" +#> [5] "cogem pathogenicity rating" #> [6] "disease association" #> [7] "gram stain" #> [8] "habitat" @@ -290,15 +297,15 @@

Explore wich attribute grou #> [12] "animal pathogen" #> [13] "antimicrobial sensitivity" #> [14] "biofilm formation" -#> [15] "Butyrate-Producing Bacteria" -#> [16] "Extreme environment" -#> [17] "Health associated" +#> [15] "butyrate-producing bacteria" +#> [16] "extreme environment" +#> [17] "health associated" #> [18] "host-associated" #> [19] "hydrogen gas producing" #> [20] "lactate producing" #> [21] "motility" #> [22] "plant pathogenity" -#> [23] "Sphingolipid producing" +#> [23] "sphingolipid producing" #> [24] "spore formation" #> [25] "coding genes" #> [26] "genome size" @@ -433,7 +440,7 @@

Session information:#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-01-17 +#> date 2024-01-19 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -445,7 +452,7 @@

Session information:#> blob 1.2.4 2023-03-17 [1] RSPM (R 4.3.0) #> bold 1.3.0 2023-05-02 [1] RSPM (R 4.3.0) #> bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) -#> bugphyzz * 0.0.1.4 2024-01-17 [1] local +#> bugphyzz * 0.0.1.4 2024-01-19 [1] local #> cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) #> cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) #> codetools 0.2-19 2023-02-01 [2] CRAN (R 4.3.2) @@ -505,7 +512,7 @@

Session information:#> utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) #> uuid 1.2-0 2024-01-14 [1] RSPM (R 4.3.0) #> vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) -#> withr 2.5.2 2023-10-30 [1] RSPM (R 4.3.0) +#> withr 3.0.0 2024-01-16 [1] RSPM (R 4.3.0) #> xfun 0.41 2023-11-01 [1] RSPM (R 4.3.0) #> xml2 1.3.6 2023-12-04 [1] RSPM (R 4.3.0) #> yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) diff --git a/articles/checks.html b/articles/checks.html index f897b96c..48e2e14a 100644 --- a/articles/checks.html +++ b/articles/checks.html @@ -137,8 +137,8 @@

Check presence and order o } else { message('No errors found.') }

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Check syntax @@ -171,8 +171,8 @@

Uncatalogued columnsdiscard(~ all(is.na(.x))) |> select(-error_type) DT::datatable(uncat_columns)

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Errors in syntax/values @@ -217,8 +217,8 @@

Errors in syntax/values#> Warning in instance$preRenderHook(instance): It seems your data is too big for #> client-side DataTables. You may consider server-side processing: #> https://rstudio.github.io/DT/server.html

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diff --git a/articles/workflow.html b/articles/workflow.html index dc381f16..4a99e4cf 100644 --- a/articles/workflow.html +++ b/articles/workflow.html @@ -110,7 +110,7 @@

Session information#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-01-17 +#> date 2024-01-19 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── diff --git a/pkgdown.yml b/pkgdown.yml index 8d5674f6..65086c04 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: checks: checks.html bugphyzz: bugphyzz.html workflow: workflow.html -last_built: 2024-01-17T06:36Z +last_built: 2024-01-19T01:29Z urls: reference: https://waldronlab.io/bugphyzz/reference article: https://waldronlab.io/bugphyzz/articles diff --git a/reference/getTaxonSignatures.html b/reference/getTaxonSignatures.html index b30c9585..772d01af 100644 --- a/reference/getTaxonSignatures.html +++ b/reference/getTaxonSignatures.html @@ -100,13 +100,13 @@

Examples

bp <- importBugphyzz() #> Importing multistate data... #> Downloading, bugphyzz_multistate.tsv. -#> Using data downloaded on 2024-01-17 06:37:00. +#> Using data downloaded on 2024-01-19 01:29:48. #> Importing binary data... #> Downloading, bugphyzz_binary.tsv. -#> Using data downloaded on 2024-01-17 06:37:15. +#> Using data downloaded on 2024-01-19 01:30:00. #> Importing numeric data... #> Downloading, bugphyzz_numeric.tsv. -#> Using data downloaded on 2024-01-17 06:37:19. +#> Using data downloaded on 2024-01-19 01:30:02. sig_names_1 <- getTaxonSignatures("562", bp) sig_names_2 <- getTaxonSignatures("Escherichia coli", bp, tax_id_type = "Taxon_name") diff --git a/reference/importBugphyzz.html b/reference/importBugphyzz.html index dffd9f4e..48ab33b7 100644 --- a/reference/importBugphyzz.html +++ b/reference/importBugphyzz.html @@ -115,35 +115,35 @@

Examples


 bp <- importBugphyzz()
 #> Importing multistate data...
-#> Using data downloaded on 2024-01-17 06:37:00.
+#> Using data downloaded on 2024-01-19 01:29:48.
 #> Importing binary data...
-#> Using data downloaded on 2024-01-17 06:37:15.
+#> Using data downloaded on 2024-01-19 01:30:00.
 #> Importing numeric data...
-#> Using data downloaded on 2024-01-17 06:37:19.
+#> Using data downloaded on 2024-01-19 01:30:02.
 names(bp)
-#>  [1] "COGEM pathogenicity rating"           
-#>  [2] "aerophilicity"                        
-#>  [3] "antimicrobial resistance"             
-#>  [4] "arrangement"                          
-#>  [5] "biosafety level"                      
+#>  [1] "aerophilicity"                        
+#>  [2] "antimicrobial resistance"             
+#>  [3] "arrangement"                          
+#>  [4] "biosafety level"                      
+#>  [5] "cogem pathogenicity rating"           
 #>  [6] "disease association"                  
 #>  [7] "gram stain"                           
 #>  [8] "habitat"                              
 #>  [9] "hemolysis"                            
 #> [10] "shape"                                
 #> [11] "spore shape"                          
-#> [12] "Butyrate-Producing Bacteria"          
-#> [13] "Extreme environment"                  
-#> [14] "Health associated"                    
-#> [15] "Sphingolipid producing"               
-#> [16] "animal pathogen"                      
-#> [17] "antimicrobial sensitivity"            
-#> [18] "biofilm formation"                    
-#> [19] "host-associated"                      
-#> [20] "hydrogen gas producing"               
-#> [21] "lactate producing"                    
-#> [22] "motility"                             
-#> [23] "plant pathogenity"                    
+#> [12] "animal pathogen"                      
+#> [13] "antimicrobial sensitivity"            
+#> [14] "biofilm formation"                    
+#> [15] "butyrate-producing bacteria"          
+#> [16] "extreme environment"                  
+#> [17] "health associated"                    
+#> [18] "host-associated"                      
+#> [19] "hydrogen gas producing"               
+#> [20] "lactate producing"                    
+#> [21] "motility"                             
+#> [22] "plant pathogenity"                    
+#> [23] "sphingolipid producing"               
 #> [24] "spore formation"                      
 #> [25] "coding genes"                         
 #> [26] "genome size"                          
diff --git a/reference/makeSignatures.html b/reference/makeSignatures.html
index aabbd0ba..017b5583 100644
--- a/reference/makeSignatures.html
+++ b/reference/makeSignatures.html
@@ -134,11 +134,11 @@ 
Examples

     

 bp <- importBugphyzz()
 #> Importing multistate data...
-#> Using data downloaded on 2024-01-17 06:37:00.
+#> Using data downloaded on 2024-01-19 01:29:48.
 #> Importing binary data...
-#> Using data downloaded on 2024-01-17 06:37:15.
+#> Using data downloaded on 2024-01-19 01:30:00.
 #> Importing numeric data...
-#> Using data downloaded on 2024-01-17 06:37:19.
+#> Using data downloaded on 2024-01-19 01:30:02.
 sigs <- lapply(bp, makeSignatures)
 sigs <- purrr::list_flatten(sigs)