diff --git a/articles/attributes.html b/articles/attributes.html index 5b68f87..3785b11 100644 --- a/articles/attributes.html +++ b/articles/attributes.html @@ -100,22 +100,22 @@

Sources and Attributes

Sources

The 17 sources of annotations in bugphyzz:

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- +
+

Attributes

Definition of attributes and attribute values. Ontology terms can be searched at OSLv3 and OSLv4.

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- +
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Sources x Attributes

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- +
+

Session info @@ -130,7 +130,7 @@

Session info#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-04-01 +#> date 2024-04-02 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -140,7 +140,7 @@

Session info#> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0) #> blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0) #> bslib 0.7.0 2024-03-29 [1] CRAN (R 4.5.0) -#> bugphyzz * 0.99.0 2024-04-01 [1] Bioconductor +#> bugphyzz * 0.99.0 2024-04-02 [1] Bioconductor #> cachem 1.0.8 2023-05-01 [1] CRAN (R 4.5.0) #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.5.0) #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.5.0) diff --git a/articles/bugphyzz.html b/articles/bugphyzz.html index 41d9aa8..0ec9d6d 100644 --- a/articles/bugphyzz.html +++ b/articles/bugphyzz.html @@ -584,7 +584,7 @@

Session information#> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC -#> date 2024-04-01 +#> date 2024-04-02 #> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -611,7 +611,7 @@

Session information#> bluster 1.13.0 2023-10-24 [1] Bioconductor #> bookdown 0.38 2024-03-04 [1] CRAN (R 4.5.0) #> bslib 0.7.0 2024-03-29 [1] CRAN (R 4.5.0) -#> bugphyzz * 0.99.0 2024-04-01 [1] Bioconductor +#> bugphyzz * 0.99.0 2024-04-02 [1] Bioconductor #> cachem 1.0.8 2023-05-01 [1] CRAN (R 4.5.0) #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.5.0) #> cluster 2.1.6 2023-12-01 [2] CRAN (R 4.5.0) @@ -638,7 +638,7 @@

Session information#> fs 1.6.3 2023-07-20 [1] CRAN (R 4.5.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0) #> GenomeInfoDb * 1.39.9 2024-03-13 [1] Bioconductor 3.19 (R 4.5.0) -#> GenomeInfoDbData 1.2.12 2024-04-01 [1] Bioconductor +#> GenomeInfoDbData 1.2.12 2024-04-02 [1] Bioconductor #> GenomicRanges * 1.55.4 2024-03-18 [1] Bioconductor 3.19 (R 4.5.0) #> ggbeeswarm 0.7.2 2023-04-29 [1] CRAN (R 4.4.0) #> ggplot2 3.5.0 2024-02-23 [1] CRAN (R 4.5.0) @@ -673,7 +673,7 @@

Session information#> mia * 1.11.9 2024-03-26 [1] Bioconductor 3.19 (R 4.5.0) #> MicrobiomeBenchmarkData * 1.5.0 2023-10-31 [1] Bioconductor #> MultiAssayExperiment * 1.29.1 2024-02-02 [1] Bioconductor 3.19 (R 4.4.0) -#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.4.0) +#> munsell 0.5.1 2024-04-01 [1] CRAN (R 4.5.0) #> nlme 3.1-164 2023-11-27 [2] CRAN (R 4.5.0) #> permute 0.9-7 2022-01-27 [1] CRAN (R 4.4.0) #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.5.0) diff --git a/pkgdown.yml b/pkgdown.yml index a8d2224..056bfdb 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: attributes: attributes.html bugphyzz: bugphyzz.html -last_built: 2024-04-01T21:36Z +last_built: 2024-04-02T15:56Z urls: reference: https://waldronlab.io/bugphyzz/reference article: https://waldronlab.io/bugphyzz/articles diff --git a/reference/getTaxonSignatures.html b/reference/getTaxonSignatures.html index 0eefe0c..1ba71f9 100644 --- a/reference/getTaxonSignatures.html +++ b/reference/getTaxonSignatures.html @@ -102,13 +102,13 @@

Examples

bp <- importBugphyzz() #> Importing binary data... #> Downloading, bugphyzz_binary.csv. -#> Using data downloaded on 2024-04-01 21:36:06. +#> Using data downloaded on 2024-04-02 15:56:17. #> Importing multistate data... #> Downloading, bugphyzz_multistate.csv. -#> Using data downloaded on 2024-04-01 21:36:09. +#> Using data downloaded on 2024-04-02 15:56:19. #> Importing numeric data... #> Downloading, bugphyzz_numeric.csv. -#> Using data downloaded on 2024-04-01 21:36:18. +#> Using data downloaded on 2024-04-02 15:56:25. sig_names_1 <- getTaxonSignatures(taxid, bp) sig_names_2 <- getTaxonSignatures(taxonName, bp, tax_id_type = "Taxon_name") diff --git a/reference/importBugphyzz.html b/reference/importBugphyzz.html index 28b6965..8f1d59d 100644 --- a/reference/importBugphyzz.html +++ b/reference/importBugphyzz.html @@ -150,11 +150,11 @@

Examples


 bp <- importBugphyzz()
 #> Importing binary data...
-#> Using data downloaded on 2024-04-01 21:36:06.
+#> Using data downloaded on 2024-04-02 15:56:17.
 #> Importing multistate data...
-#> Using data downloaded on 2024-04-01 21:36:09.
+#> Using data downloaded on 2024-04-02 15:56:19.
 #> Importing numeric data...
-#> Using data downloaded on 2024-04-01 21:36:18.
+#> Using data downloaded on 2024-04-02 15:56:25.
 names(bp)
 #>  [1] "animal pathogen"                      
 #>  [2] "antimicrobial sensitivity"            
diff --git a/reference/makeSignatures.html b/reference/makeSignatures.html
index 4af434d..51600e7 100644
--- a/reference/makeSignatures.html
+++ b/reference/makeSignatures.html
@@ -135,11 +135,11 @@ 
Examples

     

 bp <- importBugphyzz()
 #> Importing binary data...
-#> Using data downloaded on 2024-04-01 21:36:06.
+#> Using data downloaded on 2024-04-02 15:56:17.
 #> Importing multistate data...
-#> Using data downloaded on 2024-04-01 21:36:09.
+#> Using data downloaded on 2024-04-02 15:56:19.
 #> Importing numeric data...
-#> Using data downloaded on 2024-04-01 21:36:18.
+#> Using data downloaded on 2024-04-02 15:56:25.
 sigs <- purrr::map(bp, makeSignatures)
 sigs <- purrr::list_flatten(sigs, name_spec = "{inner}")