From 1d168433eddd42fe7ffaf5f1df24e7c351917ab9 Mon Sep 17 00:00:00 2001 From: sdgamboa <53412049+sdgamboa@users.noreply.github.com> Date: Fri, 22 Mar 2024 14:33:30 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20waldronl?= =?UTF-8?q?ab/bugphyzz@f6b481a8ef4766de899a6e1dc2fbe9edb00771b4=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- CODE_OF_CONDUCT.html | 2 +- CONTRIBUTING.html | 2 +- LICENSE-text.html | 2 +- SUPPORT.html | 2 +- articles/attributes.html | 16 ++++++++-------- articles/bugphyzz.html | 4 ++-- articles/index.html | 2 +- authors.html | 6 +++--- index.html | 2 +- pkgdown.yml | 2 +- reference/dot-appendLinks.html | 2 +- reference/dot-attributes.html | 2 +- reference/dot-checkColumnValues.html | 2 +- reference/dot-checkColumnValuesDF.html | 2 +- reference/dot-checkColumnValuesList.html | 2 +- reference/dot-checkRequiredColumns.html | 2 +- reference/dot-checkRequiredColumnsDF.html | 2 +- reference/dot-checkRequiredColumnsList.html | 2 +- reference/dot-errListToTable.html | 2 +- reference/dot-errorHandler.html | 2 +- reference/dot-requiredColumns.html | 2 +- reference/dot-stop_custom.html | 2 +- reference/dot-stop_invalid_column_values.html | 2 +- .../dot-stop_required_columns_misplaced.html | 2 +- reference/dot-stop_required_columns_missing.html | 2 +- .../dot-stop_required_missing_row_value.html | 2 +- reference/dot-stop_uncatalogued_column.html | 2 +- reference/dot-template.html | 2 +- reference/getTaxonSignatures.html | 8 ++++---- reference/importBugphyzz.html | 8 ++++---- reference/index.html | 2 +- reference/makeSignatures.html | 8 ++++---- reference/physiologies.html | 2 +- reference/showPhys.html | 2 +- 35 files changed, 54 insertions(+), 54 deletions(-) diff --git a/404.html b/404.html index f502eac0..cf621f72 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index b6f4475c..783f0ed6 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index b1ffedb1..9f83d0b6 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/LICENSE-text.html b/LICENSE-text.html index 30e5a141..a2afb665 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/SUPPORT.html b/SUPPORT.html index e55a85d4..15716bb3 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/articles/attributes.html b/articles/attributes.html index e57ae600..ba239d30 100644 --- a/articles/attributes.html +++ b/articles/attributes.html @@ -33,7 +33,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 @@ -96,22 +96,22 @@

Sources and Attributes

Sources

The 17 sources of annotations in bugphyzz:

-
- +
+

Attributes

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

-
- +
+

Sources x Attributes

-
- +
+

Session info @@ -136,7 +136,7 @@

Session info#> bit64 4.0.5 2020-08-30 [1] RSPM (R 4.3.0) #> blob 1.2.4 2023-03-17 [1] RSPM (R 4.3.0) #> bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) -#> bugphyzz * 0.0.1.10 2024-03-22 [1] Bioconductor +#> bugphyzz * 0.0.1.11 2024-03-22 [1] Bioconductor #> 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) #> crayon 1.5.2 2022-09-29 [1] RSPM (R 4.3.0) diff --git a/articles/bugphyzz.html b/articles/bugphyzz.html index 602d1b75..73a95473 100644 --- a/articles/bugphyzz.html +++ b/articles/bugphyzz.html @@ -33,7 +33,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11

@@ -619,7 +619,7 @@

Session information#> bold 1.3.0 2023-05-02 [1] RSPM (R 4.3.0) #> bookdown 0.38 2024-03-04 [1] RSPM (R 4.3.0) #> bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) -#> bugphyzz * 0.0.1.10 2024-03-22 [1] Bioconductor +#> bugphyzz * 0.0.1.11 2024-03-22 [1] Bioconductor #> 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) #> cluster 2.1.4 2022-08-22 [2] CRAN (R 4.3.2) diff --git a/articles/index.html b/articles/index.html index f6e8655b..00a664a2 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/authors.html b/authors.html index c306c56b..096520fd 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 @@ -89,13 +89,13 @@

Citation

Gamboa S, Waldron L, Eckenrode K, Ye J, Wokaty J (2024). bugphyzz: A harmonized data resource and software for enrichment analysis of microbial physiologies. -R package version 0.0.1.10, https://github.com/waldronlab/bugphyzz. +R package version 0.0.1.11, https://github.com/waldronlab/bugphyzz. 

@Manual{,
   title = {bugphyzz: A harmonized data resource and software for enrichment analysis of microbial physiologies},
   author = {Samuel Gamboa and Levi Waldron and Kelly Eckenrode and Jonathan Ye and Jennifer Wokaty},
   year = {2024},
-  note = {R package version 0.0.1.10},
+  note = {R package version 0.0.1.11},
   url = {https://github.com/waldronlab/bugphyzz},
 }
diff --git a/index.html b/index.html index 6965e2fc..4c7563cd 100644 --- a/index.html +++ b/index.html @@ -35,7 +35,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/pkgdown.yml b/pkgdown.yml index 0407455f..384c7616 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: attributes: attributes.html bugphyzz: bugphyzz.html -last_built: 2024-03-22T14:24Z +last_built: 2024-03-22T14:30Z urls: reference: https://waldronlab.io/bugphyzz/reference article: https://waldronlab.io/bugphyzz/articles diff --git a/reference/dot-appendLinks.html b/reference/dot-appendLinks.html index 82987ce6..af9c08d2 100644 --- a/reference/dot-appendLinks.html +++ b/reference/dot-appendLinks.html @@ -20,7 +20,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-attributes.html b/reference/dot-attributes.html index 3092d243..91b11e57 100644 --- a/reference/dot-attributes.html +++ b/reference/dot-attributes.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-checkColumnValues.html b/reference/dot-checkColumnValues.html index 77c7b637..86b0cb17 100644 --- a/reference/dot-checkColumnValues.html +++ b/reference/dot-checkColumnValues.html @@ -18,7 +18,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-checkColumnValuesDF.html b/reference/dot-checkColumnValuesDF.html index 5a6d0995..6798d6fc 100644 --- a/reference/dot-checkColumnValuesDF.html +++ b/reference/dot-checkColumnValuesDF.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-checkColumnValuesList.html b/reference/dot-checkColumnValuesList.html index 5f76f144..47618f33 100644 --- a/reference/dot-checkColumnValuesList.html +++ b/reference/dot-checkColumnValuesList.html @@ -18,7 +18,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-checkRequiredColumns.html b/reference/dot-checkRequiredColumns.html index 6ec8a5e5..d084e56e 100644 --- a/reference/dot-checkRequiredColumns.html +++ b/reference/dot-checkRequiredColumns.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-checkRequiredColumnsDF.html b/reference/dot-checkRequiredColumnsDF.html index 5906df48..1aa1e8c7 100644 --- a/reference/dot-checkRequiredColumnsDF.html +++ b/reference/dot-checkRequiredColumnsDF.html @@ -22,7 +22,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-checkRequiredColumnsList.html b/reference/dot-checkRequiredColumnsList.html index b531672e..75ca80e5 100644 --- a/reference/dot-checkRequiredColumnsList.html +++ b/reference/dot-checkRequiredColumnsList.html @@ -22,7 +22,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-errListToTable.html b/reference/dot-errListToTable.html index 77818345..3f22f63d 100644 --- a/reference/dot-errListToTable.html +++ b/reference/dot-errListToTable.html @@ -18,7 +18,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-errorHandler.html b/reference/dot-errorHandler.html index d0c0ef31..48c943e0 100644 --- a/reference/dot-errorHandler.html +++ b/reference/dot-errorHandler.html @@ -18,7 +18,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-requiredColumns.html b/reference/dot-requiredColumns.html index a84f1579..cfc92e1c 100644 --- a/reference/dot-requiredColumns.html +++ b/reference/dot-requiredColumns.html @@ -18,7 +18,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-stop_custom.html b/reference/dot-stop_custom.html index 9fcf3164..0894df69 100644 --- a/reference/dot-stop_custom.html +++ b/reference/dot-stop_custom.html @@ -21,7 +21,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-stop_invalid_column_values.html b/reference/dot-stop_invalid_column_values.html index 9b91fe45..21d8a114 100644 --- a/reference/dot-stop_invalid_column_values.html +++ b/reference/dot-stop_invalid_column_values.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-stop_required_columns_misplaced.html b/reference/dot-stop_required_columns_misplaced.html index b2550dfc..820dbacc 100644 --- a/reference/dot-stop_required_columns_misplaced.html +++ b/reference/dot-stop_required_columns_misplaced.html @@ -21,7 +21,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-stop_required_columns_missing.html b/reference/dot-stop_required_columns_missing.html index f43c5605..84bdeb26 100644 --- a/reference/dot-stop_required_columns_missing.html +++ b/reference/dot-stop_required_columns_missing.html @@ -21,7 +21,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-stop_required_missing_row_value.html b/reference/dot-stop_required_missing_row_value.html index 328422de..cc941f71 100644 --- a/reference/dot-stop_required_missing_row_value.html +++ b/reference/dot-stop_required_missing_row_value.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-stop_uncatalogued_column.html b/reference/dot-stop_uncatalogued_column.html index 5b067bf0..2cca1b1e 100644 --- a/reference/dot-stop_uncatalogued_column.html +++ b/reference/dot-stop_uncatalogued_column.html @@ -20,7 +20,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/dot-template.html b/reference/dot-template.html index 5397e1b8..7949ab2a 100644 --- a/reference/dot-template.html +++ b/reference/dot-template.html @@ -20,7 +20,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 diff --git a/reference/getTaxonSignatures.html b/reference/getTaxonSignatures.html index 3850f596..9f81e5fc 100644 --- a/reference/getTaxonSignatures.html +++ b/reference/getTaxonSignatures.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 @@ -99,13 +99,13 @@

Examples

bp <- importBugphyzz() #> Importing multistate data... #> Downloading, bugphyzz_multistate.tsv. -#> Using data downloaded on 2024-03-22 14:24:34. +#> Using data downloaded on 2024-03-22 14:30:29. #> Importing binary data... #> Downloading, bugphyzz_binary.tsv. -#> Using data downloaded on 2024-03-22 14:24:45. +#> Using data downloaded on 2024-03-22 14:30:38. #> Importing numeric data... #> Downloading, bugphyzz_numeric.tsv. -#> Using data downloaded on 2024-03-22 14:24:47. +#> Using data downloaded on 2024-03-22 14:30:41. 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 1a98cc96..4406b83a 100644 --- a/reference/importBugphyzz.html +++ b/reference/importBugphyzz.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 @@ -147,11 +147,11 @@

Examples


 bp <- importBugphyzz()
 #> Importing multistate data...
-#> Using data downloaded on 2024-03-22 14:24:34.
+#> Using data downloaded on 2024-03-22 14:30:29.
 #> Importing binary data...
-#> Using data downloaded on 2024-03-22 14:24:45.
+#> Using data downloaded on 2024-03-22 14:30:38.
 #> Importing numeric data...
-#> Using data downloaded on 2024-03-22 14:24:47.
+#> Using data downloaded on 2024-03-22 14:30:41.
 names(bp)
 #>  [1] "aerophilicity"                        
 #>  [2] "antimicrobial resistance"             
diff --git a/reference/index.html b/reference/index.html
index 03fe019c..63634f39 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
       
       
         bugphyzz
-        0.0.1.10
+        0.0.1.11
diff --git a/reference/makeSignatures.html b/reference/makeSignatures.html index af6f2d2d..6dd0dde0 100644 --- a/reference/makeSignatures.html +++ b/reference/makeSignatures.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11 @@ -132,11 +132,11 @@

Examples


 bp <- importBugphyzz()
 #> Importing multistate data...
-#> Using data downloaded on 2024-03-22 14:24:34.
+#> Using data downloaded on 2024-03-22 14:30:29.
 #> Importing binary data...
-#> Using data downloaded on 2024-03-22 14:24:45.
+#> Using data downloaded on 2024-03-22 14:30:38.
 #> Importing numeric data...
-#> Using data downloaded on 2024-03-22 14:24:47.
+#> Using data downloaded on 2024-03-22 14:30:41.
 sigs <- purrr::map(bp, makeSignatures)
 sigs <- purrr::list_flatten(sigs, name_spec = "{inner}")
 
diff --git a/reference/physiologies.html b/reference/physiologies.html
index 9c550433..f7e92f68 100644
--- a/reference/physiologies.html
+++ b/reference/physiologies.html
@@ -19,7 +19,7 @@
       
       
         bugphyzz
-        0.0.1.10
+        0.0.1.11
diff --git a/reference/showPhys.html b/reference/showPhys.html index 6f9d07ce..be895d6d 100644 --- a/reference/showPhys.html +++ b/reference/showPhys.html @@ -19,7 +19,7 @@ bugphyzz - 0.0.1.10 + 0.0.1.11