From 7c1c995b73cd470b822daa6bb7a9b56be45a4fc2 Mon Sep 17 00:00:00 2001 From: sdgamboa <53412049+sdgamboa@users.noreply.github.com> Date: Fri, 22 Mar 2024 14:27:39 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20waldronl?= =?UTF-8?q?ab/bugphyzz@d4ae70229f6de936024f616602bc0607f17de843=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 | 5 +- CODE_OF_CONDUCT.html | 5 +- CONTRIBUTING.html | 5 +- LICENSE-text.html | 5 +- SUPPORT.html | 5 +- articles/attributes.html | 135 +++++++++--------- articles/bugphyzz.html | 9 +- articles/index.html | 7 +- authors.html | 9 +- index.html | 5 +- pkgdown.yml | 3 +- reference/dot-appendLinks.html | 5 +- reference/dot-attributes.html | 5 +- reference/dot-checkColumnValues.html | 5 +- reference/dot-checkColumnValuesDF.html | 5 +- reference/dot-checkColumnValuesList.html | 5 +- reference/dot-checkRequiredColumns.html | 5 +- reference/dot-checkRequiredColumnsDF.html | 5 +- reference/dot-checkRequiredColumnsList.html | 5 +- reference/dot-errListToTable.html | 5 +- reference/dot-errorHandler.html | 5 +- reference/dot-requiredColumns.html | 5 +- reference/dot-stop_custom.html | 5 +- reference/dot-stop_invalid_column_values.html | 5 +- .../dot-stop_required_columns_misplaced.html | 5 +- .../dot-stop_required_columns_missing.html | 5 +- .../dot-stop_required_missing_row_value.html | 5 +- reference/dot-stop_uncatalogued_column.html | 5 +- reference/dot-template.html | 5 +- reference/getTaxonSignatures.html | 28 ++-- reference/importBugphyzz.html | 68 +++++++-- reference/index.html | 9 +- reference/makeSignatures.html | 41 +++--- reference/physiologies.html | 25 ++-- reference/showPhys.html | 15 +- sitemap.xml | 3 - 36 files changed, 205 insertions(+), 267 deletions(-) diff --git a/404.html b/404.html index 64878fdf..f502eac0 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ bugphyzz - 0.0.1.9 + 0.0.1.10 @@ -54,9 +54,6 @@
  • Sources and Attributes
    • -
  • - Curation Checks -
    • diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index aeca9ad5..b6f4475c 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.9 + 0.0.1.10 @@ -37,9 +37,6 @@ @@ -99,22 +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 @@ -133,65 +130,65 @@

    Session info#> pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── -#> package * version date (UTC) lib source -#> BiocFileCache 2.10.1 2023-10-26 [1] Bioconductor -#> bit 4.0.5 2022-11-15 [1] RSPM (R 4.3.0) -#> 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 * 0.0.1.9 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) -#> crosstalk 1.2.1 2023-11-23 [1] RSPM (R 4.3.0) -#> curl 5.2.1 2024-03-01 [1] RSPM (R 4.3.0) -#> DBI 1.2.2 2024-02-16 [1] RSPM (R 4.3.0) -#> dbplyr 2.5.0 2024-03-19 [1] RSPM (R 4.3.0) -#> desc 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) -#> digest 0.6.35 2024-03-11 [1] RSPM (R 4.3.0) -#> dplyr * 1.1.4 2023-11-17 [1] RSPM (R 4.3.0) -#> DT * 0.32 2024-02-19 [1] RSPM (R 4.3.0) -#> ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) -#> evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) -#> fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0) -#> fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) -#> filelock 1.0.3 2023-12-11 [1] RSPM (R 4.3.0) -#> fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) -#> generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0) -#> glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) -#> hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0) -#> htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) -#> htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) -#> httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0) -#> jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) -#> jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) -#> knitr 1.45 2023-10-30 [1] RSPM (R 4.3.0) -#> lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) -#> magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) -#> memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) -#> pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0) -#> pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0) -#> pkgdown 2.0.7 2022-12-14 [1] RSPM (R 4.3.0) -#> purrr * 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) -#> R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) -#> ragg 1.3.0 2024-03-13 [1] RSPM (R 4.3.0) -#> readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0) -#> rlang 1.1.3 2024-01-10 [1] RSPM (R 4.3.0) -#> rmarkdown 2.26 2024-03-05 [1] RSPM (R 4.3.0) -#> RSQLite 2.3.5 2024-01-21 [1] RSPM (R 4.3.0) -#> sass 0.4.9 2024-03-15 [1] RSPM (R 4.3.0) -#> sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) -#> systemfonts 1.0.6 2024-03-07 [1] RSPM (R 4.3.0) -#> textshaping 0.3.7 2023-10-09 [1] RSPM (R 4.3.0) -#> tibble 3.2.1 2023-03-20 [1] RSPM (R 4.3.0) -#> tidyselect 1.2.1 2024-03-11 [1] RSPM (R 4.3.0) -#> tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0) -#> utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) -#> vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) -#> vroom 1.6.5 2023-12-05 [1] RSPM (R 4.3.0) -#> withr 3.0.0 2024-01-16 [1] RSPM (R 4.3.0) -#> xfun 0.42 2024-02-08 [1] RSPM (R 4.3.0) -#> yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) +#> package * version date (UTC) lib source +#> BiocFileCache 2.10.1 2023-10-26 [1] Bioconductor +#> bit 4.0.5 2022-11-15 [1] RSPM (R 4.3.0) +#> 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 +#> 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) +#> crosstalk 1.2.1 2023-11-23 [1] RSPM (R 4.3.0) +#> curl 5.2.1 2024-03-01 [1] RSPM (R 4.3.0) +#> DBI 1.2.2 2024-02-16 [1] RSPM (R 4.3.0) +#> dbplyr 2.5.0 2024-03-19 [1] RSPM (R 4.3.0) +#> desc 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) +#> digest 0.6.35 2024-03-11 [1] RSPM (R 4.3.0) +#> dplyr * 1.1.4 2023-11-17 [1] RSPM (R 4.3.0) +#> DT * 0.32 2024-02-19 [1] RSPM (R 4.3.0) +#> ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) +#> evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) +#> fansi 1.0.6 2023-12-08 [1] RSPM (R 4.3.0) +#> fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) +#> filelock 1.0.3 2023-12-11 [1] RSPM (R 4.3.0) +#> fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) +#> generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0) +#> glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) +#> hms 1.1.3 2023-03-21 [1] RSPM (R 4.3.0) +#> htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) +#> htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) +#> httr 1.4.7 2023-08-15 [1] RSPM (R 4.3.0) +#> jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) +#> jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) +#> knitr 1.45 2023-10-30 [1] RSPM (R 4.3.0) +#> lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) +#> magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) +#> memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) +#> pillar 1.9.0 2023-03-22 [1] RSPM (R 4.3.0) +#> pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.3.0) +#> pkgdown 2.0.7 2022-12-14 [1] RSPM (R 4.3.0) +#> purrr * 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) +#> R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) +#> ragg 1.3.0 2024-03-13 [1] RSPM (R 4.3.0) +#> readr 2.1.5 2024-01-10 [1] RSPM (R 4.3.0) +#> rlang 1.1.3 2024-01-10 [1] RSPM (R 4.3.0) +#> rmarkdown 2.26 2024-03-05 [1] RSPM (R 4.3.0) +#> RSQLite 2.3.5 2024-01-21 [1] RSPM (R 4.3.0) +#> sass 0.4.9 2024-03-15 [1] RSPM (R 4.3.0) +#> sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) +#> systemfonts 1.0.6 2024-03-07 [1] RSPM (R 4.3.0) +#> textshaping 0.3.7 2023-10-09 [1] RSPM (R 4.3.0) +#> tibble 3.2.1 2023-03-20 [1] RSPM (R 4.3.0) +#> tidyselect 1.2.1 2024-03-11 [1] RSPM (R 4.3.0) +#> tzdb 0.4.0 2023-05-12 [1] RSPM (R 4.3.0) +#> utf8 1.2.4 2023-10-22 [1] RSPM (R 4.3.0) +#> vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) +#> vroom 1.6.5 2023-12-05 [1] RSPM (R 4.3.0) +#> withr 3.0.0 2024-01-16 [1] RSPM (R 4.3.0) +#> xfun 0.42 2024-02-08 [1] RSPM (R 4.3.0) +#> yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) #> #> [1] /usr/local/lib/R/site-library #> [2] /usr/local/lib/R/library diff --git a/articles/bugphyzz.html b/articles/bugphyzz.html index fb55bc88..602d1b75 100644 --- a/articles/bugphyzz.html +++ b/articles/bugphyzz.html @@ -33,7 +33,7 @@ bugphyzz - 0.0.1.9 + 0.0.1.10

    @@ -55,9 +55,6 @@
  • Sources and Attributes
    • -
  • - Curation Checks -
    • @@ -622,7 +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 * 0.0.1.9 2024-03-22 [1] Bioconductor +#> bugphyzz * 0.0.1.10 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) @@ -653,7 +650,7 @@

    Session information#> fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) #> generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0) #> GenomeInfoDb * 1.38.8 2024-03-15 [1] Bioconductor 3.18 (R 4.3.2) -#> GenomeInfoDbData 1.2.11 2024-03-14 [1] Bioconductor +#> GenomeInfoDbData 1.2.11 2024-03-18 [1] Bioconductor #> GenomicRanges * 1.54.1 2023-10-29 [1] Bioconductor #> ggbeeswarm 0.7.2 2023-04-29 [1] RSPM (R 4.3.0) #> ggplot2 3.5.0 2024-02-23 [1] RSPM (R 4.3.0) diff --git a/articles/index.html b/articles/index.html index 89316e2c..f6e8655b 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ bugphyzz - 0.0.1.9 + 0.0.1.10 @@ -37,9 +37,6 @@ diff --git a/pkgdown.yml b/pkgdown.yml index 12f83ce2..0407455f 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,9 +3,8 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: attributes: attributes.html - checks: checks.html bugphyzz: bugphyzz.html -last_built: 2024-03-22T01:13Z +last_built: 2024-03-22T14:24Z 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 756918dc..82987ce6 100644 --- a/reference/dot-appendLinks.html +++ b/reference/dot-appendLinks.html @@ -20,7 +20,7 @@ bugphyzz - 0.0.1.9 + 0.0.1.10 @@ -40,9 +40,6 @@