diff --git a/articles/attributes.html b/articles/attributes.html index b7f953c5..a3d0e0a2 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 diff --git a/articles/bugphyzz.html b/articles/bugphyzz.html index 64f2cc07..b26237d6 100644 --- a/articles/bugphyzz.html +++ b/articles/bugphyzz.html @@ -120,8 +120,8 @@

Import bugphyzz#> Registered S3 method overwritten by 'httr': #> method from #> print.cache_info hoardr -#> Replacing previous version downloaded on 2023-12-14 16:54:28. -#> Using data downloaded on 2023-12-14 16:55:56. +#> Replacing previous version downloaded on 2023-12-14 18:04:42. +#> Using data downloaded on 2023-12-14 18:06:25. head(bp) #> NCBI_ID Taxon_name Rank Attribute_group #> 1 105825 butyrate-producing bacterium A2-207 species hydrogen gas producing diff --git a/articles/checks.html b/articles/checks.html index 4b9fcdce..f3bb2b4d 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/pkgdown.yml b/pkgdown.yml index 39d5d786..1fde21db 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: checks: checks.html bugphyzz: bugphyzz.html workflow: workflow.html -last_built: 2023-12-14T16:52Z +last_built: 2023-12-14T18:01Z urls: reference: https://waldronlab.io/bugphyzz/reference article: https://waldronlab.io/bugphyzz/articles diff --git a/reference/getBugAnnotations.html b/reference/getBugAnnotations.html index 50bfd56a..677d48df 100644 --- a/reference/getBugAnnotations.html +++ b/reference/getBugAnnotations.html @@ -100,7 +100,7 @@

Examples

x = c('561', '562'), bp = importBugphyzz(), tax.id.type = 'NCBI_ID' ) #> Downloading, bugphyzz_export.tsv. -#> Using data downloaded on 2023-12-14 16:53:04. +#> Using data downloaded on 2023-12-14 18:01:25. x #> $`561` #> $`561`$aerophilicity diff --git a/reference/getBugphyzzSignatures.html b/reference/getBugphyzzSignatures.html index 737d3a84..ed8de89c 100644 --- a/reference/getBugphyzzSignatures.html +++ b/reference/getBugphyzzSignatures.html @@ -140,7 +140,7 @@

Examples

## Create signatures of categorical or binary attributes bp <- importBugphyzz() -#> Using data downloaded on 2023-12-14 16:53:04. +#> Using data downloaded on 2023-12-14 18:01:25. sigs <- sig_fun(bp) map(sigs, head) #> $`bugphyzz:COGEM pathogenicity rating|COGEM pathogenicity rating 1|s` diff --git a/reference/whichAttr.html b/reference/whichAttr.html index 3aeac950..fbddcb22 100644 --- a/reference/whichAttr.html +++ b/reference/whichAttr.html @@ -93,7 +93,7 @@

Value

Examples


 bp <- importBugphyzz()
-#> Using data downloaded on 2023-12-14 16:53:04.
+#> Using data downloaded on 2023-12-14 18:01:25.
 whichAttr(bp)
 #>   [1] "Acne--TRUE"                           
 #>   [2] "Arthritis--TRUE"                      
diff --git a/reference/whichAttrGrp.html b/reference/whichAttrGrp.html
index cdd07d55..4696781e 100644
--- a/reference/whichAttrGrp.html
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Value

     
Examples

     

 bp <- importBugphyzz()
-#> Using data downloaded on 2023-12-14 16:53:04.
+#> Using data downloaded on 2023-12-14 18:01:25.
 whichAttrGrp(bp)
 #>  [1] "COGEM pathogenicity rating"           
 #>  [2] "acetate producing"