diff --git a/DESCRIPTION b/DESCRIPTION index 30ceb5e1..6d116959 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.7.1.9010 +Version: 1.7.1.9011 Date: 2021-07-04 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index d9dd7b7e..d72e9568 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9010 +# `AMR` 1.7.1.9011 ## Last updated: 4 July 2021 ### Changed diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index ba932051..89592c5f 100644 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -25,7 +25,7 @@ #' Determine Bug-Drug Combinations #' -#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publicable/printable format, see *Examples*. +#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*. #' @inheritSection lifecycle Stable Lifecycle #' @inheritParams eucast_rules #' @param combine_IR a [logical] to indicate whether values R and I should be summed diff --git a/R/mo_property.R b/R/mo_property.R index d2e428fa..17226ae6 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -48,11 +48,13 @@ #' #' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.2)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics). #' +#' The functions [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()] are returned with an additional class `taxonomic_name`, which allows italic printing in [tibbles][tibble::tibble()]. +#' #' All output [will be translated][translate] where possible. #' #' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. #' -#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See the [microorganisms] data set for more info. +#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See *Source* and the [microorganisms] data set for more info. #' @inheritSection mo_matching_score Matching Score for Microorganisms #' @inheritSection catalogue_of_life Catalogue of Life #' @inheritSection as.mo Source @@ -63,9 +65,10 @@ #' - A [list] in case of [mo_taxonomy()] and [mo_info()] #' - A named [character] in case of [mo_url()] #' - A [numeric] in case of [mo_snomed()] +#' - A [character] with additional class `taxonomic_name` in case of [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()] #' - A [character] in all other cases #' @export -#' @seealso [microorganisms] +#' @seealso Data set [microorganisms] #' @inheritSection AMR Reference Data Publicly Available #' @inheritSection AMR Read more on Our Website! #' @examples @@ -783,15 +786,15 @@ print.taxonomic_name <- function(x, ...) { as.data.frame.taxonomic_name <- function(x, ...) { nm <- deparse1(substitute(x)) if (!"nm" %in% names(list(...))) { - as.data.frame.vector(x, ..., nm = nm) + as.data.frame(unclass(x), ..., nm = nm) } else { - as.data.frame.vector(x, ...) + as.data.frame(unclass(x), ...) } } # will be exported using s3_register() in R/zzz.R type_sum.taxonomic_name <- function(x, ...) { - "chr" + "chr/taxon" } # will be exported using s3_register() in R/zzz.R diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 40476a13..a6954a03 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index b5f0192a..1cf6a7e5 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9010 + 1.7.1.9011 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 1f646d8f..9fa02834 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9010 + 1.7.1.9011 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index cab789ed..50329e3a 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.7.1.9010 + 1.7.1.9011 diff --git a/docs/articles/index.html b/docs/articles/index.html index 050fc188..70aea4d0 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9010 + 1.7.1.9011 diff --git a/docs/authors.html b/docs/authors.html index b11f3d7c..8e5921d3 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9010 + 1.7.1.9011 diff --git a/docs/index.html b/docs/index.html index b7ecdd4f..5ba3ed2b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.7.1.9010 + 1.7.1.9011 @@ -227,38 +227,38 @@ - - + + - - + + - - + + - - + + @@ -266,8 +266,8 @@ - + @@ -275,8 +275,8 @@ - + @@ -284,8 +284,8 @@ - + @@ -302,8 +302,8 @@ - + @@ -311,8 +311,8 @@ - + @@ -320,8 +320,8 @@ - + diff --git a/docs/news/index.html b/docs/news/index.html index bb8f6830..f8fb0430 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9010 + 1.7.1.9011 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9010

+
+

+ Unreleased AMR 1.7.1.9011

Last updated: 4 July 2021 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 10a6fda8..9f0933e2 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-07-04T09:59Z +last_built: 2021-07-04T13:26Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index af779e8d..7cf18d2a 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -49,7 +49,7 @@ - + @@ -82,7 +82,7 @@ AMR (for R) - 1.7.1 + 1.7.1.9011

@@ -90,14 +90,14 @@
-

Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples.

+

Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publishable/printable format, see Examples.

bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 9a5d6a28..4c55f404 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
       
       
         AMR (for R)
-        1.7.1.9010
+        1.7.1.9011
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 94dd756a..65226561 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.7.1 + 1.7.1.9011 @@ -90,14 +90,14 @@
bacteriaAMK GENKAN TOBAMKKAN IPM MEM
Pseudomonas aeruginosa IR SR S
Pseudomonas aeruginosa IR SR S
Pseudomonas aeruginosa IR SR S
Pseudomonas aeruginosa S SR SR S
Pseudomonas aeruginosa S SR SR S S
Pseudomonas aeruginosa S SR SR S S
Pseudomonas aeruginosa S SR SR S
Pseudomonas aeruginosa S SR SR S
Pseudomonas aeruginosa S SR SR S S