From 93428415d0f46a73dbc093c2f7723fff2a2bd2a5 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Mon, 16 Nov 2020 20:02:20 +0100 Subject: [PATCH] (v1.4.0.9022) small bugfix --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/aa_helper_functions.R | 5 ++--- R/mo_property.R | 2 +- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 12 ++++++------ docs/pkgdown.yml | 2 +- docs/reference/index.html | 2 +- docs/survey.html | 2 +- 13 files changed, 19 insertions(+), 20 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 382f6d8b..e85e5c97 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.4.0.9021 +Version: 1.4.0.9022 Date: 2020-11-16 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 5093c630..1839e7fa 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.4.0.9021 +# AMR 1.4.0.9022 ## Last updated: 16 November 2020 ### New diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 4002720d..e53e1650 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -79,8 +79,7 @@ addin_insert_like <- function() { modifyRange <- import_fn("insertText", "rstudioapi") document_range <- import_fn("document_range", "rstudioapi") document_position <- import_fn("document_position", "rstudioapi") - # setSelectionRanges <- import_fn("setSelectionRanges", "rstudioapi") - + context <- getSourceEditorContext() current_row <- context$selection[[1]]$range$end[1] current_col <- context$selection[[1]]$range$end[2] @@ -688,7 +687,7 @@ set_clean_class <- function(x, new_class) { lvls <- levels(x) attributes(x) <- NULL levels(x) <- lvls - } else { + } else if (!is.list(x) && !is.function(x)) { attributes(x) <- NULL } class(x) <- new_class diff --git a/R/mo_property.R b/R/mo_property.R index ecc0abf0..d375ff73 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -598,7 +598,7 @@ mo_validate <- function(x, property, language, ...) { } if (property == "mo") { - return(to_class_mo(x)) + return(set_clean_class(x, new_class = c("mo", "character"))) } else if (property == "snomed") { return(as.double(eval(parse(text = x)))) } else { diff --git a/docs/404.html b/docs/404.html index 3a2193e7..c0c00da4 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9022 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 7c605413..bcc79324 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9022 diff --git a/docs/articles/index.html b/docs/articles/index.html index 537821e6..89a76757 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9022 diff --git a/docs/authors.html b/docs/authors.html index 0b6aac47..804edbc7 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9022 diff --git a/docs/index.html b/docs/index.html index 43ae6c4c..8cf902e7 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9022 diff --git a/docs/news/index.html b/docs/news/index.html index f0936704..0c08f935 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9022 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.4.0.9021 Unreleased +
+

+AMR 1.4.0.9022 Unreleased

@@ -252,14 +252,14 @@

Functions mo_is_gram_negative() and mo_is_gram_positive() as wrappers around mo_gramstain(). They always return TRUE or FALSE (except when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria. If you have the dplyr package installed, they can even determine the column with microorganisms themselves when used inside dplyr verbs:

 example_isolates %>%
-  filter(mo_is_gram_positive())
+  filter(mo_is_gram_positive())
 #> NOTE: Using column `mo` as input for mo_is_gram_positive()

  • Function mo_is_intrinsic_resistant() to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020. As with the new mo_is_gram_*() functions, if you have the dplyr package installed the column with microorganisms will be automatically determined when used inside dplyr verbs:

     example_isolates %>%
-  filter(mo_is_intrinsic_resistant(ab = "Vancomycin"))
+  filter(mo_is_intrinsic_resistant(ab = "Vancomycin"))
 #> NOTE: Using column `mo` as input for mo_is_intrinsic_resistant()

  • Functions %not_like% and %not_like_case% as wrappers around %like% and %like_case%. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert %like% and by pressing it again it will be replaced with %not_like%, etc.

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 55b5488a..5cdea038 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: 2020-11-16T15:57Z +last_built: 2020-11-16T18:55Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 91c18bcd..d7435939 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9022

    diff --git a/docs/survey.html b/docs/survey.html index 472e3707..16ad81da 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9022