From 8f868388ce96ce743d791560efc9e448766e53c8 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Wed, 21 Oct 2020 14:40:00 +0200 Subject: [PATCH] (v1.4.0.9006) bugfix --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/ggplot_rsi.R | 2 +- R/like.R | 8 ++++---- 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 | 8 ++++---- docs/pkgdown.yml | 2 +- docs/reference/index.html | 2 +- docs/survey.html | 2 +- 13 files changed, 19 insertions(+), 19 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 26b69940..e80cb630 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.4.0.9005 +Version: 1.4.0.9006 Date: 2020-10-21 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 5892ef2a..656c7fd2 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.4.0.9005 +# AMR 1.4.0.9006 ## Last updated: 21 October 2020 ### New diff --git a/R/ggplot_rsi.R b/R/ggplot_rsi.R index 69240779..cbcf7fe9 100755 --- a/R/ggplot_rsi.R +++ b/R/ggplot_rsi.R @@ -371,7 +371,7 @@ scale_rsi_colours <- function(colours = c(S = "#61a8ff", IR = "#ff6961", R = "#ff6961")) { stop_ifnot_installed("ggplot2") - meet_criteria(colours, allow_class = "character") + meet_criteria(colours, allow_class = c("character", "logical")) # previous colour: palette = "RdYlGn" # previous colours: values = c("#b22222", "#ae9c20", "#7cfc00") diff --git a/R/like.R b/R/like.R index 177e67be..0c981158 100755 --- a/R/like.R +++ b/R/like.R @@ -69,7 +69,7 @@ #' } like <- function(x, pattern, ignore.case = TRUE) { meet_criteria(x, allow_NA = TRUE) - meet_criteria(pattern, allow_class = "character") + meet_criteria(pattern, allow_NA = FALSE) meet_criteria(ignore.case, allow_class = "logical", has_length = 1) # set to fixed if no regex found @@ -154,15 +154,15 @@ like <- function(x, pattern, ignore.case = TRUE) { #' @export "%like_case%" <- function(x, pattern) { meet_criteria(x, allow_NA = TRUE) - meet_criteria(pattern, allow_class = "character") + meet_criteria(pattern, allow_NA = FALSE) like(x, pattern, ignore.case = FALSE) } # don't export his one, it's just for convenience in eucast_rules() # match all Klebsiella and Raoultella, but not K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)" "%like_perl%" <- function(x, pattern) { - meet_criteria(x) - meet_criteria(pattern, allow_class = "character") + meet_criteria(x, allow_NA = TRUE) + meet_criteria(pattern, allow_NA = FALSE) grepl(x = tolower(x), pattern = tolower(pattern), perl = TRUE, diff --git a/docs/404.html b/docs/404.html index 57b6a614..9eceb7f8 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9005 + 1.4.0.9006 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 8b76c890..e1d99796 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9005 + 1.4.0.9006 diff --git a/docs/articles/index.html b/docs/articles/index.html index 4d4b703e..a4e2ebc3 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9005 + 1.4.0.9006 diff --git a/docs/authors.html b/docs/authors.html index e097c2b0..63d3cdfc 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9005 + 1.4.0.9006 diff --git a/docs/index.html b/docs/index.html index b35154a3..39675e91 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.4.0.9005 + 1.4.0.9006 diff --git a/docs/news/index.html b/docs/news/index.html index 4d673e3b..47e0185e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9005 + 1.4.0.9006 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.4.0.9005 Unreleased +
+

+AMR 1.4.0.9006 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index ebcb532f..2fb3c63b 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: 2020-10-21T11:05Z +last_built: 2020-10-21T12:39Z 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 ebb2d05b..df3074ab 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9005 + 1.4.0.9006

diff --git a/docs/survey.html b/docs/survey.html index 66ac513b..d7b48558 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9005 + 1.4.0.9006