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AMR
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mouse-hover fixes

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dr. M.S. (Matthijs) Berends 2023-07-12 15:27:43 +01:00
parent e1b4f99f4f
commit ea2a4652e9
4 changed files with 7 additions and 6 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 2.0.0.9039
Date: 2023-07-11
Version: 2.0.0.9040
Date: 2023-07-12
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.0.0.9039
# AMR 2.0.0.9040
## New
* Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations

2
R/ab.R
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@ -548,7 +548,7 @@ pillar_shaft.ab <- function(x, ...) {
# add the names to the drugs as mouse-over!
if (tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE)) {
out[!is.na(x)] <- font_url(url = ab_name(x[!is.na(x)]),
out[!is.na(x)] <- font_url(url = paste0(x[!is.na(x)], ": ", ab_name(x[!is.na(x)])),
txt = out[!is.na(x)])
}

5
R/mo.R
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@ -583,7 +583,7 @@ mo_cleaning_regex <- function() {
# will be exported using s3_register() in R/zzz.R
pillar_shaft.mo <- function(x, ...) {
add_MO_lookup_to_AMR_env()
out <- format(x)
out <- trimws(format(x))
# grey out the kingdom (part until first "_")
out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(font_subtle("\\1"), "\\2"), out[!is.na(x)], perl = TRUE)
# and grey out every _
@ -630,7 +630,8 @@ pillar_shaft.mo <- function(x, ...) {
# add the names to the bugs as mouse-over!
if (tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE)) {
out[!x %in% c("UNKNOWN", NA)] <- font_url(url = mo_name(x[!x %in% c("UNKNOWN", NA)], keep_synonyms = TRUE),
out[!x %in% c("UNKNOWN", NA)] <- font_url(url = paste0(x[!x %in% c("UNKNOWN", NA)], ": ",
mo_name(x[!x %in% c("UNKNOWN", NA)], keep_synonyms = TRUE)),
txt = out[!x %in% c("UNKNOWN", NA)])
}