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(v3.0.1.9061) WISCA refix

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dr. M.S. (Matthijs) Berends
2026-06-23 19:43:54 +02:00
parent fd90b2c250
commit 0c1709c999
4 changed files with 9 additions and 5 deletions
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2
DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 3.0.1.9060 Version: 3.0.1.9061
Date: 2026-06-23 Date: 2026-06-23
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9060 # AMR 3.0.1.9061
Planned as v3.1.0, end of June 2026. Planned as v3.1.0, end of June 2026.

6
R/antibiogram.R
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@@ -209,10 +209,12 @@
#' ) #' )
#' #'
#' # stratified by syndrome or clinical group #' # stratified by syndrome or clinical group
#' wisca(example_isolates, #' out <- wisca(example_isolates,
#' antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), #' antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
#' syndromic_group = "ward" #' syndromic_group = "ward"
#' ) #' )
#' out
#' wisca_plot(out)
#' #'
#' # stratified using grouped tibbles (e.g. by age and gender) #' # stratified using grouped tibbles (e.g. by age and gender)
#' if (requireNamespace("dplyr")) { #' if (requireNamespace("dplyr")) {
@@ -1538,8 +1540,8 @@ wisca_plot <- function(wisca_model,
isTRUE(attributes(wisca_model)$wisca), isTRUE(attributes(wisca_model)$wisca),
"This function only applies to WISCA models." "This function only applies to WISCA models."
) )
meet_criteria(wisca_plot_type, allow_class = "character", has_length = 1, is_in = c("susceptibility_incidence", "posterior_coverage"))
wisca_plot_type <- match.arg(wisca_plot_type) wisca_plot_type <- match.arg(wisca_plot_type)
meet_criteria(wisca_plot_type, allow_class = "character", has_length = 1, is_in = c("susceptibility_incidence", "posterior_coverage"))
sep <- attributes(wisca_model)$sep %||% " + " sep <- attributes(wisca_model)$sep %||% " + "

4
man/antibiogram.Rd
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@@ -308,10 +308,12 @@ antibiogram(example_isolates,
) )
# stratified by syndrome or clinical group # stratified by syndrome or clinical group
wisca(example_isolates, out <- wisca(example_isolates,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
syndromic_group = "ward" syndromic_group = "ward"
) )
out
wisca_plot(out)
# stratified using grouped tibbles (e.g. by age and gender) # stratified using grouped tibbles (e.g. by age and gender)
if (requireNamespace("dplyr")) { if (requireNamespace("dplyr")) {