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(v3.0.0.9009) fix as.sir when uti = FALSE

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Nick Thomson
2025-07-17 23:15:52 +08:00
committed by GitHub
parent d94bdd2c6a
commit e9e3de4469
3 changed files with 18 additions and 20 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 3.0.0.9008
Version: 3.0.0.9009
Date: 2025-07-17
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

3
NEWS.md
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@ -1,4 +1,4 @@
# AMR 3.0.0.9008
# AMR 3.0.0.9009
This is primarily a bugfix release, though we added one nice feature too.
@ -13,6 +13,7 @@ This is primarily a bugfix release, though we added one nice feature too.
* Fixed a bug in `as.ab()` for antimicrobial codes with a number in it if they are preceded by a space
* Fixed a bug in `eucast_rules()` for using specific custom rules
* Fixed a bug in `as.sir()` to allow any tidyselect language (#220)
* Fixed a bug in `as.sir()` to pick right breakpoint when `uti = FALSE` (#216)
* Fixed a bug in `ggplot_sir()` when using `combine_SI = FALSE` (#213)
* Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent)
* Fixed some specific Dutch translations for antimicrobials

33
R/sir.R
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@ -1656,26 +1656,23 @@ as_sir_method <- function(method_short,
next
}
# sort on host and taxonomic rank
# (this will e.g. prefer 'species' breakpoints over 'order' breakpoints)
if (is.na(uti_current)) {
breakpoints_current <- breakpoints_current %pm>%
# `uti` is a column in the data set
# this will put UTI = FALSE first, then UTI = NA, then UTI = TRUE
pm_mutate(uti_index = ifelse(!is.na(uti) & uti == FALSE, 1,
ifelse(is.na(uti), 2,
3
)
)) %pm>%
# be as specific as possible (i.e. prefer species over genus):
pm_arrange(rank_index, uti_index)
} else if (uti_current == TRUE) {
breakpoints_current <- breakpoints_current %pm>%
subset(uti == TRUE) %pm>%
# be as specific as possible (i.e. prefer species over genus):
pm_arrange(rank_index)
# if the user explicitly set uti, keep only those rows
if (!is.na(uti_current)) {
breakpoints_current <- breakpoints_current[breakpoints_current$uti == uti_current, , drop = FALSE]
}
# build a helper factor so FALSE < NA < TRUE
uti_index <- factor(
ifelse(is.na(breakpoints_current$uti), "NA",
as.character(breakpoints_current$uti)
),
levels = c("FALSE", "NA", "TRUE")
)
# sort on host and taxonomic rank first, then by UTI
# (this will e.g. prefer 'species' breakpoints over 'order' breakpoints)
breakpoints_current <- breakpoints_current[order(breakpoints_current$rank_index, uti_index), , drop = FALSE]
# throw messages for different body sites
site <- breakpoints_current[1L, "site", drop = FALSE] # this is the one we'll take
if (is.na(site)) {