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(v2.1.1.9240) fix sir interpretation

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dr. M.S. (Matthijs) Berends 2025-04-16 15:22:12 +02:00
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 2.1.1.9239
Date: 2025-04-14
Version: 2.1.1.9240
Date: 2025-04-16
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

4
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9239
# AMR 2.1.1.9240
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*
@ -106,7 +106,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Added console colours support of `sir` class for Positron
## Other
* New website domain: <https://amr-for-r.org>! The old domain (<https://msberends.github.io/AMR>) will remain to work.
* New website domain: <https://amr-for-r.org>! The old domain (<http://amr-for-r.org>) will remain to work.
* Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
* Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
* Added Prof. Kathryn Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes

9
R/antibiogram.R
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@ -34,8 +34,8 @@
#'
#' Adhering to previously described approaches (see *Source*) and especially the Bayesian WISCA model (Weighted-Incidence Syndromic Combination Antibiogram) by Bielicki *et al.*, these functions provide flexible output formats including plots and tables, ideal for integration with R Markdown and Quarto reports.
#' @param x A [data.frame] containing at least a column with microorganisms and columns with antimicrobial results (class 'sir', see [as.sir()]).
#' @param antimicrobials A vector specifying the antimicrobials to include in the antibiogram (see *Examples*). Will be evaluated using [guess_ab_col()]. This can be:.
#' - Any antimicrobial name or code
#' @param antimicrobials A vector specifying the antimicrobials to include in the antibiogram (see *Examples*). Will be evaluated using [guess_ab_col()]. This can be:
#' - Any antimicrobial name or code that matches to a column name in `x`
#' - A column name in `x` that contains SIR values
#' - Any [antimicrobial selector][antimicrobial_selectors], such as [aminoglycosides()] or [carbapenems()]
#' - A combination of the above, using `c()`, e.g.:
@ -51,7 +51,7 @@
#' @param mo_transform A character to transform microorganism input - must be `"name"`, `"shortname"` (default), `"gramstain"`, or one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input or `NA` to consider all microorganisms 'unknown'.
#' @param ab_transform A character to transform antimicrobial input - must be one of the column names of the [antimicrobials] data set (defaults to `"name"`): `r vector_or(colnames(antimicrobials), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
#' @param syndromic_group A column name of `x`, or values calculated to split rows of `x`, e.g. by using [ifelse()] or [`case_when()`][dplyr::case_when()]. See *Examples*.
#' @param add_total_n A [logical] to indicate whether `n_tested` available numbers per pathogen should be added to the table (default is `TRUE`). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for *E. coli* 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when `wisca = TRUE`; in that case, use [retrieve_wisca_parameters()] to get the parameters used for WISCA.
#' @param add_total_n *(deprecated in favour of `formatting_type`)* A [logical] to indicate whether `n_tested` available numbers per pathogen should be added to the table (default is `TRUE`). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for *E. coli* 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when `wisca = TRUE`; in that case, use [retrieve_wisca_parameters()] to get the parameters used for WISCA.
#' @param only_all_tested (for combination antibiograms): a [logical] to indicate that isolates must be tested for all antimicrobials, see *Details*.
#' @param digits Number of digits to use for rounding the antimicrobial coverage, defaults to 1 for WISCA and 0 otherwise.
#' @param formatting_type Numeric value (1–22 for WISCA, 1-12 for non-WISCA) indicating how the 'cells' of the antibiogram table should be formatted. See *Details* > *Formatting Type* for a list of options.
@ -489,6 +489,9 @@ antibiogram.default <- function(x,
}
meet_criteria(syndromic_group, allow_class = "character", allow_NULL = TRUE, allow_NA = TRUE)
meet_criteria(add_total_n, allow_class = "logical", has_length = 1)
if (isTRUE(add_total_n) || !missing(add_total_n)) {
deprecation_warning("add_total_n", "formatting_type", fn = "antibiogram", is_argument = TRUE)
}
meet_criteria(only_all_tested, allow_class = "logical", has_length = 1)
meet_criteria(digits, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE)
meet_criteria(formatting_type, allow_class = c("numeric", "integer"), has_length = 1, is_in = c(1:22))

33
R/sir.R
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@ -44,7 +44,7 @@
#' @param uti (Urinary Tract Infection) a vector (or column name) with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.sir()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
#' @inheritParams first_isolate
#' @param guideline Defaults to `r AMR::clinical_breakpoints$guideline[1]` (the latest implemented EUCAST guideline in the [AMR::clinical_breakpoints] data set), but can be set with the package option [`AMR_guideline`][AMR-options]. Currently supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*.
#' @param capped_mic_handling A [character] string that controls how MIC values with a cap (i.e., starting with `<`, `<=`, `>`, or `>=`) are interpreted. Supports the following options:.
#' @param capped_mic_handling A [character] string that controls how MIC values with a cap (i.e., starting with `<`, `<=`, `>`, or `>=`) are interpreted. Supports the following options:
#'
#' `"none"`
#' * `<=` and `>=` are treated as-is.
@ -1261,27 +1261,28 @@ as_sir_method <- function(method_short,
# CLSI says: if MIC is not a log2 value it must be rounded up to the nearest log2 value
log2_levels <- 2^c(-9:12)
df$values <- vapply(
FUN.VALUE = double(1),
as.double(df$values),
FUN.VALUE = character(1),
df$values,
function(mic_val) {
if (is.na(mic_val)) {
return(NA_real_)
return(NA_character_)
} else {
# find the smallest log2 level that is >= mic_val
log2_val <- log2_levels[which(log2_levels >= mic_val)][1]
if (is.na(log2_val)) {
return(mic_val)
} else {
if (mic_val != log2_val && message_not_thrown_before("as.sir", "CLSI", "MICupscaling")) {
log2_val <- log2_levels[which(log2_levels >= as.double(mic_val))][1]
if (!is.na(log2_val) && as.double(mic_val) != log2_val) {
if (message_not_thrown_before("as.sir", "CLSI", "MICupscaling")) {
warning_("Some MICs were converted to the nearest higher log2 level, following the CLSI interpretation guideline.")
}
return(log2_val)
return(as.character(log2_val)) # will be MIC later
} else {
return(as.character(mic_val))
}
}
}
)
}
df$values <- as.mic(df$values)
print(df)
} else if (method == "disk") {
# when as.sir.disk is called directly
df$values <- as.disk(df$values)
@ -1583,13 +1584,13 @@ as_sir_method <- function(method_short,
if (any(breakpoints_current$site %like% "screen", na.rm = TRUE) | any(breakpoints_current$ref_tbl %like% "screen", na.rm = TRUE)) {
notes_current <- c(notes_current, "Some screening breakpoints were applied - use `include_screening = FALSE` to prevent this")
}
if (capped_mic_handling %in% c("conservative", "inverse") && any(as.character(values) %like% "^[<][0-9]")) {
if (method == "mic" && capped_mic_handling %in% c("conservative", "inverse") && any(as.character(values_bak) %like% "^[<][0-9]")) {
notes_current <- c(notes_current, paste0("MIC values with the sign '<' are all considered 'S' since capped_mic_handling = \"", capped_mic_handling, "\""))
}
if (capped_mic_handling %in% c("conservative", "inverse") && any(as.character(values) %like% "^[>][0-9]")) {
if (method == "mic" && capped_mic_handling %in% c("conservative", "inverse") && any(as.character(values_bak) %like% "^[>][0-9]")) {
notes_current <- c(notes_current, paste0("MIC values with the sign '>' are all considered 'R' since capped_mic_handling = \"", capped_mic_handling, "\""))
}
if (capped_mic_handling %in% c("conservative", "standard") && any(as.character(values) %like% "^[><]=[0-9]" & as.double(values) > breakpoints_current$breakpoint_S & as.double(values) < breakpoints_current$breakpoint_R, na.rm = TRUE)) {
if (method == "mic" && capped_mic_handling %in% c("conservative", "standard") && any(as.character(values_bak) %like% "^[><]=[0-9]" & as.double(values) > breakpoints_current$breakpoint_S & as.double(values) < breakpoints_current$breakpoint_R, na.rm = TRUE)) {
notes_current <- c(notes_current, paste0("MIC values within the breakpoint guideline range with the sign '<=' or '>=' are considered 'NI' since capped_mic_handling = \"", capped_mic_handling, "\""))
}
if (isTRUE(substitute_missing_r_breakpoint) && !is.na(breakpoints_current$breakpoint_S) && is.na(breakpoints_current$breakpoint_R)) {
@ -1600,9 +1601,9 @@ as_sir_method <- function(method_short,
if (method == "mic") {
new_sir <- case_when_AMR(
is.na(values) ~ NA_sir_,
capped_mic_handling %in% c("conservative", "inverse") & as.character(values) %like% "^[<][0-9]" ~ as.sir("S"),
capped_mic_handling %in% c("conservative", "inverse") & as.character(values) %like% "^[>][0-9]" ~ as.sir("R"),
capped_mic_handling %in% c("conservative", "standard") & as.character(values) %like% "^[><]=[0-9]" & as.double(values) > breakpoints_current$breakpoint_S & as.double(values) < breakpoints_current$breakpoint_R ~ as.sir("NI"),
capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[<][0-9]" ~ as.sir("S"),
capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[>][0-9]" ~ as.sir("R"),
capped_mic_handling %in% c("conservative", "standard") & as.character(values_bak) %like% "^[><]=[0-9]" & as.double(values) > breakpoints_current$breakpoint_S & as.double(values) < breakpoints_current$breakpoint_R ~ as.sir("NI"),
values <= breakpoints_current$breakpoint_S ~ as.sir("S"),
guideline_coerced %like% "EUCAST" & values > breakpoints_current$breakpoint_R ~ as.sir("R"),
guideline_coerced %like% "CLSI" & values >= breakpoints_current$breakpoint_R ~ as.sir("R"),

2
R/zz_deprecated.R
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@ -90,7 +90,7 @@ deprecation_warning <- function(old = NULL, new = NULL, fn = NULL, extra_msg = N
ifelse(type == "dataset",
paste0("The `", old, "` ", type, " has been renamed to `", new, "`"),
ifelse(type == "argument",
paste0("The `", old, "` ", type, " in `", fn, "()` has been renamed to `", new, "`: `", fn, "(", new, " = ...)`"),
paste0("The `", old, "` ", type, " in `", fn, "()` has been replaced with `", new, "`: `", fn, "(", new, " = ...)`"),
paste0("The `", old, "` ", type, " has been replaced with `", new, "`")
)
)

10
data-raw/gpt_training_text_v2.1.1.9239.txt → data-raw/gpt_training_text_v2.1.1.9240.txt
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@ -1,6 +1,6 @@
This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
First and foremost, you are trained on version 2.1.1.9239. Remember this whenever someone asks which AMR package version you’re at.
First and foremost, you are trained on version 2.1.1.9240. Remember this whenever someone asks which AMR package version you’re at.
Below are the contents of the NAMESPACE file, the index.md file, and all the man/*.Rd files (documentation) in the package. Every file content is split using 100 hypens.
----------------------------------------------------------------------------------------------------
@ -1723,9 +1723,9 @@ retrieve_wisca_parameters(wisca_model, ...)
\arguments{
\item{x}{A \link{data.frame} containing at least a column with microorganisms and columns with antimicrobial results (class 'sir', see \code{\link[=as.sir]{as.sir()}}).}
\item{antimicrobials}{A vector specifying the antimicrobials to include in the antibiogram (see \emph{Examples}). Will be evaluated using \code{\link[=guess_ab_col]{guess_ab_col()}}. This can be:.
\item{antimicrobials}{A vector specifying the antimicrobials to include in the antibiogram (see \emph{Examples}). Will be evaluated using \code{\link[=guess_ab_col]{guess_ab_col()}}. This can be:
\itemize{
\item Any antimicrobial name or code
\item Any antimicrobial name or code that matches to a column name in \code{x}
\item A column name in \code{x} that contains SIR values
\item Any \link[=antimicrobial_selectors]{antimicrobial selector}, such as \code{\link[=aminoglycosides]{aminoglycosides()}} or \code{\link[=carbapenems]{carbapenems()}}
\item A combination of the above, using \code{c()}, e.g.:
@ -1750,7 +1750,7 @@ retrieve_wisca_parameters(wisca_model, ...)
\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case_when]{case_when()}}. See \emph{Examples}.}
\item{add_total_n}{A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}
\item{add_total_n}{\emph{(deprecated in favour of \code{formatting_type})} A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}
\item{only_all_tested}{(for combination antibiograms): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see \emph{Details}.}
@ -3465,7 +3465,7 @@ sir_interpretation_history(clean = FALSE)
\item{uti}{(Urinary Tract Infection) a vector (or column name) with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
\item{capped_mic_handling}{A \link{character} string that controls how MIC values with a cap (i.e., starting with \code{<}, \code{<=}, \code{>}, or \code{>=}) are interpreted. Supports the following options:.
\item{capped_mic_handling}{A \link{character} string that controls how MIC values with a cap (i.e., starting with \code{<}, \code{<=}, \code{>}, or \code{>=}) are interpreted. Supports the following options:
\code{"none"}
\itemize{

6
man/antibiogram.Rd
View File

@ -46,9 +46,9 @@ retrieve_wisca_parameters(wisca_model, ...)
\arguments{
\item{x}{A \link{data.frame} containing at least a column with microorganisms and columns with antimicrobial results (class 'sir', see \code{\link[=as.sir]{as.sir()}}).}
\item{antimicrobials}{A vector specifying the antimicrobials to include in the antibiogram (see \emph{Examples}). Will be evaluated using \code{\link[=guess_ab_col]{guess_ab_col()}}. This can be:.
\item{antimicrobials}{A vector specifying the antimicrobials to include in the antibiogram (see \emph{Examples}). Will be evaluated using \code{\link[=guess_ab_col]{guess_ab_col()}}. This can be:
\itemize{
\item Any antimicrobial name or code
\item Any antimicrobial name or code that matches to a column name in \code{x}
\item A column name in \code{x} that contains SIR values
\item Any \link[=antimicrobial_selectors]{antimicrobial selector}, such as \code{\link[=aminoglycosides]{aminoglycosides()}} or \code{\link[=carbapenems]{carbapenems()}}
\item A combination of the above, using \code{c()}, e.g.:
@ -73,7 +73,7 @@ retrieve_wisca_parameters(wisca_model, ...)
\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case_when]{case_when()}}. See \emph{Examples}.}
\item{add_total_n}{A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}
\item{add_total_n}{\emph{(deprecated in favour of \code{formatting_type})} A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}
\item{only_all_tested}{(for combination antibiograms): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see \emph{Details}.}

2
man/as.sir.Rd
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@ -88,7 +88,7 @@ sir_interpretation_history(clean = FALSE)
\item{uti}{(Urinary Tract Infection) a vector (or column name) with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
\item{capped_mic_handling}{A \link{character} string that controls how MIC values with a cap (i.e., starting with \code{<}, \code{<=}, \code{>}, or \code{>=}) are interpreted. Supports the following options:.
\item{capped_mic_handling}{A \link{character} string that controls how MIC values with a cap (i.e., starting with \code{<}, \code{<=}, \code{>}, or \code{>=}) are interpreted. Supports the following options:
\code{"none"}
\itemize{