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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
parent ec937e8179
commit cf91e677c6
8 changed files with 37 additions and 33 deletions
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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, "`")
)
)