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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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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"),