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(v2.1.1.9250) Automated README and index.md

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dr. M.S. (Matthijs) Berends
2025-04-21 15:37:26 +02:00
parent be13934fe7
commit 4a336d040c
11 changed files with 715 additions and 165 deletions
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13
R/eucast_rules.R
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@ -72,7 +72,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @param administration Route of administration, either `r vector_or(dosage$administration)`.
#' @param only_sir_columns A [logical] to indicate whether only antimicrobial columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`).
#' @param custom_rules Custom rules to apply, created with [custom_eucast_rules()].
#' @param overwrite A [logical] indicating whether to overwrite non-`NA` values (default: `FALSE`). When `FALSE`, only `NA` values are modified. To ensure compliance with EUCAST guidelines, **this should remain** `FALSE`, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant.".
#' @param overwrite A [logical] indicating whether to overwrite non-`NA` values (default: `FALSE`). When `FALSE`, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, **this should remain** `FALSE`, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".
#' @inheritParams first_isolate
#' @details
#' **Note:** This function does not translate MIC values to SIR values. Use [as.sir()] for that. \cr
@ -1248,7 +1248,7 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 15) {
meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
# show used version_breakpoints number once per session (AMR_env will reload every session)
if (message_not_thrown_before("eucast_dosage", "v", gsub("[^0-9]", "", version_breakpoints), entire_session = TRUE)) {
if (missing(version_breakpoints) && message_not_thrown_before("eucast_dosage", "v", gsub("[^0-9]", "", version_breakpoints), entire_session = TRUE)) {
message_(
"Dosages for antimicrobial drugs, as meant for ",
format_eucast_version_nr(version_breakpoints, markdown = FALSE), ". ",
@ -1259,18 +1259,19 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 15) {
ab <- as.ab(ab)
lst <- vector("list", length = length(ab))
for (i in seq_len(length(ab))) {
df <- AMR::dosage[which(AMR::dosage$ab == ab[i] & AMR::dosage$administration == administration), , drop = FALSE]
df <- AMR::dosage[which(AMR::dosage$eucast_version == version_breakpoints & AMR::dosage$ab == ab[i] & AMR::dosage$administration == administration), , drop = FALSE]
lst[[i]] <- list(
ab = "",
name = "",
standard_dosage = ifelse("standard_dosage" %in% df$type,
df[which(df$type == "standard_dosage"), "original_txt", drop = TRUE],
trimws2(df[which(df$type == "standard_dosage"), "original_txt", drop = TRUE]),
NA_character_
),
high_dosage = ifelse("high_dosage" %in% df$type,
df[which(df$type == "high_dosage"), "original_txt", drop = TRUE],
trimws2(df[which(df$type == "high_dosage"), "original_txt", drop = TRUE]),
NA_character_
)
),
eucast_version = df$eucast_version[1]
)
}
out <- do.call(rbind_AMR, lapply(lst, as.data.frame, stringsAsFactors = FALSE))