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(v2.1.1.9198) support eucast expert rules 14 and 13.1

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dr. M.S. (Matthijs) Berends
2025-03-14 10:10:35 +01:00
parent eafe9bd113
commit e134e01418
34 changed files with 604 additions and 175 deletions
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7
R/ab.R
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@ -211,6 +211,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
next
}
# screening, but written without the hyphen, e.g., FOXS instead of FOX-S
if (substr(x[i], 4, 4) == "S" && paste0(substr(x[i], 1, 3), "-S") %in% AMR_env$AB_lookup$ab) {
x_new[i] <- paste0(substr(x[i], 1, 3), "-S")
next
}
if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") {
from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], translate_ab = FALSE)[[1]]),
error = function(e) character(0)
@ -306,7 +312,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
next
}
# try if name ends with it
found <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
if (nchar(x[i]) >= 4 && length(found) > 0) {