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(v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N

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dr. M.S. (Matthijs) Berends
2024-06-14 22:39:01 +02:00
parent de17de1be9
commit 9bf7584d58
57 changed files with 4375 additions and 135 deletions
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2
R/antibiogram.R
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@ -352,7 +352,7 @@ antibiogram <- function(x,
} else {
S_values <- "S"
}
other_values <- setdiff(c("S", "SDD", "I", "R", "N"), S_values)
other_values <- setdiff(c("S", "SDD", "I", "R", "NI"), S_values)
x_transposed <- as.list(as.data.frame(t(x[, abx, drop = FALSE]), stringsAsFactors = FALSE))
if (isTRUE(only_all_tested)) {
x[new_colname] <- as.sir(vapply(FUN.VALUE = character(1), x_transposed, function(x) ifelse(anyNA(x), NA_character_, ifelse(any(x %in% S_values), "S", "R")), USE.NAMES = FALSE))