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new SDD and N for as.sir()

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dr. M.S. (Matthijs) Berends
2024-05-20 15:27:04 +02:00
parent b68f47d985
commit 08a27922a8
28 changed files with 225 additions and 172 deletions
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4
R/antibiogram.R
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@ -348,11 +348,11 @@ antibiogram <- function(x,
} else {
# determine whether this new column should contain S, I, R, or NA
if (isTRUE(combine_SI)) {
S_values <- c("S", "I")
S_values <- c("S", "SDD", "I")
} else {
S_values <- "S"
}
other_values <- setdiff(c("S", "I", "R"), S_values)
other_values <- setdiff(c("S", "SDD", "I", "R", "N"), 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))