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(v2.1.1.9253) parallel computing
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@ -573,6 +573,8 @@ antibiogram.default <- function(x,
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for (ab in abx) {
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# make sure they are SIR columns
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x[, ab] <- as.sir(x[, ab, drop = TRUE])
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# set NI as NA
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x[[ab]][x[[ab]] == "NI"] <- NA_sir_
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}
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new_colname <- paste0(trimws(abx), collapse = sep)
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if (length(abx) == 1) {
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@ -584,7 +586,7 @@ antibiogram.default <- function(x,
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} else {
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S_values <- "S"
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}
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other_values <- setdiff(c("S", "SDD", "I", "R", "NI"), S_values)
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other_values <- setdiff(c("S", "SDD", "I", "R"), S_values)
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x_transposed <- as.list(as.data.frame(t(x[, abx, drop = FALSE]), stringsAsFactors = FALSE))
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if (isTRUE(only_all_tested)) {
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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))
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