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(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

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Fixes #246
Fixes #254
Fixes #255
Fixes #256
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-02-08 23:15:40 +01:00
parent 2df2911cf4
commit ba4c159154
31 changed files with 394 additions and 165 deletions
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12
R/antibiogram.R
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@@ -560,12 +560,11 @@ antibiogram.default <- function(x,
next
} else {
# determine whether this new column should contain S, I, R, or NA
S_values <- c("S", "WT")
if (isTRUE(combine_SI)) {
S_values <- c("S", "SDD", "I")
} else {
S_values <- "S"
S_values <- c(S_values, "SDD", "I")
}
other_values <- setdiff(c("S", "SDD", "I", "R"), S_values)
other_values <- setdiff(c("S", "SDD", "I", "R", "WT", "NWT", "NS"), 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))
@@ -615,10 +614,9 @@ antibiogram.default <- function(x,
counts <- out
out$n_susceptible <- out$S + out$WT
if (isTRUE(combine_SI)) {
out$n_susceptible <- out$S + out$I + out$SDD
} else {
out$n_susceptible <- out$S
out$n_susceptible <- out$n_susceptible + out$I + out$SDD
}
if (all(out$n_tested < minimum, na.rm = TRUE) && wisca == FALSE) {
warning_("All combinations had less than `minimum = ", minimum, "` results, returning an empty antibiogram")