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(v2.1.1.9041) antibiotics update

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dr. M.S. (Matthijs) Berends
2024-06-08 17:35:25 +02:00
parent e2acc513a5
commit af74e1d4f2
26 changed files with 110 additions and 67 deletions
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11
R/mic.R
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@@ -43,6 +43,9 @@ VALID_MIC_LEVELS <- c(t(vapply(FUN.VALUE = character(length(VALID_MIC_LEVELS)),
c("<", "<=", "", ">=", ">"),
paste0,
VALID_MIC_LEVELS)))
COMMON_MIC_VALUES <- c(0.001, 0.002, 0.004, 0.008, 0.016, 0.032, 0.064,
0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32,
64, 128, 256, 512, 1024)
#' Transform Input to Minimum Inhibitory Concentrations (MIC)
#'
@@ -300,10 +303,10 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
}
# create a manual factor with levels only within desired range
expanded <- range_as_table(x,
expand = TRUE,
keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
mic_range = mic_range)
expanded <- plotrange_as_table(x,
expand = TRUE,
keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
mic_range = mic_range)
if (keep_operators == "edges") {
names(expanded)[1] <- paste0("<=", names(expanded)[1])
names(expanded)[length(expanded)] <- paste0(">=", names(expanded)[length(expanded)])