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use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

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dr. M.S. (Matthijs) Berends
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions
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R/mean_amr_distance.R
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@ -137,7 +137,7 @@ mean_amr_distance.data.frame <- function(x, ..., combine_SI = TRUE) {
if (!is.null(out)) {
df <- df[, out, drop = FALSE]
} else {
df <- pm_select(df, ...)
df <- select(df, ...)
}
}
df_classes <- colnames(df)[vapply(FUN.VALUE = logical(1), df, function(x) is.disk(x) | is.mic(x) | is.disk(x), USE.NAMES = FALSE)]