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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
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8
R/mean_amr_distance.R
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@ -49,13 +49,13 @@
#' sir <- random_sir(10)
#' sir
#' mean_amr_distance(sir)
#'
#'
#' mic <- random_mic(10)
#' mic
#' mean_amr_distance(mic)
#' # equal to the Z-score of their log2:
#' (log2(mic) - mean(log2(mic))) / sd(log2(mic))
#'
#'
#' disk <- random_disk(10)
#' disk
#' mean_amr_distance(disk)
@ -143,7 +143,7 @@ mean_amr_distance.data.frame <- function(x, ..., combine_SI = TRUE) {
df_classes <- colnames(df)[vapply(FUN.VALUE = logical(1), df, function(x) is.disk(x) | is.mic(x) | is.disk(x), USE.NAMES = FALSE)]
df_antibiotics <- unname(get_column_abx(df, info = FALSE))
df <- df[, colnames(df)[colnames(df) %in% union(df_classes, df_antibiotics)], drop = FALSE]
stop_if(ncol(df) < 2,
"data set must contain at least two variables",
call = -2
@ -151,7 +151,7 @@ mean_amr_distance.data.frame <- function(x, ..., combine_SI = TRUE) {
if (message_not_thrown_before("mean_amr_distance", "groups")) {
message_("Calculating mean AMR distance based on columns ", vector_and(colnames(df), sort = FALSE))
}
res <- vapply(
FUN.VALUE = double(nrow(df)),
df,