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cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-31 13:25:41 +01:00
parent 796b972f8a
commit d20caae54b
7 changed files with 53 additions and 41 deletions
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R/ab.R
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@ -498,6 +498,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
data.frame(
x = x,
ab = x_new,
x_bak = x_bak[match(x, x_bak_clean)],
stringsAsFactors = FALSE
),
stringsAsFactors = FALSE
@ -513,7 +514,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
x_unknown <- c(x_unknown,
AMR_env$ab_previously_coerced$x[which(AMR_env$ab_previously_coerced$x %in% x & is.na(AMR_env$ab_previously_coerced$ab))])
AMR_env$ab_previously_coerced$x_bak[which(AMR_env$ab_previously_coerced$x %in% x & is.na(AMR_env$ab_previously_coerced$ab))])
if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_(
"in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",