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fix add manual ab

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-18 22:53:38 +02:00
parent ad68b50ecd
commit e5e6d2200d
6 changed files with 19 additions and 7 deletions
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10
R/add_custom_antimicrobials.R
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@ -112,13 +112,19 @@ add_custom_antimicrobials <- function(x) {
AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
class(AMR_env$AB_lookup$ab) <- "character"
bind_rows <- import_fn("bind_rowtts", "dplyr", error_on_fail = FALSE)
bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
if (is.null(bind_rows)) {
# do the binding in base R
new_df <- AMR_env$AB_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
rownames(new_df) <- NULL
list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list)
for (l in which(list_cols)) {
# prevent binding NULLs in lists, replace with NA
new_df[, l] <- as.list(NA_character_)
}
for (col in colnames(x)) {
new_df[, col] <- x[, col, drop = TRUE]
# assign new values
new_df[, col] <- x[, col, drop = TRUE]
}
AMR_env$AB_lookup <- unique(rbind(AMR_env$AB_lookup, new_df))
} else {