P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 13:01:51 +02:00
Code Releases Activity

fix antibiotics error

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-30 21:05:46 +01:00
parent d40e0ef20b
commit 9444ed6d1d
37 changed files with 86 additions and 97 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
R/ab.R
View File

@ -492,14 +492,17 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
# save to package env to save time for next time
AMR_env$ab_previously_coerced <- unique(rbind(AMR_env$ab_previously_coerced,
data.frame(
x = x,
ab = x_new,
if (initial_search == TRUE) {
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE]
AMR_env$ab_previously_coerced <- unique(rbind(AMR_env$ab_previously_coerced,
data.frame(
x = x,
ab = x_new,
stringsAsFactors = FALSE
),
stringsAsFactors = FALSE
),
stringsAsFactors = FALSE
))
))
}
# take failed ATC codes apart from rest
if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
@ -509,7 +512,8 @@ 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))])
if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_(
"in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",