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fix for NA in as.ab()

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dr. M.S. (Matthijs) Berends
2022-10-10 15:44:59 +02:00
parent 43c638d122
commit 4fe90092c7
13 changed files with 67 additions and 47 deletions
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24
R/ab.R
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@ -135,7 +135,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
abnames <- abnames[!abnames %in% c("clavulanic acid", "avibactam")]
}
if (length(abnames) > 1) {
message_(
warning_(
"More than one result was found for item ", index, ": ",
vector_and(abnames, quotes = FALSE)
)
@ -164,13 +164,19 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
USE.NAMES = FALSE
)]
x_new[known_codes_cid] <- AB_lookup$ab[match(x[known_codes_cid], AB_lookup$cid)]
already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid
previously_coerced <- x %in% AMR_env$ab_previously_coerced$x
x_new[previously_coerced & is.na(x_new)] <- AMR_env$ab_previously_coerced$ab[match(x[is.na(x_new) & x %in% AMR_env$ab_previously_coerced$x], AMR_env$ab_previously_coerced$x)]
already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid | previously_coerced
# fix for NAs
x_new[is.na(x)] <- NA
already_known[is.na(x)] <- FALSE
if (initial_search == TRUE && sum(already_known) < length(x)) {
progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
on.exit(close(progress))
}
for (i in which(!already_known)) {
if (initial_search == TRUE) {
progress$tick()
@ -481,6 +487,16 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
if (initial_search == TRUE && sum(already_known) < length(x)) {
close(progress)
}
# save to package env to save time for next time
AMR_env$ab_previously_coerced <- unique(rbind(AMR_env$ab_previously_coerced,
data.frame(
x = x,
ab = x_new,
stringsAsFactors = FALSE
),
stringsAsFactors = FALSE
))
# take failed ATC codes apart from rest
if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {