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fixes

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dr. M.S. (Matthijs) Berends
2026-03-20 15:17:34 +01:00
parent 51f689b069
commit d28671c34d
8 changed files with 94 additions and 92 deletions
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11
R/ab.R
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@@ -191,12 +191,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_new[known_codes_cid] <- AMR_env$AB_lookup$ab[match(x[known_codes_cid], AMR_env$AB_lookup$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)]
previously_coerced_mention <- x %in% AMR_env$ab_previously_coerced$x & !x %in% AMR_env$AB_lookup$ab & !x %in% AMR_env$AB_lookup$generalised_name
previously_coerced_mention <- !is.na(x) & x %in% AMR_env$ab_previously_coerced$x & !x %in% AMR_env$AB_lookup$ab & !x %in% AMR_env$AB_lookup$generalised_name
if (any(previously_coerced_mention) && isTRUE(info) && message_not_thrown_before("as.ab", entire_session = TRUE)) {
only_one <- length(unique(which(x[which(previously_coerced)] %in% x_bak_clean))) == 1
message_(
"Returning previously coerced ",
ifelse(length(unique(which(x[which(previously_coerced)] %in% x_bak_clean))) > 1, "value for an antimicrobial", "values for various antimicrobials"),
". Run `ab_reset_session()` to reset this. This note will be shown once per session."
"Returning ", ifelse(only_one, "a ", ""), "previously coerced ",
ifelse(only_one, "value for an antimicrobial", "values for various antimicrobials"),
". Run {.help [{.fun ab_reset_session}](AMR::ab_reset_session)} to reset this. This note will be shown once per session."
)
}
@@ -464,6 +465,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
}
# Throw note about uncertainties
x_uncertain <- x_uncertain[!is.na(x_uncertain)]
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[!is.na(AMR_env$ab_previously_coerced$x), ]
if (isTRUE(info) && length(x_uncertain) > 0 && fast_mode == FALSE) {
x_uncertain <- unique(x_uncertain)
if (message_not_thrown_before("as.ab", "uncertainties", x_bak)) {