mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 21:01:57 +02:00
(v2.1.1.9158) updated as.ab
This commit is contained in:
20
R/ab.R
20
R/ab.R
@ -349,6 +349,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), loop_time = loop_time + 2))
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if (length(found) > 0 && !is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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}
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@ -358,6 +359,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
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if (length(found) > 0 && !is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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}
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@ -392,6 +394,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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if (length(found_perms) > 0) {
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found <- found_perms[order(nchar(found_perms), decreasing = TRUE)][1]
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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}
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@ -418,6 +421,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 2))
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if (!is.na(x_translated_guess)) {
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x_new[i] <- x_translated_guess
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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@ -441,6 +445,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 2))
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if (!is.na(x_translated_guess)) {
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x_new[i] <- x_translated_guess
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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@ -449,6 +454,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i], perl = TRUE), loop_time = loop_time + 2))
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if (!is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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}
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@ -457,6 +463,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
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if (!is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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@ -471,6 +478,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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}
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if (!is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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@ -483,6 +491,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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found <- suppressWarnings(as.ab(substr(x[i], 1, 7), loop_time = loop_time + 2))
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if (!is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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@ -495,6 +504,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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}
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if (!is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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@ -507,6 +517,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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}
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if (!is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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@ -519,6 +530,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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found <- suppressWarnings(as.ab(x_spelling, loop_time = loop_time + 2, already_regex = TRUE))
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if (!is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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@ -540,6 +552,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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}
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if (!is.na(found)) {
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x_new[i] <- found[1L]
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x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
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next
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}
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} # end of loop_time <= 2
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@ -590,11 +603,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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# Throw note about uncertainties
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if (isTRUE(info) && length(x_uncertain) > 0 && fast_mode == FALSE) {
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x_uncertain <- unique(x_uncertain)
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if (message_not_thrown_before("as.ab", "uncertainties", x_bak)) {
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plural <- c("", "this")
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if (length(x_uncertain) > 1) {
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plural <- c("s", "these uncertainties")
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}
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if (length(x_uncertain) <= 3) {
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examples <- vector_and(
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paste0(
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@ -603,7 +613,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
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", ", AMR_env$ab_previously_coerced$ab[which(AMR_env$ab_previously_coerced$x_bak %in% x_uncertain)], ")"),
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quotes = FALSE)
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} else {
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examples <- paste0(nr2char(length(x_uncertain)), " antimicrobial", plural[1])
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examples <- paste0(nr2char(length(x_uncertain)), " antimicrobials")
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}
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message_("Antimicrobial translation was uncertain for ", examples,
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". If required, use `add_custom_antimicrobials()` to add custom entries.")
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