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(v2.1.1.9158) updated as.ab

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dr. M.S. (Matthijs) Berends
2025-02-26 13:32:16 +01:00
parent 195dfb4b91
commit 122bca0f95
9 changed files with 21 additions and 11 deletions
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20
R/ab.R
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@ -349,6 +349,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), loop_time = loop_time + 2))
if (length(found) > 0 && !is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
}
@ -358,6 +359,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
if (length(found) > 0 && !is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
}
@ -392,6 +394,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
if (length(found_perms) > 0) {
found <- found_perms[order(nchar(found_perms), decreasing = TRUE)][1]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
}
@ -418,6 +421,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 2))
if (!is.na(x_translated_guess)) {
x_new[i] <- x_translated_guess
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -441,6 +445,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 2))
if (!is.na(x_translated_guess)) {
x_new[i] <- x_translated_guess
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -449,6 +454,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i], perl = TRUE), loop_time = loop_time + 2))
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
}
@ -457,6 +463,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -471,6 +478,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -483,6 +491,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(substr(x[i], 1, 7), loop_time = loop_time + 2))
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -495,6 +504,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -507,6 +517,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -519,6 +530,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
found <- suppressWarnings(as.ab(x_spelling, loop_time = loop_time + 2, already_regex = TRUE))
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
@ -540,6 +552,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
if (!is.na(found)) {
x_new[i] <- found[1L]
x_uncertain <- c(x_uncertain, x_bak[x[i] == x_bak_clean][1])
next
}
} # end of loop_time <= 2
@ -590,11 +603,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# Throw note about uncertainties
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)) {
plural <- c("", "this")
if (length(x_uncertain) > 1) {
plural <- c("s", "these uncertainties")
}
if (length(x_uncertain) <= 3) {
examples <- vector_and(
paste0(
@ -603,7 +613,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
", ", AMR_env$ab_previously_coerced$ab[which(AMR_env$ab_previously_coerced$x_bak %in% x_uncertain)], ")"),
quotes = FALSE)
} else {
examples <- paste0(nr2char(length(x_uncertain)), " antimicrobial", plural[1])
examples <- paste0(nr2char(length(x_uncertain)), " antimicrobials")
}
message_("Antimicrobial translation was uncertain for ", examples,
". If required, use `add_custom_antimicrobials()` to add custom entries.")