P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 19:41:58 +02:00
Code Releases Activity

allow column name for ab in as.sir()

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-05-20 21:29:13 +02:00
parent fc269e667d
commit d214f74e25
10 changed files with 139 additions and 106 deletions
Download Patch File Download Diff File Expand all files Collapse all files

27
R/ab.R
View File

@ -322,13 +322,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
# INITIAL SEARCH - More uncertain results ----
if (loop_time <= 2 && fast_mode == FALSE) {
# only run on first and second try
# try by removing all spaces
if (x[i] %like% " ") {
found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), loop_time = loop_time + 1))
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)
next
@ -337,7 +336,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# try by removing all spaces and numbers
if (x[i] %like% " " || x[i] %like% "[0-9]") {
found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), loop_time = loop_time + 1))
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)
next
@ -363,7 +362,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
)[[1]],
collapse = "/"
)
x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 1))
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
next
@ -375,7 +374,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
strsplit(x_translated, "[^A-Z0-9 ]"),
function(y) {
for (i in seq_len(length(y))) {
y_name <- suppressWarnings(ab_name(y[i], language = NULL, loop_time = loop_time + 1))
y_name <- suppressWarnings(ab_name(y[i], language = NULL, loop_time = loop_time + 2))
y[i] <- ifelse(!is.na(y_name),
y_name,
y[i]
@ -386,7 +385,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
)[[1]],
collapse = "/"
)
x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 1))
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
next
@ -394,7 +393,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# try by removing all trailing capitals
if (x[i] %like_case% "[a-z]+[A-Z]+$") {
found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i], perl = TRUE), loop_time = loop_time + 1))
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)
next
@ -402,7 +401,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
# keep only letters
found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i], perl = TRUE), loop_time = loop_time + 1))
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)
next
@ -413,7 +412,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
if (flag_multiple_results == TRUE) {
found <- from_text[1L]
} else {
found <- tryCatch(suppressWarnings(ab_from_text(x[i], loop_time = loop_time + 1, translate_ab = FALSE)[[1]][1L]),
found <- tryCatch(suppressWarnings(ab_from_text(x[i], loop_time = loop_time + 2, translate_ab = FALSE)[[1]][1L]),
error = function(e) NA_character_
)
}
@ -423,12 +422,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
}
# first 5 except for cephalosporins, then first 7 (those cephalosporins all start quite the same!)
found <- suppressWarnings(as.ab(substr(x[i], 1, 5), loop_time = loop_time + 1))
found <- suppressWarnings(as.ab(substr(x[i], 1, 5), loop_time = loop_time + 2))
if (!is.na(found) && ab_group(found, loop_time = loop_time + 1) %unlike% "cephalosporins") {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
found <- suppressWarnings(as.ab(substr(x[i], 1, 7), loop_time = loop_time + 1))
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)
next
@ -436,7 +435,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# make all consonants facultative
search_str <- gsub("([BCDFGHJKLMNPQRSTVWXZ])", "\\1*", x[i], perl = TRUE)
found <- suppressWarnings(as.ab(search_str, loop_time = loop_time + 1, already_regex = TRUE))
found <- suppressWarnings(as.ab(search_str, loop_time = loop_time + 2, already_regex = TRUE))
# keep at least 4 normal characters
if (nchar(gsub(".\\*", "", search_str, perl = TRUE)) < 4) {
found <- NA
@ -448,7 +447,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
# make all vowels facultative
search_str <- gsub("([AEIOUY])", "\\1*", x[i], perl = TRUE)
found <- suppressWarnings(as.ab(search_str, loop_time = loop_time + 1, already_regex = TRUE))
found <- suppressWarnings(as.ab(search_str, loop_time = loop_time + 2, already_regex = TRUE))
# keep at least 5 normal characters
if (nchar(gsub(".\\*", "", search_str, perl = TRUE)) < 5) {
found <- NA
@ -464,7 +463,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_spelling <- gsub("I+", "[AEIOU]+", x_spelling, fixed = TRUE)
x_spelling <- gsub("O+", "[AEIOU]+", x_spelling, fixed = TRUE)
x_spelling <- gsub("U+", "[AEIOU]+", x_spelling, fixed = TRUE)
found <- suppressWarnings(as.ab(x_spelling, loop_time = loop_time + 1, already_regex = TRUE))
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)
next