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(v1.2.0.9017) ab_from_text() improvement

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dr. M.S. (Matthijs) Berends
2020-06-26 12:31:27 +02:00
parent b31003c0b6
commit 4f6f056077
19 changed files with 239 additions and 118 deletions
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111
R/ab.R
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@ -24,6 +24,7 @@
#' Use this function to determine the antibiotic code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
#' @inheritSection lifecycle Maturing lifecycle
#' @param x character vector to determine to antibiotic ID
#' @param flag_multiple_results logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.
#' @param ... arguments passed on to internal functions
#' @rdname as.ab
#' @inheritSection WHOCC WHOCC
@ -67,7 +68,7 @@
#' # they use as.ab() internally:
#' ab_name("J01FA01") # "Erythromycin"
#' ab_name("eryt") # "Erythromycin"
as.ab <- function(x, ...) {
as.ab <- function(x, flag_multiple_results = TRUE, ...) {
check_dataset_integrity()
@ -75,7 +76,7 @@ as.ab <- function(x, ...) {
return(x)
}
initial <- is.null(list(...)$initial)
initial_search <- is.null(list(...)$initial_search)
already_regex <- isTRUE(list(...)$already_regex)
if (all(toupper(x) %in% antibiotics$ab)) {
@ -114,7 +115,24 @@ as.ab <- function(x, ...) {
x_new <- rep(NA_character_, length(x))
x_unknown <- character(0)
note_if_more_than_one_found <- function(found, index, from_text) {
if (initial_search == TRUE & isTRUE(length(from_text) > 1)) {
message(font_blue(paste0("NOTE: more than one result was found for item ", index, ": ",
paste0(ab_name(from_text, tolower = TRUE, initial_search = FALSE), collapse = ", "))))
}
found[1L]
}
if (initial_search == TRUE) {
progress <- progress_estimated(n = length(x), n_min = 25) # start if n >= 25
on.exit(close(progress))
}
for (i in seq_len(length(x))) {
if (initial_search == TRUE) {
progress$tick()
}
if (is.na(x[i]) | is.null(x[i])) {
next
}
@ -127,31 +145,37 @@ as.ab <- function(x, ...) {
next
}
if (isTRUE(flag_multiple_results) & x[i] %like% "[ ]") {
from_text <- suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE))
} else {
from_text <- character(0)
}
# exact AB code
found <- antibiotics[which(antibiotics$ab == x[i]), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# exact ATC code
found <- antibiotics[which(antibiotics$atc == x[i]), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# exact CID code
found <- antibiotics[which(antibiotics$cid == x[i]), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# exact name
found <- antibiotics[which(toupper(antibiotics$name) == x[i]), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
@ -160,7 +184,7 @@ as.ab <- function(x, ...) {
function(s) x[i] %in% s))
found <- antibiotics$ab[loinc_found == TRUE]
if (length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
@ -169,7 +193,7 @@ as.ab <- function(x, ...) {
function(s) x[i] %in% toupper(s)))
found <- antibiotics$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
@ -178,7 +202,7 @@ as.ab <- function(x, ...) {
function(a) x[i] %in% toupper(a)))
found <- antibiotics$ab[abbr_found == TRUE]
if (length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
@ -213,13 +237,13 @@ as.ab <- function(x, ...) {
# try if name starts with it
found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# try if name ends with it
found <- antibiotics[which(antibiotics$name %like% paste0(x_spelling, "$")), ]$ab
if (nchar(x[i]) >= 4 & length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# and try if any synonym starts with it
@ -227,29 +251,29 @@ as.ab <- function(x, ...) {
function(s) any(s %like% paste0("^", x_spelling))))
found <- antibiotics$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# INITIAL - More uncertain results ----
# INITIAL SEARCH - More uncertain results ----
if (initial == TRUE) {
if (initial_search == TRUE) {
# only run on first try
# try by removing all spaces
if (x[i] %like% " ") {
found <- suppressWarnings(as.ab(gsub(" +", "", x[i]), initial = FALSE))
found <- suppressWarnings(as.ab(gsub(" +", "", x[i]), initial_search = FALSE))
if (length(found) > 0 & !is.na(found)) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
}
# 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]), initial = FALSE))
found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i]), initial_search = FALSE))
if (length(found) > 0 & !is.na(found)) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
}
@ -266,7 +290,7 @@ as.ab <- function(x, ...) {
y
})[[1]],
collapse = "/")
x_translated_guess <- suppressWarnings(as.ab(x_translated, initial = FALSE))
x_translated_guess <- suppressWarnings(as.ab(x_translated, initial_search = FALSE))
if (!is.na(x_translated_guess)) {
x_new[i] <- x_translated_guess
next
@ -276,7 +300,7 @@ as.ab <- function(x, ...) {
x_translated <- paste(lapply(strsplit(x_translated, "[^A-Z0-9 ]"),
function(y) {
for (i in seq_len(length(y))) {
y_name <- suppressWarnings(ab_name(y[i], language = NULL, initial = FALSE))
y_name <- suppressWarnings(ab_name(y[i], language = NULL, initial_search = FALSE))
y[i] <- ifelse(!is.na(y_name),
y_name,
y[i])
@ -284,7 +308,7 @@ as.ab <- function(x, ...) {
y
})[[1]],
collapse = "/")
x_translated_guess <- suppressWarnings(as.ab(x_translated, initial = FALSE))
x_translated_guess <- suppressWarnings(as.ab(x_translated, initial_search = FALSE))
if (!is.na(x_translated_guess)) {
x_new[i] <- x_translated_guess
next
@ -292,60 +316,65 @@ as.ab <- function(x, ...) {
# try by removing all trailing capitals
if (x[i] %like_case% "[a-z]+[A-Z]+$") {
found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i]), initial = FALSE))
found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i]), initial_search = FALSE))
if (!is.na(found)) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
}
# keep only letters
found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i]), initial = FALSE))
found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i]), initial_search = FALSE))
if (!is.na(found)) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# try from a bigger text, like from a health care record, see ?ab_from_text
found <- suppressWarnings(ab_from_text(x[i], initial = FALSE, translate_ab = FALSE)[1L])
# already calculated above if flag_multiple_results = TRUE
if (isTRUE(flag_multiple_results)) {
found <- from_text[1L]
} else {
found <- suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[1L])
}
if (!is.na(found)) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# first 5 except for cephalosporins, then first 7 (those cephalosporins all start quite the same!)
found <- suppressWarnings(as.ab(substr(x[i], 1, 5), initial = FALSE))
if (!is.na(found) && !ab_group(found, initial = FALSE) %like% "cephalosporins") {
x_new[i] <- found[1L]
found <- suppressWarnings(as.ab(substr(x[i], 1, 5), initial_search = FALSE))
if (!is.na(found) && !ab_group(found, initial_search = FALSE) %like% "cephalosporins") {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
found <- suppressWarnings(as.ab(substr(x[i], 1, 7), initial = FALSE))
found <- suppressWarnings(as.ab(substr(x[i], 1, 7), initial_search = FALSE))
if (!is.na(found)) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# make all consonants facultative
search_str <- gsub("([BCDFGHJKLMNPQRSTVWXZ])", "\\1*", x[i])
found <- suppressWarnings(as.ab(search_str, initial = FALSE, already_regex = TRUE))
found <- suppressWarnings(as.ab(search_str, initial_search = FALSE, already_regex = TRUE))
# keep at least 4 normal characters
if (nchar(gsub(".\\*", "", search_str)) < 4) {
found <- NA
}
if (!is.na(found)) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# make all vowels facultative
search_str <- gsub("([AEIOUY])", "\\1*", x[i])
found <- suppressWarnings(as.ab(search_str, initial = FALSE, already_regex = TRUE))
found <- suppressWarnings(as.ab(search_str, initial_search = FALSE, already_regex = TRUE))
# keep at least 5 normal characters
if (nchar(gsub(".\\*", "", search_str)) < 5) {
found <- NA
}
if (!is.na(found)) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
@ -355,17 +384,21 @@ as.ab <- function(x, ...) {
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, initial = FALSE, already_regex = TRUE))
found <- suppressWarnings(as.ab(x_spelling, initial_search = FALSE, already_regex = TRUE))
if (!is.na(found)) {
x_new[i] <- found[1L]
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
} # end of initial = TRUE
} # end of initial_search = TRUE
# not found
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
}
if (initial_search == TRUE) {
close(progress)
}
# take failed ATC codes apart from rest
x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]