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(v1.2.0.9022) as.ab() improvement

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dr. M.S. (Matthijs) Berends
2020-07-01 16:21:36 +02:00
parent afc660dc33
commit 298e67a45b
15 changed files with 84 additions and 29 deletions
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40
R/ab.R
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@ -29,6 +29,13 @@
#' @rdname as.ab
#' @inheritSection WHOCC WHOCC
#' @details All entries in the [antibiotics] data set have three different identifiers: a human readable EARS-Net code (column `ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO), and a CID code (column `cid`, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.
#'
#' All these properties will be searched for the user input. The [as.ab()] can correct for different forms of misspelling:
#'
#' * Wrong spelling of drug names (like "tobramicin" or "gentamycin"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.
#' * Too few or too many vowels or consonants
#' * Switching two characters (like "mreopenem", often the case in clinical data, when doctors typed too fast)
#' * Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.
#'
#' Use the [ab_property()] functions to get properties based on the returned antibiotic ID, see Examples.
#'
@ -231,7 +238,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
# replace spaces and slashes with a possibility on both
x_spelling <- gsub("[ /]", "( .*|.*/)", x_spelling)
# correct for digital reading text (OCR)
x_spelling <- gsub("[NRD]", "[NRD]", x_spelling)
x_spelling <- gsub("[NRD8B]", "[NRD8B]", x_spelling)
x_spelling <- gsub("(O|0)", "(O|0)+", x_spelling)
x_spelling <- gsub("++", "+", x_spelling, fixed = TRUE)
}
# try if name starts with it
@ -246,6 +255,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# and try if any synonym starts with it
synonym_found <- unlist(lapply(antibiotics$synonyms,
function(s) any(s %like% paste0("^", x_spelling))))
@ -254,7 +264,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
next
}
# INITIAL SEARCH - More uncertain results ----
if (initial_search == TRUE) {
@ -341,7 +351,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
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_search = FALSE))
if (!is.na(found) && !ab_group(found, initial_search = FALSE) %like% "cephalosporins") {
@ -365,7 +375,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
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_search = FALSE, already_regex = TRUE))
@ -390,8 +400,28 @@ as.ab <- function(x, flag_multiple_results = TRUE, ...) {
next
}
# try with switched character, like "mreopenem"
for (j in seq_len(nchar(x[i]))) {
x_switched <- paste0(
# beginning part:
substr(x[i], 1, j - 1),
# here is the switching of 2 characters:
substr(x[i], j + 1, j + 1),
substr(x[i], j, j),
# ending part:
substr(x[i], j + 2, nchar(x[i])))
found <- suppressWarnings(as.ab(x_switched, initial_search = FALSE))
if (!is.na(found)) {
break
}
}
if (!is.na(found)) {
x_new[i] <- found[1L]
next
}
} # end of initial_search = TRUE
# not found
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
}