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(v1.3.0.9023) optimalisation

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dr. M.S. (Matthijs) Berends
2020-09-19 11:54:01 +02:00
parent 4e40e42011
commit d049cce69b
30 changed files with 104 additions and 578 deletions
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12
R/ab.R
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@ -104,7 +104,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
}
x <- unique(x_bak_clean)
x <- unique(x_bak_clean) # this means that every x is in fact generalise_antibiotic_name(x)
x_new <- rep(NA_character_, length(x))
x_unknown <- character(0)
@ -174,7 +174,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
# exact LOINC code
loinc_found <- unlist(lapply(AB_lookup$generalised_loinc,
function(s) generalise_antibiotic_name(x[i]) %in% s))
function(s) x[i] %in% s))
found <- antibiotics$ab[loinc_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
@ -183,7 +183,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
# exact synonym
synonym_found <- unlist(lapply(AB_lookup$generalised_synonyms,
function(s) generalise_antibiotic_name(x[i]) %in% s))
function(s) x[i] %in% s))
found <- antibiotics$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
@ -192,7 +192,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
# exact abbreviation
abbr_found <- unlist(lapply(AB_lookup$generalised_abbreviations,
function(s) generalise_antibiotic_name(x[i]) %in% s))
function(s) x[i] %in% s))
found <- antibiotics$ab[abbr_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
@ -244,7 +244,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
# and try if any synonym starts with it
synonym_found <- unlist(lapply(AB_lookup$generalised_synonyms,
function(s) any(generalise_antibiotic_name(s) %like% paste0("^", x_spelling))))
function(s) any(s %like% paste0("^", x_spelling))))
found <- antibiotics$ab[synonym_found == TRUE]
if (length(found) > 0) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)
@ -532,7 +532,7 @@ generalise_antibiotic_name <- function(x) {
# remove part between brackets if that's followed by another string
x <- gsub("(.*)+ [(].*[)]", "\\1", x)
# keep only max 1 space
x <- trimws(gsub(" +", " ", x))
x <- trimws2(gsub(" +", " ", x))
# non-character, space or number should be a slash
x <- gsub("[^A-Z0-9 -]", "/", x)
# spaces around non-characters must be removed: amox + clav -> amox/clav