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ab_info, other bug fixes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-05-16 21:20:00 +02:00
parent f6bf54b37d
commit 4c3cf85a65
57 changed files with 519 additions and 430 deletions
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47
R/ab.R
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@ -52,7 +52,7 @@
#' as.ab(" eryt 123")
#' as.ab("ERYT")
#' as.ab("ERY")
#' as.ab("erytromicine") # spelled wrong
#' as.ab("eritromicine") # spelled wrong, yet works
#' as.ab("Erythrocin") # trade name
#' as.ab("Romycin") # trade name
#'
@ -64,13 +64,20 @@ as.ab <- function(x) {
if (is.ab(x)) {
return(x)
}
if (all(toupper(x) %in% AMR::antibiotics$ab)) {
# valid AB code, but not yet right class
return(structure(.Data = toupper(x),
class = "ab"))
}
x_bak <- x
# remove suffices
x_bak_clean <- gsub("_(mic|rsi|disk|disc)$", "", x)
x_bak_clean <- gsub("_(mic|rsi|disk|disc)$", "", x, ignore.case = TRUE)
# remove disk concentrations, like LVX_NM -> LVX
x_bak_clean <- gsub("_[A-Z]{2}[0-9_]{0,3}$", "", x_bak_clean, ignore.case = TRUE)
# clean rest of it
x_bak_clean <- gsub("[^a-zA-Z0-9/-]", "", x_bak_clean)
x_bak_clean <- gsub("[^A-Z0-9/-]", "", x_bak_clean, ignore.case = TRUE)
# keep only a-z when it's not an ATC code or only numbers
x_bak_clean[!x_bak_clean %like% "^([A-Z][0-9]{2}[A-Z]{2}[0-9]{2}|[0-9]+)$"] <- gsub("[^a-zA-Z]+",
"",
@ -156,19 +163,25 @@ as.ab <- function(x) {
x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
next
}
x_spelling <- x[i]
x_spelling <- gsub("[iy]+", "[iy]+", x_spelling, ignore.case = TRUE)
x_spelling <- gsub("[sz]+", "[sz]+", x_spelling, ignore.case = TRUE)
x_spelling <- gsub("(c|k|q|qu)+", "(c|k|q|qu)+", x_spelling, ignore.case = TRUE)
x_spelling <- gsub("(ph|f|v)+", "(ph|f|v)+", x_spelling, ignore.case = TRUE)
x_spelling <- gsub("(th|t)+", "(th|t)+", x_spelling, ignore.case = TRUE)
x_spelling <- gsub("a+", "a+", x_spelling, ignore.case = TRUE)
x_spelling <- gsub("e+", "e+", x_spelling, ignore.case = TRUE)
x_spelling <- gsub("o+", "o+", x_spelling, ignore.case = TRUE)
x_spelling <- tolower(x[i])
x_spelling <- gsub("[iy]+", "[iy]+", x_spelling)
x_spelling <- gsub("[sz]+", "[sz]+", x_spelling)
x_spelling <- gsub("(c|k|q|qu)+", "(c|k|q|qu)+", x_spelling)
x_spelling <- gsub("(ph|f|v)+", "(ph|f|v)+", x_spelling)
x_spelling <- gsub("(th|t)+", "(th|t)+", x_spelling)
x_spelling <- gsub("(x|ks)+", "(x|ks)+", x_spelling)
x_spelling <- gsub("a+", "a+", x_spelling)
x_spelling <- gsub("e+", "e+", x_spelling)
x_spelling <- gsub("o+", "o+", x_spelling)
# allow start with C/S/Z
x_spelling <- gsub("^(\\(c\\|k\\|q\\|qu\\)|\\[sz\\])", "(c|k|q|qu|s|z)", x_spelling)
x_spelling <- gsub("(c|k|q|qu)+[sz]", "(c|k|q|qu|s|x|z)", x_spelling, fixed = TRUE)
# allow any ending of -in/-ine and -im/-ime
x_spelling <- gsub("(\\[iy\\]\\+(n|m)|\\[iy\\]\\+(n|m)e\\+)$", "[iy]+(n|m)e*", x_spelling, ignore.case = TRUE)
x_spelling <- gsub("(\\[iy\\]\\+(n|m)|\\[iy\\]\\+(n|m)e\\+)$", "[iy]+(n|m)e*", x_spelling)
# allow any ending of -ol/-ole
x_spelling <- gsub("(o\\+l|o\\+le\\+)$", "o+le*", x_spelling, ignore.case = TRUE)
x_spelling <- gsub("(o\\+l|o\\+le\\+)$", "o+le*", x_spelling)
# allow any ending of -on/-one
x_spelling <- gsub("(o\\+n|o\\+ne\\+)$", "o+ne*", x_spelling)
# try if name starts with it
found <- AMR::antibiotics[which(AMR::antibiotics$name %like% paste0("^", x_spelling)),]$ab
if (length(found) > 0) {
@ -203,11 +216,15 @@ as.ab <- function(x) {
left_join(data.frame(x = x, x_new = x_new, stringsAsFactors = FALSE), by = "x") %>%
pull(x_new)
if (length(x_result) == 0) {
x_result <- NA_character_
}
structure(.Data = x_result,
class = "ab")
}
#' @rdname as.atc
#' @rdname as.ab
#' @export
is.ab <- function(x) {
identical(class(x), "ab")