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(v0.7.1.9102) lintr

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-10-11 17:21:02 +02:00
parent 59af355a89
commit 00cdb498a0
65 changed files with 620 additions and 812 deletions
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26
R/ab.R
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@ -79,8 +79,6 @@ as.ab <- function(x, ...) {
x_bak_clean <- gsub("_[A-Z]{2}[0-9_]{0,3}$", "", x_bak_clean, ignore.case = TRUE)
# remove part between brackets if that's followed by another string
x_bak_clean <- gsub("(.*)+ [(].*[)]", "\\1", x_bak_clean)
# keep only a-Z, 0-9, space, slash and dash
# x_bak_clean <- gsub("[^A-Z0-9 /-]", "", x_bak_clean, ignore.case = TRUE)
# keep only max 1 space
x_bak_clean <- trimws(gsub(" +", " ", x_bak_clean, ignore.case = TRUE))
# non-character, space or number should be a slash
@ -93,7 +91,7 @@ as.ab <- function(x, ...) {
x_new <- rep(NA_character_, length(x))
x_unknown <- character(0)
for (i in 1:length(x)) {
for (i in seq_len(length(x))) {
if (is.na(x[i]) | is.null(x[i])) {
next
}
@ -108,28 +106,28 @@ as.ab <- function(x, ...) {
}
# exact AB code
found <- AMR::antibiotics[which(AMR::antibiotics$ab == toupper(x[i])),]$ab
found <- AMR::antibiotics[which(AMR::antibiotics$ab == toupper(x[i])), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
next
}
# exact ATC code
found <- AMR::antibiotics[which(AMR::antibiotics$atc == toupper(x[i])),]$ab
found <- AMR::antibiotics[which(AMR::antibiotics$atc == toupper(x[i])), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
next
}
# exact CID code
found <- AMR::antibiotics[which(AMR::antibiotics$cid == x[i]),]$ab
found <- AMR::antibiotics[which(AMR::antibiotics$cid == x[i]), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
next
}
# exact name
found <- AMR::antibiotics[which(toupper(AMR::antibiotics$name) == toupper(x[i])),]$ab
found <- AMR::antibiotics[which(toupper(AMR::antibiotics$name) == toupper(x[i])), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
next
@ -163,7 +161,7 @@ as.ab <- function(x, ...) {
# first >=4 characters of name
if (nchar(x[i]) >= 4) {
found <- AMR::antibiotics[which(toupper(AMR::antibiotics$name) %like% paste0("^", x[i])),]$ab
found <- AMR::antibiotics[which(toupper(AMR::antibiotics$name) %like% paste0("^", x[i])), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
next
@ -193,7 +191,7 @@ as.ab <- function(x, ...) {
x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
# try if name starts with it
found <- AMR::antibiotics[which(AMR::antibiotics$name %like% paste0("^", x_spelling)),]$ab
found <- AMR::antibiotics[which(AMR::antibiotics$name %like% paste0("^", x_spelling)), ]$ab
if (length(found) > 0) {
x_new[i] <- found[1L]
next
@ -233,7 +231,7 @@ as.ab <- function(x, ...) {
# transform back from other languages and try again
x_translated <- paste(lapply(strsplit(x[i], "[^a-zA-Z0-9 ]"),
function(y) {
for (i in 1:length(y)) {
for (i in seq_len(length(y))) {
y[i] <- ifelse(tolower(y[i]) %in% tolower(translations_file$replacement),
translations_file[which(tolower(translations_file$replacement) == tolower(y[i]) &
!isFALSE(translations_file$fixed)), "pattern"],
@ -252,7 +250,7 @@ as.ab <- function(x, ...) {
# now also try to coerce brandname combinations like "Amoxy/clavulanic acid"
x_translated <- paste(lapply(strsplit(x_translated, "[^a-zA-Z0-9 ]"),
function(y) {
for (i in 1:length(y)) {
for (i in seq_len(length(y))) {
y_name <- suppressWarnings(ab_name(y[i], language = NULL, initial_search = FALSE, initial_search2 = FALSE))
y[i] <- ifelse(!is.na(y_name),
y_name,
@ -278,14 +276,14 @@ as.ab <- function(x, ...) {
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
if (length(x_unknown_ATCs) > 0) {
warning("These ATC codes are not (yet) in the antibiotics data set: ",
paste('"', sort(unique(x_unknown_ATCs)), '"', sep = "", collapse = ', '),
paste('"', sort(unique(x_unknown_ATCs)), '"', sep = "", collapse = ", "),
".",
call. = FALSE)
}
if (length(x_unknown) > 0) {
warning("These values could not be coerced to a valid antimicrobial ID: ",
paste('"', sort(unique(x_unknown)), '"', sep = "", collapse = ', '),
paste('"', sort(unique(x_unknown)), '"', sep = "", collapse = ", "),
".",
call. = FALSE)
}
@ -319,7 +317,7 @@ print.ab <- function(x, ...) {
#' @exportMethod as.data.frame.ab
#' @export
#' @noRd
as.data.frame.ab <- function (x, ...) {
as.data.frame.ab <- function(x, ...) {
# same as as.data.frame.character but with removed stringsAsFactors
nm <- paste(deparse(substitute(x), width.cutoff = 500L),
collapse = " ")