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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
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22
R/av_from_text.R
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@ -69,26 +69,26 @@ av_from_text <- function(text,
if (missing(type)) {
type <- type[1L]
}
meet_criteria(text)
meet_criteria(type, allow_class = "character", has_length = 1)
meet_criteria(collapse, has_length = 1, allow_NULL = TRUE)
meet_criteria(translate_av, allow_NULL = FALSE) # get_translate_av() will be more informative about what's allowed
meet_criteria(thorough_search, allow_class = "logical", has_length = 1, allow_NULL = TRUE)
meet_criteria(info, allow_class = "logical", has_length = 1)
type <- tolower(trimws2(type))
text <- tolower(as.character(text))
text_split_all <- strsplit(text, "[ ;.,:\\|]")
progress <- progress_ticker(n = length(text_split_all), n_min = 5, print = info)
on.exit(close(progress))
if (type %like% "(drug|ab|anti)") {
translate_av <- get_translate_av(translate_av)
if (isTRUE(thorough_search) ||
(isTRUE(is.null(thorough_search)) && max(vapply(FUN.VALUE = double(1), text_split_all, length), na.rm = TRUE) <= 3)) {
(isTRUE(is.null(thorough_search)) && max(vapply(FUN.VALUE = double(1), text_split_all, length), na.rm = TRUE) <= 3)) {
text_split_all <- text_split_all[nchar(text_split_all) >= 4 & grepl("[a-z]+", text_split_all)]
result <- lapply(text_split_all, function(text_split) {
progress$tick()
@ -125,9 +125,9 @@ av_from_text <- function(text,
)
})
}
close(progress)
result <- lapply(result, function(out) {
out <- out[!is.na(out)]
if (length(out) == 0) {
@ -149,7 +149,7 @@ av_from_text <- function(text,
text_split <- as.double(gsub("[^0-9.]", "", text_split))
# minimal 100 units/mg and no years that unlikely doses
text_split <- text_split[text_split >= 100 & !text_split %in% c(1951:1999, 2001:2049)]
if (length(text_split) > 0) {
text_split
} else {
@ -170,7 +170,7 @@ av_from_text <- function(text,
} else {
stop_("`type` must be either 'drug', 'dose' or 'administration'")
}
# collapse text if needed
if (!is.null(collapse)) {
result <- vapply(FUN.VALUE = character(1), result, function(x) {
@ -181,6 +181,6 @@ av_from_text <- function(text,
}
})
}
result
}