P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 19:01:51 +02:00
Code Releases Activity

(v1.1.0.9010) lose dependencies

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-05-18 11:09:02 +02:00
parent bf0402a653
commit d659c9baef
14 changed files with 37 additions and 46 deletions
Download Patch File Download Diff File Expand all files Collapse all files

14
R/guess_ab_col.R
View File

@ -79,8 +79,8 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
if (search_string.ab %in% colnames(x)) {
ab_result <- colnames(x)[colnames(x) == search_string.ab][1L]
} else if (any(tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations"))))) {
ab_result <- colnames(x)[tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations")))][1L]
} else if (any(tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations", language = NULL))))) {
ab_result <- colnames(x)[tolower(colnames(x)) %in% tolower(unlist(ab_property(search_string.ab, "abbreviations", language = NULL)))][1L]
} else {
# sort colnames on length - longest first
@ -96,13 +96,13 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
if (length(ab_result) == 0) {
if (verbose == TRUE) {
message(paste0("No column found as input for `", search_string,
"` (", ab_name(search_string, language = "en", tolower = TRUE), ")."))
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ")."))
}
return(NULL)
} else {
if (verbose == TRUE) {
message(font_blue(paste0("NOTE: Using column `", font_bold(ab_result), "` as input for `", search_string,
"` (", ab_name(search_string, language = "en", tolower = TRUE), ").")))
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").")))
}
return(ab_result)
}
@ -173,11 +173,11 @@ get_column_abx <- function(x,
for (i in seq_len(length(x))) {
if (verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
message(font_blue(paste0("NOTE: Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE), ").")))
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")))
}
if (names(x[i]) %in% names(duplicates)) {
warning(font_red(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE),
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
"), although it was matched for multiple antibiotics or columns.")),
call. = FALSE,
immediate. = verbose)
@ -210,7 +210,7 @@ get_column_abx <- function(x,
}
generate_warning_abs_missing <- function(missing, any = FALSE) {
missing <- paste0(missing, " (", ab_name(missing, tolower = TRUE), ")")
missing <- paste0(missing, " (", ab_name(missing, tolower = TRUE, language = NULL), ")")
if (any == TRUE) {
any_txt <- c(" any of", "is")
} else {