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(v1.4.0.9030) as.mo() fix for known lab codes

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dr. M.S. (Matthijs) Berends
2020-12-03 16:59:04 +01:00
parent 4c114ff4b4
commit e03b3c96d3
40 changed files with 136 additions and 124 deletions
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18
R/guess_ab_col.R
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@ -44,7 +44,7 @@
#' # [1] "tetr"
#'
#' guess_ab_col(df, "J01AA07", verbose = TRUE)
#' # NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).
#' # NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).
#' # [1] "tetr"
#'
#' # WHONET codes
@ -94,16 +94,16 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE) {
if (length(ab_result) == 0) {
if (verbose == TRUE) {
message_("No column found as input for `", search_string,
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").",
message_("No column found as input for ", search_string,
" (", ab_name(search_string, language = NULL, tolower = TRUE), ").",
add_fn = font_black,
as_note = FALSE)
}
return(NULL)
} else {
if (verbose == TRUE) {
message_("Using column `", font_bold(ab_result), "` as input for `", search_string,
"` (", ab_name(search_string, language = NULL, tolower = TRUE), ").")
message_("Using column '", font_bold(ab_result), "' as input for ", search_string,
" (", ab_name(search_string, language = NULL, tolower = TRUE), ").")
}
return(ab_result)
}
@ -204,12 +204,12 @@ get_column_abx <- function(x,
for (i in seq_len(length(x))) {
if (info == TRUE & verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
message_("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
message_("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
" (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
}
if (info == TRUE & names(x[i]) %in% names(duplicates)) {
warning_(paste0("Using column `", font_bold(x[i]), "` as input for `", names(x)[i],
"` (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
warning_(paste0("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
" (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
"), although it was matched for multiple antibiotics or columns."),
add_fn = font_red,
call = FALSE,