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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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6
R/aa_helper_functions.R
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@ -146,7 +146,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
# WHONET support
found <- sort(colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"])[1]
if (!any(class(pm_pull(x, found)) %in% c("Date", "POSIXct"))) {
stop(font_red(paste0("ERROR: Found column `", font_bold(found), "` to be used as input for `col_", type,
stop(font_red(paste0("Found column '", font_bold(found), "' to be used as input for `col_", type,
"`, but this column contains no valid dates. Transform its values to valid dates first.")),
call. = FALSE)
}
@ -178,7 +178,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
if (!is.null(found)) {
# this column should contain logicals
if (!is.logical(x[, found, drop = TRUE])) {
message_("Column `", font_bold(found), "` found as input for `col_", type,
message_("Column '", font_bold(found), "' found as input for `col_", type,
"`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.",
add_fn = font_red)
found <- NULL
@ -187,7 +187,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
}
if (!is.null(found) & info == TRUE) {
msg <- paste0("Using column `", font_bold(found), "` as input for `col_", type, "`.")
msg <- paste0("Using column '", found, "' as input for `col_", type, "`.")
if (type %in% c("keyantibiotics", "specimen")) {
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
}