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(v0.7.1.9066) bug-drug fix

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dr. M.S. (Matthijs) Berends
2019-08-27 23:00:00 +02:00
parent 248638ad91
commit e2b78fa428
12 changed files with 24 additions and 17 deletions
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5
R/bug_drug_combinations.R
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@ -25,6 +25,7 @@
#' @inheritParams eucast_rules
#' @param combine_IR logical to indicate whether values R and I should be summed
#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column
#' @param ... argumments passed on to \code{\link{mo_name}}
#' @inheritParams rsi_df
#' @importFrom dplyr rename
#' @importFrom tidyr spread
@ -75,14 +76,14 @@ bug_drug_combinations <- function(x, col_mo = NULL, minimum = 30) {
#' @exportMethod format.bug_drug_combinations
#' @export
#' @rdname bug_drug_combinations
format.bug_drug_combinations <- function(x, combine_IR = FALSE, add_ab_group = TRUE) {
format.bug_drug_combinations <- function(x, combine_IR = FALSE, add_ab_group = TRUE, ...) {
if (combine_IR == FALSE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I
}
y <- x %>%
mutate(mo = mo_name(mo),
mutate(mo = mo_name(mo, ...),
txt = paste0(percent(isolates / total, force_zero = TRUE),
" (", trimws(format(isolates, big.mark = ",")), "/",
trimws(format(total, big.mark = ",")), ")")) %>%