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(v1.3.0.9014) as.mo() speed improvement

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dr. M.S. (Matthijs) Berends
2020-09-03 12:31:48 +02:00
parent 18e52f2725
commit c4b87fe241
93 changed files with 739 additions and 609 deletions
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4
R/bug_drug_combinations.R
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@ -33,8 +33,6 @@
#' @inheritParams rsi_df
#' @inheritParams base::formatC
#' @details The function [format()] calculates the resistance per bug-drug combination. Use `combine_IR = FALSE` (default) to test R vs. S+I and `combine_IR = TRUE` to test R+I vs. S.
#'
#' The language of the output can be overwritten with `options(AMR_locale)`, please see [translate].
#' @export
#' @rdname bug_drug_combinations
#' @return The function [bug_drug_combinations()] returns a [`data.frame`] with columns "mo", "ab", "S", "I", "R" and "total".
@ -71,7 +69,7 @@ bug_drug_combinations <- function(x,
x_class <- class(x)
x <- as.data.frame(x, stringsAsFactors = FALSE)
x[, col_mo] <- FUN(x[, col_mo, drop = TRUE])
x[, col_mo] <- FUN(x[, col_mo, drop = TRUE], ...)
x <- x[, c(col_mo, names(which(sapply(x, is.rsi)))), drop = FALSE]
unique_mo <- sort(unique(x[, col_mo, drop = TRUE]))