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(v0.7.1.9064) bug-drug fix

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dr. M.S. (Matthijs) Berends
2019-08-27 19:15:04 +02:00
parent 93be16484b
commit f3276592b7
11 changed files with 22 additions and 22 deletions
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8
R/bug_drug_combinations.R
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@ -23,12 +23,12 @@
#'
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
#' @inheritParams eucast_rules
#' @param combine_RI logical to indicate whether values R and I should be summed
#' @param combine_IR logical to indicate whether values R and I should be summed
#' @inheritParams rsi_df
#' @importFrom dplyr rename
#' @importFrom tidyr spread
#' @importFrom clean freq
#' @details The function \code{format} calculated the resistance per bug-drug combination. Use \code{combine_RI = FALSE} (default) to test R vs. S+I and \code{combine_RI = TRUE} to test R+I vs. S.
#' @details The function \code{format} calculated the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
#' @export
#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' @inheritSection AMR Read more on our website!
@ -72,8 +72,8 @@ bug_drug_combinations <- function(x, col_mo = NULL, minimum = 30) {
#' @importFrom tidyr spread
#' @exportMethod format.bugdrug
#' @export
format.bugdrug <- function(x, combine_RI = FALSE, add_ab_group = TRUE, ...) {
if (combine_RI == FALSE) {
format.bugdrug <- function(x, combine_IR = FALSE, add_ab_group = TRUE, ...) {
if (combine_IR == FALSE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I