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(v0.7.1.9063) septic_patients -> example_isolates

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dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
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8
R/bug_drug_combinations.R
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@ -23,16 +23,18 @@
#'
#' 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
#' @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.
#' @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!
#' @examples
#' \donttest{
#' x <- bug_drug_combinations(septic_patients)
#' x <- bug_drug_combinations(example_isolates)
#' x
#' format(x)
#' }
@ -70,8 +72,8 @@ bug_drug_combinations <- function(x, col_mo = NULL, minimum = 30) {
#' @importFrom tidyr spread
#' @exportMethod format.bugdrug
#' @export
format.bugdrug <- function(x, combine_SI = TRUE, add_ab_group = TRUE, ...) {
if (combine_SI == TRUE) {
format.bugdrug <- function(x, combine_RI = FALSE, add_ab_group = TRUE, ...) {
if (combine_RI == FALSE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I