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add confidence intervals (fixed #70), remove combine_IR

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dr. M.S. (Matthijs) Berends
2022-10-20 16:08:01 +02:00
parent 85e2fbe4a3
commit aa2c0639d0
19 changed files with 248 additions and 144 deletions
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10
R/bug_drug_combinations.R
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@ -31,7 +31,7 @@
#'
#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*.
#' @inheritParams eucast_rules
#' @param combine_IR a [logical] to indicate whether values R and I should be summed
#' @param combine_SI a [logical] to indicate whether values S and I should be summed, so resistance will be based on only R, defaults to `TRUE`
#' @param add_ab_group a [logical] to indicate where the group of the antimicrobials must be included as a first column
#' @param remove_intrinsic_resistant [logical] to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table
#' @param FUN the function to call on the `mo` column to transform the microorganism codes, defaults to [mo_shortname()]
@ -39,11 +39,11 @@
#' @param ... arguments passed on to `FUN`
#' @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.
#' @details The function [format()] calculates the resistance per bug-drug combination. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S.
#' @export
#' @rdname bug_drug_combinations
#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "I", "R" and "total".
#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition}, 2022, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
#' @examples
#' \donttest{
#' x <- bug_drug_combinations(example_isolates)
@ -174,7 +174,6 @@ format.bug_drug_combinations <- function(x,
language = get_AMR_locale(),
minimum = 30,
combine_SI = TRUE,
combine_IR = FALSE,
add_ab_group = TRUE,
remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"),
@ -185,7 +184,6 @@ format.bug_drug_combinations <- function(x,
language <- validate_language(language)
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
meet_criteria(combine_IR, allow_class = "logical", has_length = 1)
meet_criteria(add_ab_group, allow_class = "logical", has_length = 1)
meet_criteria(remove_intrinsic_resistant, allow_class = "logical", has_length = 1)
meet_criteria(decimal.mark, allow_class = "character", has_length = 1)
@ -218,7 +216,7 @@ format.bug_drug_combinations <- function(x,
if (remove_intrinsic_resistant == TRUE) {
x <- subset(x, R != total)
}
if (combine_SI == TRUE || combine_IR == FALSE) {
if (combine_SI == TRUE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I