P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 15:02:00 +02:00
Code Releases Activity

(v2.1.1.9226) update intrinsic_resistant, unit test fixes

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-27 15:20:22 +01:00
parent e6f88241b2
commit 969a42cc8c
29 changed files with 139318 additions and 244254 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
R/amr_selectors.R
View File

@ -612,9 +612,9 @@ administrable_iv <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
#' @rdname antimicrobial_selectors
#' @inheritParams eucast_rules
#' @details The [not_intrinsic_resistant()] function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of *E. coli* and *K. pneumoniae* and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies `r format_eucast_version_nr(names(EUCAST_VERSION_EXPERT_RULES[1]))` to determine intrinsic resistance, using the [eucast_rules()] function internally. Because of this determination, this function is quite slow in terms of performance.
#' @details The [not_intrinsic_resistant()] function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of *E. coli* and *K. pneumoniae* and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies `r format_eucast_version_nr(names(EUCAST_VERSION_EXPECTED_PHENOTYPES[1]))` to determine intrinsic resistance, using the [eucast_rules()] function internally. Because of this determination, this function is quite slow in terms of performance.
#' @export
not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, version_expertrules = 3.3, ...) {
not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, version_expected_phenotypes = 1.2, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
# get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
# but it only takes a couple of milliseconds
@ -629,8 +629,9 @@ not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, ver
sapply(
eucast_rules(vars_df,
col_mo = col_mo,
version_expertrules = version_expertrules,
rules = "expert",
version_expected_phenotypes = version_expected_phenotypes,
rules = "expected_phenotypes",
overwrite = TRUE,
info = FALSE
),
function(col) {