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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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4
R/bug_drug_combinations.R
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@ -35,7 +35,7 @@
#' @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 - the default is [mo_shortname()]
#' @param translate_ab a [character] of length 1 containing column names of the [antibiotics] data set
#' @param translate_ab a [character] of length 1 containing column names of the [antimicrobials] data set
#' @param include_n_rows a [logical] to indicate if the total number of rows must be included in the output
#' @param ... arguments passed on to `FUN`
#' @inheritParams sir_df
@ -93,7 +93,7 @@ bug_drug_combinations <- function(x,
unique_mo <- sort(unique(x[, col_mo, drop = TRUE]))
# select only groups and antibiotics
# select only groups and antimicrobials
if (is_null_or_grouped_tbl(x.bak)) {
data_has_groups <- TRUE
groups <- get_group_names(x.bak)