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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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12
R/bug_drug_combinations.R
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@ -37,7 +37,7 @@
#' @param FUN the function to call on the `mo` column to transform the microorganism codes, defaults to [mo_shortname()]
#' @param translate_ab a [character] of length 1 containing column names of the [antibiotics] data set
#' @param ... arguments passed on to `FUN`
#' @inheritParams rsi_df
#' @inheritParams sir_df
#' @inheritParams base::formatC
#' @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
@ -67,7 +67,7 @@ bug_drug_combinations <- function(x,
col_mo = NULL,
FUN = mo_shortname,
...) {
meet_criteria(x, allow_class = "data.frame", contains_column_class = "rsi")
meet_criteria(x, allow_class = "data.frame", contains_column_class = "sir")
meet_criteria(col_mo, allow_class = "character", is_in = colnames(x), has_length = 1, allow_NULL = TRUE)
meet_criteria(FUN, allow_class = "function", has_length = 1)
@ -90,10 +90,10 @@ bug_drug_combinations <- function(x,
if (is_null_or_grouped_tbl(x.bak)) {
data_has_groups <- TRUE
groups <- setdiff(names(attributes(x.bak)$groups), ".rows")
x <- x[, c(groups, col_mo, colnames(x)[vapply(FUN.VALUE = logical(1), x, is.rsi)]), drop = FALSE]
x <- x[, c(groups, col_mo, colnames(x)[vapply(FUN.VALUE = logical(1), x, is.sir)]), drop = FALSE]
} else {
data_has_groups <- FALSE
x <- x[, c(col_mo, names(which(vapply(FUN.VALUE = logical(1), x, is.rsi)))), drop = FALSE]
x <- x[, c(col_mo, names(which(vapply(FUN.VALUE = logical(1), x, is.sir)))), drop = FALSE]
}
run_it <- function(x) {
@ -113,8 +113,8 @@ bug_drug_combinations <- function(x,
}
for (i in seq_len(length(unique_mo))) {
# filter on MO group and only select R/SI columns
x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.rsi))), drop = FALSE]
# filter on MO group and only select SIR columns
x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.sir))), drop = FALSE]
# turn and merge everything
pivot <- lapply(x_mo_filter, function(x) {
m <- as.matrix(table(x))