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new SDD and N for as.sir()

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dr. M.S. (Matthijs) Berends
2024-05-20 15:27:04 +02:00
parent b68f47d985
commit 08a27922a8
28 changed files with 225 additions and 172 deletions
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10
R/bug_drug_combinations.R
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@ -42,7 +42,7 @@
#' @details The function [format()] calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. [knitr::kable()].
#' @export
#' @rdname bug_drug_combinations
#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "I", "R" and "total".
#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "SDD", "I", "R", and "total".
#' @examples
#' # example_isolates is a data set available in the AMR package.
#' # run ?example_isolates for more info.
@ -105,6 +105,7 @@ bug_drug_combinations <- function(x,
mo = character(0),
ab = character(0),
S = integer(0),
SDD = integer(0),
I = integer(0),
R = integer(0),
total = integer(0),
@ -122,13 +123,14 @@ bug_drug_combinations <- function(x,
# turn and merge everything
pivot <- lapply(x_mo_filter, function(x) {
m <- as.matrix(table(x))
data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
data.frame(S = m["S", ], SDD = m["SDD", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
})
merged <- do.call(rbind_AMR, pivot)
out_group <- data.frame(
mo = rep(unique_mo[i], NROW(merged)),
ab = rownames(merged),
S = merged$S,
SDD = merged$SSD,
I = merged$I,
R = merged$R,
total = merged$S + merged$I + merged$R,
@ -203,10 +205,12 @@ format.bug_drug_combinations <- function(x,
mo = gsub("(.*)%%(.*)", "\\1", names(idx)),
ab = gsub("(.*)%%(.*)", "\\2", names(idx)),
S = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$S[i], na.rm = TRUE)),
SDD = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$SDD[i], na.rm = TRUE)),
I = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$I[i], na.rm = TRUE)),
R = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$R[i], na.rm = TRUE)),
total = vapply(FUN.VALUE = double(1), idx, function(i) {
sum(x$S[i], na.rm = TRUE) +
sum(x$SDD[i], na.rm = TRUE) +
sum(x$I[i], na.rm = TRUE) +
sum(x$R[i], na.rm = TRUE)
}),
@ -223,7 +227,7 @@ format.bug_drug_combinations <- function(x,
if (combine_SI == TRUE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I
x$isolates <- x$R + x$I + x$SDD
}
give_ab_name <- function(ab, format, language) {