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(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

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Fixes #246
Fixes #254
Fixes #255
Fixes #256
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-02-08 23:15:40 +01:00
parent 2df2911cf4
commit ba4c159154
31 changed files with 394 additions and 165 deletions
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27
R/bug_drug_combinations.R
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@@ -43,7 +43,7 @@
#' @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", "SDD", "I", "R", and "total".
#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "SDD", "I", "R", "WT, "NWT", and "total".
#' @examples
#' # example_isolates is a data set available in the AMR package.
#' # run ?example_isolates for more info.
@@ -111,6 +111,8 @@ bug_drug_combinations <- function(x,
SDD = integer(0),
I = integer(0),
R = integer(0),
WT = integer(0),
NWT = integer(0),
total = integer(0),
total_rows = integer(0),
stringsAsFactors = FALSE
@@ -133,6 +135,9 @@ bug_drug_combinations <- function(x,
I = m["I", ],
R = m["R", ],
NI = m["NI", ],
WT = m["WT", ],
NWT = m["NWT", ],
NS = m["NS", ],
na = m[which(is.na(rownames(m))), ],
stringsAsFactors = FALSE
)
@@ -146,8 +151,11 @@ bug_drug_combinations <- function(x,
I = merged$I,
R = merged$R,
NI = merged$NI,
total = merged$S + merged$SDD + merged$I + merged$R + merged$NI,
total_rows = merged$S + merged$SDD + merged$I + merged$R + merged$NI + merged$na,
WT = merged$WT,
NWT = merged$NWT,
NS = merged$NS,
total = merged$S + merged$SDD + merged$I + merged$R + merged$NI + merged$WT + merged$NWT + merged$NS,
total_rows = merged$S + merged$SDD + merged$I + merged$R + merged$NI + merged$WT + merged$NWT + merged$NS + merged$na,
stringsAsFactors = FALSE
)
if (data_has_groups) {
@@ -229,12 +237,17 @@ format.bug_drug_combinations <- function(x,
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)),
NI = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NI[i], na.rm = TRUE)),
WT = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$WT[i], na.rm = TRUE)),
NWT = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NWT[i], na.rm = TRUE)),
NS = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NS[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) +
sum(x$NI[i], na.rm = TRUE)
sum(x$WT[i], na.rm = TRUE) +
sum(x$NWT[i], na.rm = TRUE) +
sum(x$NS[i], na.rm = TRUE)
}),
stringsAsFactors = FALSE
)
@@ -246,10 +259,10 @@ format.bug_drug_combinations <- function(x,
if (remove_intrinsic_resistant == TRUE) {
x <- subset(x, R != total)
}
x$isolates <- x$R + x$NWT
if (combine_SI == TRUE) {
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I + x$SDD
x$isolates <- x$isolates + x$I + x$SDD
}
give_ab_name <- function(ab, format, language) {