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(v2.1.1.9275) include guideline name in MDRO verbose output

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dr. M.S. (Matthijs) Berends
2025-05-13 18:56:12 +02:00
parent 7d45ca9fbf
commit 48a59ee31a
5 changed files with 30 additions and 14 deletions
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31
R/mdro.R
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@ -141,6 +141,8 @@
#' The rules set (the `custom` object in this case) could be exported to a shared file location using [saveRDS()] if you collaborate with multiple users. The custom rules set could then be imported using [readRDS()].
#' @inheritSection as.sir Interpretation of SIR
#' @return
#' - If `verbose` is set to `TRUE`:\cr
#' A [data.frame] containing columns `row_number`, `microorganism`, `MDRO`, `reason`, `all_nonsusceptible_columns`, `guideline`
#' - CMI 2012 paper - function [mdr_cmi2012()] or [mdro()]:\cr
#' Ordered [factor] with levels `Negative` < `Multi-drug-resistant (MDR)` < `Extensively drug-resistant (XDR)` < `Pandrug-resistant (PDR)`
#' - TB guideline - function [mdr_tb()] or [`mdro(..., guideline = "TB")`][mdro()]:\cr
@ -148,7 +150,7 @@
#' - German guideline - function [mrgn()] or [`mdro(..., guideline = "MRGN")`][mdro()]:\cr
#' Ordered [factor] with levels `Negative` < `3MRGN` < `4MRGN`
#' - Everything else, except for custom guidelines:\cr
#' Ordered [factor] with levels `Negative` < `Positive, unconfirmed` < `Positive`. The value `"Positive, unconfirmed"` means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests
#' Ordered [factor] with levels `Negative` < `Positive, unconfirmed` < `Positive`. The value `"Positive, unconfirmed"` means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. genotypic) tests
#' @rdname mdro
#' @aliases MDR XDR PDR BRMO 3MRGN 4MRGN
#' @export
@ -349,17 +351,26 @@ mdro <- function(x = NULL,
))))
}
}
if (isTRUE(verbose)) {
x$reason[is.na(x$reason)] <- "not covered by guideline"
x$microorganism <- NA_character_
x$guideline <- "Custom guideline"
return(x[, c(
"row_number",
"microorganism",
"MDRO",
"reason",
"all_nonsusceptible_columns"
)])
"all_nonsusceptible_columns",
"guideline"
),
drop = FALSE
])
} else {
return(x$MDRO)
}
}
} # end of custom MDRO guideline
guideline <- tolower(gsub("[^a-zA-Z0-9.]+", "", guideline))
if (is.null(guideline)) {
# default to the paper by Magiorakos et al. (2012)
@ -772,10 +783,10 @@ mdro <- function(x = NULL,
function(y) y %in% search_result
)
paste(
sort(c(
unique(sort(c(
unlist(strsplit(x[row, "all_nonsusceptible_columns", drop = TRUE], ", ", fixed = TRUE)),
names(cols_nonsus)[cols_nonsus]
)),
))),
collapse = ", "
)
}
@ -849,7 +860,7 @@ mdro <- function(x = NULL,
rows,
function(row, group_vct = lst_vector) {
cols_nonsus <- vapply(FUN.VALUE = logical(1), x[row, group_vct, drop = FALSE], function(y) y %in% search_result)
paste(sort(names(cols_nonsus)[cols_nonsus]), collapse = ", ")
paste(unique(sort(names(cols_nonsus)[cols_nonsus])), collapse = ", ")
}
)
}
@ -1943,12 +1954,14 @@ mdro <- function(x = NULL,
# format data set
colnames(x)[colnames(x) == col_mo] <- "microorganism"
x$microorganism <- mo_name(x$microorganism, language = NULL)
x$guideline <- paste0(guideline$author, " - ", guideline$name, ", ", guideline$version, ")")
x[, c(
"row_number",
"microorganism",
"MDRO",
"reason",
"all_nonsusceptible_columns"
"all_nonsusceptible_columns",
"guideline"
),
drop = FALSE
]
@ -2119,7 +2132,7 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
all_nonsusceptible_columns <- vapply(
FUN.VALUE = character(1),
all_nonsusceptible_columns,
function(x) paste0(rownames(all_nonsusceptible_columns)[which(x)], collapse = " ")
function(x) paste0(rownames(all_nonsusceptible_columns)[which(x)], collapse = ", ")
)
all_nonsusceptible_columns[is.na(out)] <- NA_character_