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(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement

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dr. M.S. (Matthijs) Berends
2021-02-02 23:57:35 +01:00
parent 20d638c193
commit 2eca8c3f01
246 changed files with 1171 additions and 965 deletions
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34
R/mdro.R
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@ -1,6 +1,6 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
@ -20,7 +20,7 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Determine Multidrug-Resistant Organisms (MDRO)
@ -153,6 +153,7 @@ mdro <- function(x,
pct_required_classes = 0.5,
combine_SI = TRUE,
verbose = FALSE,
only_rsi_columns = any(is.rsi(x)),
...) {
if (missing(x)) {
x <- get_current_data(arg_name = "x", call = -2)
@ -432,6 +433,7 @@ mdro <- function(x,
"MNO"),
verbose = verbose,
info = info,
only_rsi_columns = only_rsi_columns,
...)
} else if (guideline$code == "eucast3.2") {
cols_ab <- get_column_abx(x = x,
@ -457,8 +459,9 @@ mdro <- function(x,
"TOB",
"TZD",
"VAN"),
info = info,
verbose = verbose,
info = info,
only_rsi_columns = only_rsi_columns,
...)
} else if (guideline$code == "tb") {
cols_ab <- get_column_abx(x = x,
@ -470,8 +473,9 @@ mdro <- function(x,
"RIF",
"RIB",
"RFP"),
info = info,
verbose = verbose,
info = info,
only_rsi_columns = only_rsi_columns,
...)
} else if (guideline$code == "mrgn") {
cols_ab <- get_column_abx(x = x,
@ -483,11 +487,13 @@ mdro <- function(x,
"CIP"),
verbose = verbose,
info = info,
only_rsi_columns = only_rsi_columns,
...)
} else {
cols_ab <- get_column_abx(x = x,
verbose = verbose,
info = info,
only_rsi_columns = only_rsi_columns,
...)
}
@ -1509,55 +1515,55 @@ run_custom_mdro_guideline <- function(df, guideline) {
#' @rdname mdro
#' @export
brmo <- function(x, guideline = "BRMO", ...) {
brmo <- function(x, guideline = "BRMO", only_rsi_columns = any(is.rsi(x)), ...) {
if (missing(x)) {
x <- get_current_data(arg_name = "x", call = -2)
}
meet_criteria(x, allow_class = "data.frame")
meet_criteria(guideline, allow_class = "character", has_length = 1)
mdro(x, guideline = "BRMO", ...)
mdro(x, guideline = "BRMO", only_rsi_columns = only_rsi_columns, ...)
}
#' @rdname mdro
#' @export
mrgn <- function(x, guideline = "MRGN", ...) {
mrgn <- function(x, guideline = "MRGN", only_rsi_columns = any(is.rsi(x)), ...) {
if (missing(x)) {
x <- get_current_data(arg_name = "x", call = -2)
}
meet_criteria(x, allow_class = "data.frame")
meet_criteria(guideline, allow_class = "character", has_length = 1)
mdro(x = x, guideline = "MRGN", ...)
mdro(x = x, guideline = "MRGN", only_rsi_columns = only_rsi_columns, ...)
}
#' @rdname mdro
#' @export
mdr_tb <- function(x, guideline = "TB", ...) {
mdr_tb <- function(x, guideline = "TB", only_rsi_columns = any(is.rsi(x)), ...) {
if (missing(x)) {
x <- get_current_data(arg_name = "x", call = -2)
}
meet_criteria(x, allow_class = "data.frame")
meet_criteria(guideline, allow_class = "character", has_length = 1)
mdro(x = x, guideline = "TB", ...)
mdro(x = x, guideline = "TB", only_rsi_columns = only_rsi_columns, ...)
}
#' @rdname mdro
#' @export
mdr_cmi2012 <- function(x, guideline = "CMI2012", ...) {
mdr_cmi2012 <- function(x, guideline = "CMI2012", only_rsi_columns = any(is.rsi(x)), ...) {
if (missing(x)) {
x <- get_current_data(arg_name = "x", call = -2)
}
meet_criteria(x, allow_class = "data.frame")
meet_criteria(guideline, allow_class = "character", has_length = 1)
mdro(x = x, guideline = "CMI2012", ...)
mdro(x = x, guideline = "CMI2012", only_rsi_columns = only_rsi_columns, ...)
}
#' @rdname mdro
#' @export
eucast_exceptional_phenotypes <- function(x, guideline = "EUCAST", ...) {
eucast_exceptional_phenotypes <- function(x, guideline = "EUCAST", only_rsi_columns = any(is.rsi(x)), ...) {
if (missing(x)) {
x <- get_current_data(arg_name = "x", call = -2)
}
meet_criteria(x, allow_class = "data.frame")
meet_criteria(guideline, allow_class = "character", has_length = 1)
mdro(x = x, guideline = "EUCAST", ...)
mdro(x = x, guideline = "EUCAST", only_rsi_columns = only_rsi_columns, ...)
}