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(v1.6.0.9021) join functions update

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dr. M.S. (Matthijs) Berends
2021-05-12 18:15:03 +02:00
parent 3319fbae58
commit 29dbfa2f49
119 changed files with 973 additions and 1040 deletions
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22
R/mdro.R
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@ -34,7 +34,7 @@
#' @inheritParams eucast_rules
#' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
#' @param combine_SI a [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
#' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
#' @inheritSection eucast_rules Antibiotics
#' @details
#' These functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*.
@ -136,7 +136,7 @@
#' @export
#' @inheritSection AMR Read more on Our Website!
#' @source
#' See the supported guidelines above for the list of publications used for this function.
#' See the supported guidelines above for the [list] of publications used for this function.
#' @examples
#' mdro(example_isolates, guideline = "EUCAST")
#'
@ -232,7 +232,7 @@ mdro <- function(x = NULL,
}
}
# force regular data.frame, not a tibble or data.table
# force regular [data.frame], not a tibble or data.table
x <- as.data.frame(x, stringsAsFactors = FALSE)
if (pct_required_classes > 1) {
@ -252,7 +252,7 @@ mdro <- function(x = NULL,
if (info == TRUE) {
txt <- paste0("Determining MDROs based on custom rules",
ifelse(isTRUE(attributes(guideline)$as_factor),
paste0(", resulting in factor levels: ", paste0(attributes(guideline)$values, collapse = " < ")),
paste0(", resulting in [factor] levels: ", paste0(attributes(guideline)$values, collapse = " < ")),
""),
".")
txt <- word_wrap(txt)
@ -361,7 +361,7 @@ mdro <- function(x = NULL,
if (guideline$code == "cmi2012") {
cols_ab <- get_column_abx(x = x,
soft_dependencies = c(
# table 1 (S aureus):
# [table] 1 (S aureus):
"GEN",
"RIF",
"CPT",
@ -384,7 +384,7 @@ mdro <- function(x = NULL,
"TCY",
"DOX",
"MNO",
# table 2 (Enterococcus)
# [table] 2 (Enterococcus)
"GEH",
"STH",
"IPM",
@ -402,7 +402,7 @@ mdro <- function(x = NULL,
"QDA",
"DOX",
"MNO",
# table 3 (Enterobacteriaceae)
# [table] 3 (Enterobacteriaceae)
"GEN",
"TOB",
"AMK",
@ -434,7 +434,7 @@ mdro <- function(x = NULL,
"TCY",
"DOX",
"MNO",
# table 4 (Pseudomonas)
# [table] 4 (Pseudomonas)
"GEN",
"TOB",
"AMK",
@ -452,7 +452,7 @@ mdro <- function(x = NULL,
"FOS",
"COL",
"PLB",
# table 5 (Acinetobacter)
# [table] 5 (Acinetobacter)
"GEN",
"TOB",
"AMK",
@ -1340,7 +1340,7 @@ mdro <- function(x = NULL,
ab
}
drug_is_R <- function(ab) {
# returns logical vector
# returns [logical] vector
ab <- prepare_drug(ab)
if (length(ab) == 0) {
rep(FALSE, NROW(x))
@ -1351,7 +1351,7 @@ mdro <- function(x = NULL,
}
}
drug_is_not_R <- function(ab) {
# returns logical vector
# returns [logical] vector
ab <- prepare_drug(ab)
if (length(ab) == 0) {
rep(TRUE, NROW(x))