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(v0.8.0.9033) antivirals data set, cleanup

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dr. M.S. (Matthijs) Berends
2019-11-18 12:10:47 +01:00
parent 67f3f4387b
commit 267320f15f
97 changed files with 1131 additions and 644 deletions
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17
R/mdro.R
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@ -54,29 +54,24 @@
#' @rdname mdro
#' @aliases MDR XDR PDR BRMO 3MRGN 4MRGN
#' @importFrom dplyr %>% filter_at vars all_vars pull mutate_at
#' @importFrom crayon blue bold italic
#' @importFrom crayon blue bold italic red
#' @importFrom cleaner percentage
#' @export
#' @inheritSection AMR Read more on our website!
#' @source
#' Please see Details for the list of publications used for this function.
#' @examples
#' \donttest{
#' library(dplyr)
#'
#' example_isolates %>%
#' mdro() %>%
#' freq()
#'
#' \donttest{
#' example_isolates %>%
#' mutate(EUCAST = eucast_exceptional_phenotypes(.),
#' BRMO = brmo(.),
#' MRGN = mrgn(.))
#'
#' example_isolates %>%
#' rename(PIP = TZP) %>% # no piperacillin, so take piperacillin/tazobactam
#' mrgn() %>% # check German guideline
#' freq() # check frequencies
#' }
mdro <- function(x,
guideline = NULL,
@ -155,7 +150,7 @@ mdro <- function(x,
guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
guideline$author <- "Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
guideline$version <- "N/A"
guideline$source <- "Magiorakos et al. (2012) Clinical Microbiology and Infection 18:3. DOI: 10.1111/j.1469-0691.2011.03570.x"
guideline$source <- "Clinical Microbiology and Infection 18:3, 2012. DOI: 10.1111/j.1469-0691.2011.03570.x"
} else if (guideline$code == "eucast") {
guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Exceptional Phenotypes Tables\""
@ -174,7 +169,7 @@ mdro <- function(x,
guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
guideline$author <- "M\u00fcller J, Voss A, K\u00f6ck R, ..., Kern WV, Wendt C, Friedrich AW"
guideline$version <- "N/A"
guideline$source <- "M\u00fcller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6"
guideline$source <- "Antimicrobial Resistance and Infection Control 4:7, 2015. DOI: 10.1186/s13756-015-0047-6"
} else if (guideline$code == "brmo") {
guideline$name <- "WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)"
@ -422,9 +417,9 @@ mdro <- function(x,
if (info == TRUE) {
if (combine_SI == TRUE) {
cat("\nOnly results with 'R' are considered as resistance. Use `combine_SI = FALSE` to also consider 'I' as resistance.\n")
cat(red("\nOnly results with 'R' are considered as resistance. Use `combine_SI = FALSE` to also consider 'I' as resistance.\n"))
} else {
cat("\nResults with 'R' or 'I' are considered as resistance. Use `combine_SI = TRUE` to only consider 'R' as resistance.\n")
cat(red("\nResults with 'R' or 'I' are considered as resistance. Use `combine_SI = TRUE` to only consider 'R' as resistance.\n"))
}
cat("\nDetermining multidrug-resistant organisms (MDRO), according to:\n",
bold("Guideline: "), italic(guideline$name), "\n",