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dr. M.S. (Matthijs) Berends
2022-08-21 16:37:20 +02:00
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R/eucast_rules.R
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@ -52,7 +52,6 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
#'
#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
#' @inheritSection lifecycle Stable Lifecycle
#' @param x data with antibiotic columns, such as `amox`, `AMX` and `AMC`
#' @param info a [logical] to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions
#' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
@ -76,11 +75,11 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#'
#' Custom rules can be created using [custom_eucast_rules()], e.g.:
#'
#' ```
#' ```{r}
#' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
#'
#' eucast_rules(example_isolates, rules = "custom", custom_rules = x)
#' eucast_rules(example_isolates, rules = "custom", custom_rules = x, info = FALSE)
#' ```
#'
#'
@ -113,8 +112,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx)
#' @inheritSection AMR Reference Data Publicly Available
#' @inheritSection AMR Read more on Our Website!
#' @examples
#' \donttest{
#' a <- data.frame(mo = c("Staphylococcus aureus",
@ -131,33 +131,26 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' FOX = "S", # Cefoxitin
#' stringsAsFactors = FALSE)
#'
#' a
#' # mo VAN AMX COL CAZ CXM PEN FOX
#' # 1 Staphylococcus aureus - - - - - S S
#' # 2 Enterococcus faecalis - - - - - S S
#' # 3 Escherichia coli - - - - - S S
#' # 4 Klebsiella pneumoniae - - - - - S S
#' # 5 Pseudomonas aeruginosa - - - - - S S
#' head(a)
#'
#'
#' # apply EUCAST rules: some results wil be changed
#' b <- eucast_rules(a)
#'
#' b
#' # mo VAN AMX COL CAZ CXM PEN FOX
#' # 1 Staphylococcus aureus - S R R S S S
#' # 2 Enterococcus faecalis - - R R R S R
#' # 3 Escherichia coli R - - - - R S
#' # 4 Klebsiella pneumoniae R R - - - R S
#' # 5 Pseudomonas aeruginosa R R - - R R R
#' head(b)
#'
#'
#' # do not apply EUCAST rules, but rather get a data.frame
#' # containing all details about the transformations:
#' c <- eucast_rules(a, verbose = TRUE)
#' head(c)
#' }
#'
#' # Dosage guidelines:
#'
#' eucast_dosage(c("tobra", "genta", "cipro"), "iv")
#'
#' eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
eucast_rules <- function(x,
col_mo = NULL,
info = interactive(),