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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling

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dr. M.S. (Matthijs) Berends
2021-12-11 13:41:31 +01:00
parent e18c49ed93
commit 77ba4318ea
64 changed files with 51141 additions and 9840 deletions
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R/data.R
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@ -262,20 +262,24 @@
#'
#' Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
#' @format A [data.frame] with `r format(nrow(intrinsic_resistant), big.mark = ",")` observations and `r ncol(intrinsic_resistant)` variables:
#' - `microorganism`\cr Name of the microorganism
#' - `antibiotic`\cr Name of the antibiotic drug
#' - `microorganism`\cr Official taxonomic name of the microorganism, according to the LPSN
#' - `antibiotic`\cr Official name of the antibiotic drug, according to the WHOCC
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
#'
#' This data set is based on `r format_eucast_version_nr(3.2)`.
#' This data set is based on `r format_eucast_version_nr(3.3)`.
#' @inheritSection AMR Reference Data Publicly Available
#' @inheritSection AMR Read more on Our Website!
#' @examples
#' subset(intrinsic_resistant,
#' antibiotic == "Vancomycin" & microorganism %like% "Enterococcus")$microorganism
#' #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#'
#' \donttest{
#' if (require("dplyr")) {
#' intrinsic_resistant %>%
#' filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>%
#' filter(antibiotic == "Vancomycin" & microorganism %like% "Enterococcus") %>%
#' pull(microorganism)
#' # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#' #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#' }
#' }
"intrinsic_resistant"