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(v1.3.0.9002) intrinsic_resistant data set

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dr. M.S. (Matthijs) Berends
2020-08-14 13:36:10 +02:00
parent 7d16bec21f
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@ -70,7 +70,7 @@
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <http://ec.europa.eu/health/documents/community-register/html/atc.htm>
#' @inheritSection WHOCC WHOCC
#' @inheritSection AMR Read more on our website!
#' @seealso [microorganisms]
#' @seealso [microorganisms], [intrinsic_resistant]
"antibiotics"
#' @rdname antibiotics
@ -119,7 +119,7 @@
#'
#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date> and <https://lpsn.dsmz.de> (check included version with [catalogue_of_life_version()]).
#' @inheritSection AMR Read more on our website!
#' @seealso [as.mo()], [mo_property()], [microorganisms.codes]
#' @seealso [as.mo()], [mo_property()], [microorganisms.codes], [intrinsic_resistant]
"microorganisms"
catalogue_of_life <- list(
@ -235,4 +235,25 @@ catalogue_of_life <- list(
#' - `uti`\cr A logical value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
#' @inheritSection AMR Read more on our website!
#' @seealso [intrinsic_resistant]
"rsi_translation"
#' Data set with bacterial intrinsic resistance
#'
#' 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
#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/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 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r EUCAST_VERSION_EXPERT_RULES`.
#' @inheritSection AMR Read more on our website!
#' @examples
#' if (require("dplyr")) {
#' intrinsic_resistant %>%
#' filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>%
#' pull(microorganism)
#' # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
#' }
#' @seealso [intrinsic_resistant]
"intrinsic_resistant"