#' A data set containing all antibiotics. Use \code{\link{as.ab}} or one of the \code{\link{ab_property}} functions to retrieve values from this data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
#' \item{\code{ab}}{Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available}
#' \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}
#' \item{\code{cid}}{Compound ID as found in PubChem}
#' \item{\code{name}}{Official name as used by WHONET/EARS-Net or the WHO}
#' \item{\code{group}}{A short and concise group name, based on WHONET and WHOCC definitions}
#' \item{\code{atc_group1}}{Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like \code{"Macrolides, lincosamides and streptogramins"}}
#' \item{\code{atc_group2}}{Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like \code{"Macrolides"}}
#' \item{\code{abbr}}{List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)}
#' \item{\code{synonyms}}{Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID}
#' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: \code{atc_group1}, \code{atc_group2}, \code{oral_ddd}, \code{oral_units}, \code{iv_ddd} and \code{iv_units}
#' @section About the records from DSMZ (see source):
#' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#'
#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link{catalogue_of_life_version}()}).
#' A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by \code{\link{as.mo}}.
#' @inheritSection catalogue_of_life Catalogue of Life
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#' An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This \code{data.frame} can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
#' \item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
#' This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The data itself was based on our \code{\link{septic_patients}} data set.
#' @format A \code{\link{data.frame}} with 500 observations and 53 variables:
#' \describe{
#' \item{\code{Identification number}}{ID of the sample}
#' \item{\code{Specimen number}}{ID of the specimen}
#' \item{\code{Organism}}{Name of the microorganism. Before analysis, you should transform this to a valid microbial class, using \code{\link{as.mo}}.}
#' \item{\code{AMP_ND10:CIP_EE}}{27 different antibiotics. You can lookup the abbreviatons in the \code{\link{antibiotics}} data set, or use e.g. \code{\link{atc_name}("AMP")} to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using \code{\link{as.rsi}}.}
#' Data set to interpret MIC and disk diffusion to RSI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use \code{\link{as.rsi}} to transform MICs or disks measurements to RSI values.
#' @format A \code{\link{data.frame}} with 11,559 observations and 9 variables:
#' \describe{
#' \item{\code{guideline}}{Name of the guideline}
#' \item{\code{mo}}{Microbial ID, see \code{\link{as.mo}}}
#' \item{\code{ab}}{Antibiotic ID, see \code{\link{as.ab}}}
#' \item{\code{ref_tbl}}{Info about where the guideline rule can be found}
#' \item{\code{S_mic}}{Lowest MIC value that leads to "S"}
#' \item{\code{R_mic}}{Highest MIC value that leads to "R"}
#' \item{\code{dose_disk}}{Dose of the used disk diffusion method}
#' \item{\code{S_disk}}{Lowest number of millimeters that leads to "S"}
#' \item{\code{R_disk}}{Highest number of millimeters that leads to "R"}
