% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Data Set with 5 063 Common Microorganism Codes}
\format{
A \link[tibble:tibble]{tibble} with 5 063 observations and 2 variables:
\itemize{
\item \code{code}\cr Commonly used code of a microorganism. \emph{\strong{This is a unique identifier.}}
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
}
}
\usage{
microorganisms.codes
}
\description{
A data set containing commonly used codes for microorganisms, from laboratory systems and \href{https://whonet.org}{WHONET}. Define your own with \code{\link[=set_mo_source]{set_mo_source()}}. They will all be searched when using \code{\link[=as.mo]{as.mo()}} and consequently all the \code{\link[=mo_property]{mo_*}} functions.
}
\section{Download Our Reference Data}{

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}

\examples{
microorganisms.codes

# 'ECO' or 'eco' is the WHONET code for E. coli:
microorganisms.codes[microorganisms.codes$code == "ECO", ]

# and therefore, 'eco' will be understood as E. coli in this package:
mo_info("eco")

# works for all AMR functions:
mo_is_intrinsic_resistant("eco", ab = "vancomycin")
}
\seealso{
\code{\link[=as.mo]{as.mo()}} \link{microorganisms}
}
\keyword{datasets}