AMR/man/microorganisms.codes.Rd

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
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\name{microorganisms.codes}
\alias{microorganisms.codes}
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\title{Data Set with 4 971 Common Microorganism Codes}
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\format{
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A \link[tibble:tibble]{tibble} with 4 971 observations and 2 variables:
\itemize{
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\item \code{code}\cr Commonly used code of a microorganism. \emph{This is a unique identifier.}
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
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}
}
\usage{
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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.
}
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\details{
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
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}
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\examples{
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microorganisms.codes
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# '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")
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}
\seealso{
\code{\link[=as.mo]{as.mo()}} \link{microorganisms}
}
\keyword{datasets}