mirror of https://github.com/msberends/AMR.git
39 lines
1.6 KiB
R
39 lines
1.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/data.R
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\docType{data}
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\name{microorganisms.codes}
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\alias{microorganisms.codes}
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\title{Data Set with 4 957 Common Microorganism Codes}
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\format{
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A \link[tibble:tibble]{tibble} with 4 957 observations and 2 variables:
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\itemize{
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\item \code{code}\cr Commonly used code of a microorganism
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\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
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}
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}
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\usage{
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microorganisms.codes
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}
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\description{
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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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}
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\details{
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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:
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microorganisms.codes[microorganisms.codes$code == "ECO", ]
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# and therefore, 'eco' will be understood as E. coli in this package:
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mo_info("eco")
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# works for all AMR functions:
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mo_is_intrinsic_resistant("eco", ab = "vancomycin")
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}
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\seealso{
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\code{\link[=as.mo]{as.mo()}} \link{microorganisms}
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}
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\keyword{datasets}
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