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dr. M.S. (Matthijs) Berends
eb9a9c2fa5
WHONET names are now matched exactly (also outdated names, after removing qualifiers), then on GBIF identifier, and fuzzy results are only kept if consistent with that; otherwise the genus or UNKNOWN is used. A code refers to the record of the name it was named after (e.g. EAE is Enterobacter aerogenes) if that name refers to the same taxon. Every remap of an existing code to another taxon must be listed in data-raw/whonet_remaps_reviewed.csv; the 198 remaps of this rebuild were reviewed.
46 lines
2.5 KiB
R
46 lines
2.5 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 6 293 Common Microorganism Codes}
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\format{
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A \link[tibble:tibble]{tibble} with 6 293 observations and 3 variables:
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\itemize{
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\item \code{code}\cr Commonly used code of a microorganism. \emph{\strong{This is a unique identifier.}}
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\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set. This is the record of the name that the code was named after, also if that name is outdated, so that the code and the microorganism ID remain relatable: e.g., the WHONET code \code{EAE} refers to \emph{Enterobacter aerogenes} (\code{B_ENTRBC_AERG}). \code{\link[=as.mo]{as.mo()}} returns the current name, here \emph{Klebsiella aerogenes}. Codes for organisms that are not in the \link{microorganisms} data set, such as viruses, refer to \code{UNKNOWN}.
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\item \code{source}\cr Source of the code, with the name it refers to, e.g. \code{"WHONET (Enterobacter aerogenes)"}, or \code{NA} if the source is unknown
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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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\section{Download Our Reference Data}{
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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.
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For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
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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/datasets}{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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