mirror of https://github.com/msberends/AMR.git
45 lines
2.8 KiB
R
45 lines
2.8 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.old}
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\alias{microorganisms.old}
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\title{Data Set with Previously Accepted Taxonomic Names}
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\format{
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A \link[tibble:tibble]{tibble} with 14,338 observations and 4 variables:
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\itemize{
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\item \code{fullname}\cr Old full taxonomic name of the microorganism
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\item \code{fullname_new}\cr New full taxonomic name of the microorganism
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\item \code{ref}\cr Author(s) and year of concerning scientific publication
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\item \code{prevalence}\cr Prevalence of the microorganism, see \code{\link[=as.mo]{as.mo()}}
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}
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}
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\source{
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Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
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Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
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}
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\usage{
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microorganisms.old
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}
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\description{
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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]{as.mo()}}.
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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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\section{Catalogue of Life}{
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\if{html}{\figure{logo_col.png}{options: height="40" style=margin-bottom:"5"} \cr}
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This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/CatalogueOfLife/general}{CoL+ project} is finished, which we await.
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\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
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}
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\examples{
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microorganisms.old
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}
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\seealso{
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\code{\link[=as.mo]{as.mo()}} \code{\link[=mo_property]{mo_property()}} \link{microorganisms}
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}
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\keyword{datasets}
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