mirror of https://github.com/msberends/AMR.git
44 lines
2.5 KiB
R
44 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.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 \code{\link{data.frame}} with 12,709 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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\section{Catalogue of Life}{
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\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
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This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
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\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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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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