AMR/man/microorganisms.old.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{microorganisms.old}
\alias{microorganisms.old}
\title{Data set with previously accepted taxonomic names}
\format{
A \code{\link{data.frame}} with 12,709 observations and 4 variables:
\itemize{
\item \code{fullname}\cr Old full taxonomic name of the microorganism
\item \code{fullname_new}\cr New full taxonomic name of the microorganism
\item \code{ref}\cr Author(s) and year of concerning scientific publication
\item \code{prevalence}\cr Prevalence of the microorganism, see \code{\link[=as.mo]{as.mo()}}
}
}
\source{
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()}}).

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
}
\usage{
microorganisms.old
}
\description{
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()}}.
}
\section{Catalogue of Life}{

\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
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.

\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()}}.
}

\section{Read more on our website!}{

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}.
}

\seealso{
\code{\link[=as.mo]{as.mo()}} \code{\link[=mo_property]{mo_property()}} \link{microorganisms}
}
\keyword{datasets}