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(v0.8.0.9036) complete documentation rewrite

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dr. M.S. (Matthijs) Berends
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man/microorganisms.Rd
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@ -5,38 +5,38 @@
\alias{microorganisms}
\title{Data set with ~70,000 microorganisms}
\format{A \code{\link{data.frame}} with 69,447 observations and 16 variables:
\describe{
\item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID}
\item{\code{fullname}}{Full name, like \code{"Escherichia coli"}}
\item{\code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}}{Taxonomic rank of the microorganism}
\item{\code{rank}}{Text of the taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}}
\item{\code{ref}}{Author(s) and year of concerning scientific publication}
\item{\code{species_id}}{ID of the species as used by the Catalogue of Life}
\item{\code{source}}{Either "CoL", "DSMZ" (see Source) or "manually added"}
\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{col_id}\cr Catalogue of Life ID
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}
\item \code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}\cr Taxonomic rank of the microorganism
\item \code{rank}\cr Text of the taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}
\item \code{ref}\cr Author(s) and year of concerning scientific publication
\item \code{species_id}\cr ID of the species as used by the Catalogue of Life
\item \code{source}\cr Either "CoL", "DSMZ" (see Source) or "manually added"
\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: 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()}}).
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link{catalogue_of_life_version}()}).
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
}
\usage{
microorganisms
}
\description{
A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link[=as.mo]{as.mo()}}.
}
\details{
Manually added were:
\itemize{
\item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
\item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
\item{1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)}
\item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
\item{6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not in the Catalogue of Life}
\item{12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications}
\item 11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
\item 2 entries of \emph{Staphylococcus} (coagulase-negative \link{CoNS} and coagulase-positive \link{CoPS})
\item 3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)
\item 1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
\item 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
\item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not in the Catalogue of Life
\item 12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
}
}
\section{About the records from DSMZ (see source)}{
@ -51,7 +51,7 @@ From: \url{https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloa
\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}()}.
\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!}{
@ -60,6 +60,6 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
}
\seealso{
\code{\link{as.mo}}, \code{\link{mo_property}}, \code{\link{microorganisms.codes}}
\code{\link[=as.mo]{as.mo()}}, \code{\link[=mo_property]{mo_property()}}, \link{microorganisms.codes}
}
\keyword{datasets}