mirror of https://github.com/msberends/AMR.git
64 lines
4.1 KiB
R
Executable File
64 lines
4.1 KiB
R
Executable File
% 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}
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\alias{microorganisms}
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\title{Data set with ~70,000 microorganisms}
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\format{A \code{\link{data.frame}} with 69,855 observations and 16 variables:
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\describe{
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\item{\code{mo}}{ID of microorganism as used by this package}
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\item{\code{col_id}}{Catalogue of Life ID}
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\item{\code{fullname}}{Full name, like \code{"Escherichia coli"}}
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\item{\code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}}{Taxonomic rank of the microorganism}
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\item{\code{rank}}{Text of the taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}}
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\item{\code{ref}}{Author(s) and year of concerning scientific publication}
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\item{\code{species_id}}{ID of the species as used by the Catalogue of Life}
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\item{\code{source}}{Either "CoL", "DSMZ" (see Source) or "manually added"}
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\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
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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}()}).
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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}()}).
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}
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\usage{
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microorganisms
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}
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\description{
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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}}.
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}
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\details{
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Manually added were:
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\itemize{
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\item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
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\item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
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\item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
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\item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
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\item{8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
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}
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}
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\section{About the records from DSMZ (see source)}{
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Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
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From: \url{https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html}
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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}()}.
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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 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}}, \code{\link{mo_property}}, \code{\link{microorganisms.codes}}
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}
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\keyword{datasets}
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