mirror of https://github.com/msberends/AMR.git
48 lines
3.1 KiB
R
Executable File
48 lines
3.1 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 taxonomic data from ITIS}
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\format{A \code{\link{data.frame}} with 18,833 observations and 15 variables:
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\describe{
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\item{\code{mo}}{ID of microorganism}
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\item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
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\item{\code{genus}}{Taxonomic genus of the microorganism as found in ITIS, see Source}
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\item{\code{species}}{Taxonomic species of the microorganism as found in ITIS, see Source}
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\item{\code{subspecies}}{Taxonomic subspecies of the microorganism as found in ITIS, see Source}
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\item{\code{fullname}}{Full name, like \code{"Echerichia coli"}}
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\item{\code{family}}{Taxonomic family of the microorganism as found in ITIS, see Source}
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\item{\code{order}}{Taxonomic order of the microorganism as found in ITIS, see Source}
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\item{\code{class}}{Taxonomic class of the microorganism as found in ITIS, see Source}
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\item{\code{phylum}}{Taxonomic phylum of the microorganism as found in ITIS, see Source}
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\item{\code{subkingdom}}{Taxonomic subkingdom of the microorganism as found in ITIS, see Source}
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\item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
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\item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungi"}}
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\item{\code{prevalence}}{An integer based on estimated prevalence of the microorganism in humans. Used internally by \code{\link{as.mo}}, otherwise quite meaningless. It has a value of 25 for manually added items and a value of 1000 for all unprevalent microorganisms whose genus was somewhere in the top 250 (with another species).}
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\item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
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}}
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\source{
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[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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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 complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using \code{\link{as.mo}}.
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}
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\section{ITIS}{
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\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
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This package contains the \strong{complete microbial taxonomic data} (with all seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
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All (sub)species from the \strong{taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This \strong{allows users to use authoritative taxonomic information} for their data analysis on any microorganism, not only human pathogens. It also helps to \strong{quickly determine the Gram stain of bacteria}, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.
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ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
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}
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\seealso{
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\code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
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}
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\keyword{datasets}
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