AMR/man/microorganisms.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with taxonomic data from ITIS}
\format{A \code{\link{data.frame}} with 18,833 observations and 15 variables:
\describe{
  \item{\code{mo}}{ID of microorganism}
  \item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
  \item{\code{genus}}{Taxonomic genus of the microorganism as found in ITIS, see Source}
  \item{\code{species}}{Taxonomic species of the microorganism as found in ITIS, see Source}
  \item{\code{subspecies}}{Taxonomic subspecies of the microorganism as found in ITIS, see Source}
  \item{\code{fullname}}{Full name, like \code{"Echerichia coli"}}
  \item{\code{family}}{Taxonomic family of the microorganism as found in ITIS, see Source}
  \item{\code{order}}{Taxonomic order of the microorganism as found in ITIS, see Source}
  \item{\code{class}}{Taxonomic class of the microorganism as found in ITIS, see Source}
  \item{\code{phylum}}{Taxonomic phylum of the microorganism as found in ITIS, see Source}
  \item{\code{subkingdom}}{Taxonomic subkingdom of the microorganism as found in ITIS, see Source}
  \item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
  \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungi"}}
  \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).}
  \item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
}}
\source{
[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
}
\usage{
microorganisms
}
\description{
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}}.
}
\section{ITIS}{

\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
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}).

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.

ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
}

\seealso{
\code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
}
\keyword{datasets}