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 18,831 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}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
  \item{\code{mo.old}}{The old ID for package versions 0.3.0 and lower.}
}}
\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 \code{AMR} package contains the \strong{complete microbial taxonomic data} from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa (from subkingdom to the subspecies level) are included in this package.
}

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