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 ~20,000 microorganisms}
\format{A \code{\link{data.frame}} with 19,456 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{kingdom}}{Taxonomic kingdom of the microorganism as found in ITIS, see Source}
  \item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
  \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{
Integrated Taxonomic Information System (ITIS) public online database, \url{https://www.itis.gov}.
}
\usage{
microorganisms
}
\description{
A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using \code{\link{as.mo}}.
}
\details{
Manually added were:
\itemize{
  \item{605 species of Aspergillus (as Aspergillus misses from ITIS, list from https://en.wikipedia.org/wiki/List_of_Aspergillus_species on 2019-02-05)}
  \item{23 species of Trichophyton (as Trichophyton misses from ITIS, list from https://en.wikipedia.org/wiki/Trichophyton on 2019-02-05)}
  \item{9 species of Streptococcus (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
  \item{2 species of Straphylococcus (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
  \item{1 species of Candida (C. glabrata)}
  \item{2 other undefined (unknown Gram negatives and unknown Gram positives)}
}

These manual entries have no Taxonomic Serial Number (TSN), so can be looked up with \code{filter(microorganisms, is.na(tsn)}.
}
\section{ITIS}{

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This package contains the \strong{complete microbial taxonomic data} (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).

All ~20,000 (sub)species from \strong{the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package}, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.

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

\section{Read more on our website!}{

\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive 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}.
}

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