AMR/man/microorganisms.codes.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Translation table for microorganism codes}
\format{A \code{\link{data.frame}} with 4,731 observations and 2 variables:
\describe{
  \item{\code{certe}}{Commonly used code of a microorganism}
  \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}
}}
\usage{
microorganisms.codes
}
\description{
A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with \code{\link{set_mo_source}}.
}
\section{Catalogue of Life}{

\if{html}{\figure{logo_col.png}{options: height=60px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). This data is updated annually - check the included version with \code{\link{catalogue_of_life_version}}.

Included are:
\itemize{
  \item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
  \item{All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
  \item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
  \item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies}
  \item{The responsible author(s) and year of scientific publication}
}

The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.

The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R}.
}

\section{Read more on our website!}{

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{microorganisms}}
}
\keyword{datasets}