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first inclusion of ITIS data

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dr. M.S. (Matthijs) Berends
2018-09-24 23:33:29 +02:00
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man/microorganisms.Rd
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\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with human pathogenic microorganisms}
\format{A \code{\link{tibble}} with 2,642 observations and 14 variables:
\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{bactsys}}{Bactsyscode of microorganism}
\item{\code{genus}}{Genus name of microorganism, like \code{"Echerichia"}}
\item{\code{species}}{Species name of microorganism, like \code{"coli"}}
\item{\code{subspecies}}{Subspecies name of bio-/serovar of microorganism, like \code{"EHEC"}}
\item{\code{fullname}}{Full name, like \code{"Echerichia coli (EHEC)"}}
\item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
\item{\code{aerobic}}{Logical whether bacteria is aerobic}
\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{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
\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{
Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
}
\usage{
microorganisms
}
\description{
A data set containing (potential) human pathogenic microorganisms. MO codes can be looked up using \code{\link{guess_mo}}.
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{guess_mo}} \code{\link{antibiotics}} \code{\link{microorganisms.umcg}}
\code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
}
\keyword{datasets}