mirror of https://github.com/msberends/AMR.git
44 lines
2.5 KiB
R
Executable File
44 lines
2.5 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/data.R
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\docType{data}
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\name{microorganisms}
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\alias{microorganisms}
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\title{Data set with taxonomic data from ITIS}
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\format{A \code{\link{data.frame}} with 18,831 observations and 15 variables:
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\describe{
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\item{\code{mo}}{ID of microorganism}
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\item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
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\item{\code{genus}}{Taxonomic genus of the microorganism as found in ITIS, see Source}
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\item{\code{species}}{Taxonomic species of the microorganism as found in ITIS, see Source}
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\item{\code{subspecies}}{Taxonomic subspecies of the microorganism as found in ITIS, see Source}
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\item{\code{fullname}}{Full name, like \code{"Echerichia coli"}}
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\item{\code{family}}{Taxonomic family of the microorganism as found in ITIS, see Source}
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\item{\code{order}}{Taxonomic order of the microorganism as found in ITIS, see Source}
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\item{\code{class}}{Taxonomic class of the microorganism as found in ITIS, see Source}
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\item{\code{phylum}}{Taxonomic phylum of the microorganism as found in ITIS, see Source}
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\item{\code{subkingdom}}{Taxonomic subkingdom of the microorganism as found in ITIS, see Source}
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\item{\code{gramstain}}{Gram of microorganism, like \code{"Gram negative"}}
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\item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungi"}}
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\item{\code{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
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\item{\code{mo.old}}{The old ID for package versions 0.3.0 and lower.}
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}}
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\source{
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[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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}
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\usage{
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microorganisms
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}
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\description{
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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}}.
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}
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\section{ITIS}{
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\if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
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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.
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}
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\seealso{
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\code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
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}
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\keyword{datasets}
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