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added taxonomic data from ITIS

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dr. M.S. (Matthijs) Berends
2018-09-17 20:53:32 +02:00
parent 7680e4edd8
commit 5d80cef338
13 changed files with 150 additions and 80 deletions
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14
man/microorganisms.Rd
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@ -4,20 +4,26 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with human pathogenic microorganisms}
\format{A \code{\link{tibble}} with 2,642 observations and 11 variables:
\format{A \code{\link{tibble}} with 2,642 observations and 14 variables:
\describe{
\item{\code{mo}}{ID of microorganism}
\item{\code{bactsys}}{Bactsyscode of microorganism}
\item{\code{family}}{Family name 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{aerobic}}{Logical whether bacteria is aerobic}
\item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
\item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
\item{\code{aerobic}}{Logical whether bacteria is aerobic}
\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{prevalence}}{A rounded integer based on prevalence of the microorganism. Used internally by \code{\link{as.mo}}, otherwise quite meaningless.}
}}
\source{
Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
}
\usage{
microorganisms
}