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mo codes for WHONET

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dr. M.S. (Matthijs) Berends
2019-02-08 16:06:54 +01:00
parent 3d3366faf7
commit ed30312048
60 changed files with 1103 additions and 615 deletions
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15
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~20,000 microorganisms}
\format{A \code{\link{data.frame}} with 18,833 observations and 15 variables:
\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}
@ -31,6 +31,19 @@ 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}{
\if{html}{\figure{logo_itis.jpg}{options: height=60px style=margin-bottom:5px} \cr}