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(v1.8.1.9013) add Toxoplasma

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dr. M.S. (Matthijs) Berends
2022-06-10 13:15:23 +02:00
parent b84d647cac
commit 7f981e7778
29 changed files with 432 additions and 124 deletions
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15
man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data Set with 70,760 Microorganisms}
\title{Data Set with 70,764 Microorganisms}
\format{
A \link{data.frame} with 70,760 observations and 16 variables:
A \link{data.frame} with 70,764 observations and 16 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}
@ -54,6 +54,7 @@ For convenience, some entries were added manually:
\item 11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
\item 2 entries of \emph{Staphylococcus} (coagulase-negative (CoNS) and coagulase-positive (CoPS))
\item 3 entries of \emph{Trichomonas} (\emph{T. vaginalis}, and its family and genus)
\item 4 entries of \emph{Toxoplasma} (\emph{T. gondii}, and its order, family and genus)
\item 1 entry of \emph{Candida} (\emph{C. krusei}), that is not (yet) in the Catalogue of Life
\item 1 entry of \emph{Blastocystis} (\emph{B. hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
\item 1 entry of \emph{Moraxella} (\emph{M. catarrhalis}), which was formally named \emph{Branhamella catarrhalis} (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
@ -64,15 +65,9 @@ For convenience, some entries were added manually:
\subsection{Direct download}{
This data set is available as 'flat file' for use even without \R - you can find the file here:
\itemize{
\item \url{https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt}
}
This data set is available as 'flat file' for use even without \R - you can find the file here: \url{https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt}.
The file in \R format (with preserved data structure) can be found here:
\itemize{
\item \url{https://github.com/msberends/AMR/raw/main/data/microorganisms.rda}
}
The file in \R format (with preserved data structure) can be found here: \url{https://github.com/msberends/AMR/raw/main/data/microorganisms.rda}.
}
}
\section{About the Records from LPSN (see \emph{Source})}{