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(v1.2.0.9026) move to github

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dr. M.S. (Matthijs) Berends
2020-07-08 14:48:06 +02:00
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12
man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with 67,108 microorganisms}
\title{Data set with 67,150 microorganisms}
\format{
A \code{\link{data.frame}} with 67,108 observations and 16 variables:
A \code{\link{data.frame}} with 67,150 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"}
@ -40,18 +40,18 @@ Manually added were:
\item 1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
\item 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
\item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
\item 7,369 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
\item 7,411 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
}
\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://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt}
\item \url{https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt}
}
The file in R format (with preserved data structure) can be found here:
\itemize{
\item \url{https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda}
\item \url{https://github.com/msberends/AMR/raw/master/data/microorganisms.rda}
}
}
}
@ -72,7 +72,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
\section{Read more on our website!}{
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\seealso{