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(v1.1.0.9021) 1st isolates update

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dr. M.S. (Matthijs) Berends
2020-05-28 10:51:56 +02:00
parent 86d44054f0
commit d9a4b0bcaf
51 changed files with 483 additions and 1106 deletions
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6
man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with 67,107 microorganisms}
\title{Data set with 67,108 microorganisms}
\format{
A \code{\link{data.frame}} with 67,107 observations and 16 variables:
A \code{\link{data.frame}} with 67,108 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"}
@ -40,7 +40,7 @@ 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 7,368 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
\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
}
\subsection{Direct download}{

2
man/microorganisms.old.Rd
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@ -5,7 +5,7 @@
\alias{microorganisms.old}
\title{Data set with previously accepted taxonomic names}
\format{
A \code{\link{data.frame}} with 12,709 observations and 4 variables:
A \code{\link{data.frame}} with 12,708 observations and 4 variables:
\itemize{
\item \code{fullname}\cr Old full taxonomic name of the microorganism
\item \code{fullname_new}\cr New full taxonomic name of the microorganism