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(v0.8.0.9007) Enterobacterales order

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dr. M.S. (Matthijs) Berends
2019-10-30 23:02:50 +01:00
parent 7ff2ad8188
commit 09c4b04cd0
22 changed files with 156 additions and 55 deletions
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7
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~70,000 microorganisms}
\format{A \code{\link{data.frame}} with 69,465 observations and 16 variables:
\format{A \code{\link{data.frame}} with 69,447 observations and 16 variables:
\describe{
\item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID}
@ -33,9 +33,10 @@ Manually added were:
\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{Trichomonas vaginalis}, and its family and genus)}
\item{1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel et al. 2005, PMID 15634993)}
\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{9,460 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications}
\item{6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not in the Catalogue of Life}
\item{12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications}
}
}
\section{About the records from DSMZ (see source)}{

2
man/mo_property.Rd
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@ -134,7 +134,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
mo_kingdom("E. coli") # "Bacteria"
mo_phylum("E. coli") # "Proteobacteria"
mo_class("E. coli") # "Gammaproteobacteria"
mo_order("E. coli") # "Enterobacteriales"
mo_order("E. coli") # "Enterobacterales" ()
mo_family("E. coli") # "Enterobacteriaceae"
mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli"