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(v1.1.0.9020) updated taxonomy

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dr. M.S. (Matthijs) Berends
2020-05-27 16:37:49 +02:00
parent ae1969b941
commit 86d44054f0
55 changed files with 68063 additions and 70233 deletions
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1
man/as.mo.Rd
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@ -166,7 +166,6 @@ as.mo("Zthafilokkoockus oureuz") # handles incorrect spelling
as.mo("MRSA") # Methicillin Resistant S. aureus
as.mo("VISA") # Vancomycin Intermediate S. aureus
as.mo("VRSA") # Vancomycin Resistant S. aureus
as.mo(22242419) # Catalogue of Life ID
as.mo(115329001) # SNOMED CT code
# Dyslexia is no problem - these all work:

10
man/catalogue_of_life.Rd
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@ -42,9 +42,9 @@ catalogue_of_life_version()
# Get a note when a species was renamed
mo_shortname("Chlamydia psittaci")
# Note: 'Chlamydia psittaci' (Page, 1968) was renamed
# 'Chlamydophila psittaci' (Everett et al., 1999)
mo_shortname("Chlamydophila psittaci")
# Note: 'Chlamydophila psittaci' (Everett et al., 1999) was renamed back to
# 'Chlamydia psittaci' (Page, 1968)
# [1] "C. psittaci"
# Get any property from the entire taxonomic tree for all included species
@ -62,9 +62,9 @@ mo_ref("E. coli")
# Do not get mistaken - this package is about microorganisms
mo_kingdom("C. elegans")
# [1] "Bacteria" # Bacteria?!
# [1] "Fungi" # Fungi?!
mo_name("C. elegans")
# [1] "Chroococcus limneticus elegans" # Because a microorganism was found
# [1] "Cladosporium elegans" # Because a microorganism was found
}
\seealso{
Data set \link{microorganisms} for the actual data. \cr

9
man/microorganisms.Rd
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@ -3,12 +3,11 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with 69,447 microorganisms}
\title{Data set with 67,107 microorganisms}
\format{
A \code{\link{data.frame}} with 69,447 observations and 17 variables:
A \code{\link{data.frame}} with 67,107 observations and 16 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{col_id}\cr Catalogue of Life ID
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}
\item \code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}\cr Taxonomic rank of the microorganism
\item \code{rank}\cr Text of the taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}
@ -22,6 +21,8 @@ A \code{\link{data.frame}} with 69,447 observations and 17 variables:
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
}
\usage{
@ -39,7 +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 12,600 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
\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
}
\subsection{Direct download}{

4
man/microorganisms.codes.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Translation table for common microorganism codes}
\title{Translation table with 5,582 common microorganism codes}
\format{
A \code{\link{data.frame}} with 5,585 observations and 2 variables:
A \code{\link{data.frame}} with 5,582 observations and 2 variables:
\itemize{
\item \code{code}\cr Commonly used code of a microorganism
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set

7
man/microorganisms.old.Rd
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@ -5,17 +5,18 @@
\alias{microorganisms.old}
\title{Data set with previously accepted taxonomic names}
\format{
A \code{\link{data.frame}} with 24,253 observations and 5 variables:
A \code{\link{data.frame}} with 12,709 observations and 4 variables:
\itemize{
\item \code{col_id}\cr Catalogue of Life ID that was originally given
\item \code{col_id_new}\cr New Catalogue of Life ID that responds to an entry in the \link{microorganisms} data set
\item \code{fullname}\cr Old full taxonomic name of the microorganism
\item \code{fullname_new}\cr New full taxonomic name of the microorganism
\item \code{ref}\cr Author(s) and year of concerning scientific publication
\item \code{prevalence}\cr Prevalence of the microorganism, see \code{\link[=as.mo]{as.mo()}}
}
}
\source{
Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; doi: 10.1099/ijsem.0.002786
}
\usage{
microorganisms.old