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DSMZ data

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dr. M.S. (Matthijs) Berends
2019-03-18 14:29:41 +01:00
parent b561de462a
commit c6a12266e7
38 changed files with 575 additions and 363 deletions
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8
man/mo_property.Rd
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@@ -67,7 +67,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
\item{...}{other parameters passed on to \code{\link{as.mo}}}
\item{open}{browse the URL using \code{\link[utils]{browseURL}}}
\item{open}{browse the URL using \code{\link[utils]{browseURL}()}}
\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}}
}
@@ -90,9 +90,9 @@ All functions will return the most recently known taxonomic property according t
\item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
}
The Gram stain - \code{mo_gramstain()} - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes (ref: \url{https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097}). These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value \code{NA}.
The Gram stain - \code{mo_gramstain()} - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value \code{NA}.
The function \code{mo_url()} will return the direct URL to the species in the Catalogue of Life.
The function \code{mo_url()} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
}
\section{Supported languages}{
@@ -169,7 +169,7 @@ mo_shortname("K. pneu rh") # "K. pneumoniae"
# Becker classification, see ?as.mo
mo_fullname("S. epi") # "Staphylococcus epidermidis"
mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
mo_fullname("S. epi", Becker = TRUE) # "Coagulase-negative Staphylococcus (CoNS)"
mo_shortname("S. epi") # "S. epidermidis"
mo_shortname("S. epi", Becker = TRUE) # "CoNS"