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speed improvement eucast_rules(), support more old MO codes

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dr. M.S. (Matthijs) Berends
2019-05-20 12:00:18 +02:00
parent b0033dae1b
commit 4ca00e1868
35 changed files with 590 additions and 683 deletions
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7
man/mo_property.Rd
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@@ -72,7 +72,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
\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"}}
\item{property}{one of the column names of the \code{\link{microorganisms}} data set or \code{"shortname"}}
}
\value{
\itemize{
@@ -88,7 +88,7 @@ Use these functions to return a specific property of a microorganism from the \c
\details{
All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
\itemize{
\item{\code{mo_fullname("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)}
\item{\code{mo_name("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)}
\item{\code{mo_ref("Chlamydia psittaci")} will return \code{"Page, 1968"} (with a warning about the renaming)}
\item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
}
@@ -162,9 +162,10 @@ mo_species("VISA") # "aureus"
# Known subspecies
mo_name("doylei") # "Campylobacter jejuni doylei"
mo_genus("doylei") # "Campylobacter"
mo_species("doylei") # "jejuni"
mo_fullname("doylei") # "Campylobacter jejuni doylei"
mo_subspecies("doylei") # "doylei"
mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
mo_shortname("K. pneu rh") # "K. pneumoniae"