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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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6
man/as.mo.Rd
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@ -112,16 +112,16 @@ Use \code{mo_uncertainties()} to get a data.frame with all values that were coer
Use \code{mo_renamed()} to get a vector with all values that could be coerced based on an old, previously accepted taxonomic name.
\strong{Microbial prevalence of pathogens in humans} \cr
The intelligent rules takes into account microbial prevalence of pathogens in humans. It uses three groups and all (sub)species are in only one group. These groups are:
The intelligent rules take into account microbial prevalence of pathogens in humans. It uses three groups and all (sub)species are in only one group. These groups are:
\itemize{
\item{1 (most prevalent): class is Gammaproteobacteria \strong{or} genus is one of: \emph{Enterococcus}, \emph{Staphylococcus}, \emph{Streptococcus}.}
\item{2: phylum is one of: Proteobacteria, Firmicutes, Actinobacteria, Sarcomastigophora \strong{or} genus is one of: \emph{Aspergillus}, \emph{Bacteroides}, \emph{Candida}, \emph{Capnocytophaga}, \emph{Chryseobacterium}, \emph{Cryptococcus}, \emph{Elisabethkingia}, \emph{Flavobacterium}, \emph{Fusobacterium}, \emph{Giardia}, \emph{Leptotrichia}, \emph{Mycoplasma}, \emph{Prevotella}, \emph{Rhodotorula}, \emph{Treponema}, \emph{Trichophyton}, \emph{Ureaplasma}.}
\item{3 (least prevalent): all others.}
}
Group 1 contains all common Gram negatives, like all Enterobacteriaceae and e.g. \emph{Pseudomonas} and \emph{Legionella}.
Group 1 contains all common Gram positives and Gram negatives, like all Enterobacteriaceae and e.g. \emph{Pseudomonas} and \emph{Legionella}.
Group 2 probably contains all other microbial pathogens ever found in humans.
Group 2 probably contains less microbial pathogens; all other members of phyla that were found in humans in the Northern Netherlands between 2001 and 2018.
}
\section{Source}{

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"