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AI improvements for microorganisms

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dr. M.S. (Matthijs) Berends
2018-09-09 12:11:44 +02:00
parent 936198372e
commit 4816419f0c
5 changed files with 39 additions and 37 deletions
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10
man/mo_property.Rd
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@ -20,7 +20,7 @@
\usage{
mo_family(x)
mo_genus(x)
mo_genus(x, language = NULL)
mo_species(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
@ -42,6 +42,8 @@ mo_property(x, property = "fullname", Becker = FALSE,
\arguments{
\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}}
\item{language}{language of the returned text, defaults to the systems language. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).}
\item{Becker}{a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1].
This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
@ -50,8 +52,6 @@ mo_property(x, property = "fullname", Becker = FALSE,
This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
\item{language}{language of the returned text, defaults to the systems language. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).}
\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"mo"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}}
}
\value{
@ -126,10 +126,10 @@ mo_gramstain("E. coli", language = "nl") # "Negatieve staven"
mo_gramstain("E. coli", language = "es") # "Bacilos negativos"
mo_gramstain("Giardia", language = "pt") # "Parasitas"
mo_fullname("S. pyo",
mo_fullname("S. pyogenes",
Lancefield = TRUE,
language = "de") # "Streptococcus Gruppe A"
mo_fullname("S. pyo",
mo_fullname("S. pyogenes",
Lancefield = TRUE,
language = "nl") # "Streptococcus groep A"
}