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support for portuguese, language determination based on system

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dr. M.S. (Matthijs) Berends
2018-09-08 16:06:47 +02:00
parent b8a6c9af19
commit 26f5be0033
19 changed files with 307 additions and 106 deletions
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49
man/mo_property.Rd
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@@ -18,32 +18,30 @@
[2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
}
\usage{
mo_property(x, property = "fullname", Becker = FALSE,
Lancefield = FALSE)
mo_family(x)
mo_genus(x)
mo_species(x, Becker = FALSE, Lancefield = FALSE)
mo_species(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_subspecies(x, Becker = FALSE, Lancefield = FALSE)
mo_subspecies(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_fullname(x, Becker = FALSE, Lancefield = FALSE)
mo_fullname(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_shortname(x, Becker = FALSE, Lancefield = FALSE)
mo_shortname(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
mo_type(x, language = "en")
mo_type(x, language = NULL)
mo_gramstain(x, language = "en")
mo_gramstain(x, language = NULL)
mo_aerobic(x)
mo_property(x, property = "fullname", Becker = FALSE,
Lancefield = FALSE, language = NULL)
}
\arguments{
\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}}
\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"}}
\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".}
@@ -52,7 +50,9 @@ mo_aerobic(x)
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, either one of \code{"en"} (English), \code{"de"} (German) or \code{"nl"} (Dutch)}
\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{
Character or logical (only \code{mo_aerobic})
@@ -72,14 +72,6 @@ mo_type("E. coli") # "Bacteria"
mo_gramstain("E. coli") # "Negative rods"
mo_aerobic("E. coli") # TRUE
# language support for Spanish, German and Dutch
mo_type("E. coli", "es") # "Bakteria"
mo_type("E. coli", "de") # "Bakterien"
mo_type("E. coli", "nl") # "Bacterie"
mo_gramstain("E. coli", "es") # "Bacilos negativos"
mo_gramstain("E. coli", "de") # "Negative Staebchen"
mo_gramstain("E. coli", "nl") # "Negatieve staven"
# Abbreviations known in the field
mo_genus("MRSA") # "Staphylococcus"
@@ -123,6 +115,23 @@ mo_fullname("S. pyo") # "Streptococcus pyogenes"
mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
mo_shortname("S. pyo") # "S. pyogenes"
mo_shortname("S. pyo", Lancefield = TRUE) # "GAS"
# Language support for German, Dutch, Spanish and Portuguese
mo_type("E. coli", language = "de") # "Bakterium"
mo_type("E. coli", language = "nl") # "Bacterie"
mo_type("E. coli", language = "es") # "Bakteria"
mo_gramstain("E. coli", language = "de") # "Negative Staebchen"
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",
Lancefield = TRUE,
language = "de") # "Streptococcus Gruppe A"
mo_fullname("S. pyo",
Lancefield = TRUE,
language = "nl") # "Streptococcus groep A"
}
\seealso{
\code{\link{microorganisms}}