support for portuguese, language determination based on system

man/AMR.Rd

@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{AMR}
+\alias{AMR}
+\title{The \code{AMR} Package}
+\description{
+Welcome to the \code{AMR} package. This page gives some additional contact information abount the authors.
+}
+\details{
+This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
+
+This package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
+}
+\section{Authors}{
+
+Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2],  Corinna Glasner[1],  Alex W. Friedrich[1],  Bhanu Sinha[1] \cr
+
+[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{rug.nl} \url{umcg.nl} \cr
+[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{certe.nl}
+}
+
+\section{Contact us}{
+
+For suggestions, comments or questions, please contact us at:
+
+Matthijs S. Berends \cr
+m.s.berends [at] umcg [dot] nl \cr
+Department of Medical Microbiology, University of Groningen \cr
+University Medical Center Groningen \cr
+Post Office Box 30001 \cr
+9700 RB Groningen
+
+If you have found a bug, please file a new issue at: \cr
+\url{https://github.com/msberends/AMR/issues}
+}
+

man/as.mo.Rd

@@ -44,7 +44,6 @@ Some exceptions have been built in to get more logical results, based on prevale
 \itemize{
   \item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
   \item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae}}
-  \item{Something like \code{"s pyo"} will return the ID of \emph{Streptococcus pyogenes} and not \emph{Actinomyes pyogenes}}
   \item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
   \item{Something like \code{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
 }

man/microorganisms.Rd

@@ -4,7 +4,7 @@
 \name{microorganisms}
 \alias{microorganisms}
 \title{Data set with human pathogenic microorganisms}
-\format{A \code{\link{tibble}} with 2,669 observations and 16 variables:
+\format{A \code{\link{tibble}} with 2,669 observations and 10 variables:
 \describe{
   \item{\code{mo}}{ID of microorganism}
   \item{\code{bactsys}}{Bactsyscode of microorganism}
@@ -16,12 +16,6 @@
   \item{\code{aerobic}}{Logical whether bacteria is aerobic}
   \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
   \item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
-  \item{\code{type_de}}{Type of microorganism in German, like \code{"Bakterien"} and \code{"Pilz/Hefe"}}
-  \item{\code{gramstain_de}}{Gram of microorganism in German, like \code{"Negative Staebchen"}}
-  \item{\code{type_nl}}{Type of microorganism in Dutch, like \code{"Bacterie"} and \code{"Schimmel/gist"}}
-  \item{\code{gramstain_nl}}{Gram of microorganism in Dutch, like \code{"Negatieve staven"}}
-  \item{\code{type_es}}{Type of microorganism in Spanish, like \code{"Bacteria"} and \code{"Hongo/levadura"}}
-  \item{\code{gramstain_es}}{Gram of microorganism in Spanish, like \code{"Bacilos negativos"}}
 }}
 \usage{
 microorganisms

man/mo_property.Rd

@@ -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}}