mirror of https://github.com/msberends/AMR.git
116 lines
4.6 KiB
R
116 lines
4.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mo_property.R
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\name{mo_property}
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\alias{mo_property}
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\alias{mo_family}
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\alias{mo_genus}
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\alias{mo_species}
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\alias{mo_subspecies}
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\alias{mo_fullname}
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\alias{mo_type}
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\alias{mo_gramstain}
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\alias{mo_aerobic}
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\title{Property of a microorganism}
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\source{
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[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
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[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}
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}
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\usage{
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mo_property(x, property = "fullname", Becker = FALSE,
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Lancefield = FALSE)
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mo_family(x)
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mo_genus(x)
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mo_species(x, Becker = FALSE, Lancefield = FALSE)
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mo_subspecies(x, Becker = FALSE, Lancefield = FALSE)
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mo_fullname(x, Becker = FALSE, Lancefield = FALSE)
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mo_type(x, language = "en")
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mo_gramstain(x, language = "en")
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mo_aerobic(x)
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}
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\arguments{
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\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}}
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\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"}}
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\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].
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This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
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\item{Lancefield}{a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These \emph{Streptococci} will be categorised in their first group, i.e. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
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This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
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\item{language}{language of the returned text, either one of \code{"en"} (English), \code{"de"} (German) or \code{"nl"} (Dutch)}
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}
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\description{
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Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
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}
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\examples{
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# All properties
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mo_family("E. coli") # "Enterobacteriaceae"
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mo_genus("E. coli") # "Escherichia"
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mo_species("E. coli") # "coli"
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mo_subspecies("E. coli") # <NA>
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mo_fullname("E. coli") # "Escherichia coli"
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mo_type("E. coli") # "Bacteria"
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mo_gramstain("E. coli") # "Negative rods"
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mo_aerobic("E. coli") # TRUE
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# language support for Spanish, German and Dutch
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mo_type("E. coli", "es") # "Bakteria"
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mo_type("E. coli", "de") # "Bakterien"
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mo_type("E. coli", "nl") # "Bacterie"
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mo_gramstain("E. coli", "es") # "Bacilos negativos"
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mo_gramstain("E. coli", "de") # "Negative Staebchen"
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mo_gramstain("E. coli", "nl") # "Negatieve staven"
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# Abbreviations known in the field
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mo_genus("MRSA") # "Staphylococcus"
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mo_species("MRSA") # "aureus"
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mo_gramstain("MRSA") # "Positive cocci"
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mo_genus("VISA") # "Staphylococcus"
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mo_species("VISA") # "aureus"
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# Known subspecies
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mo_genus("EHEC") # "Escherichia"
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mo_species("EHEC") # "coli"
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mo_subspecies("EHEC") # "EHEC"
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mo_fullname("EHEC") # "Escherichia coli (EHEC)"
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mo_genus("doylei") # "Campylobacter"
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mo_species("doylei") # "jejuni"
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mo_fullname("doylei") # "Campylobacter jejuni (doylei)"
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mo_fullname("K. pneu rh") # "Klebsiella pneumoniae (rhinoscleromatis)"
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# Anaerobic bacteria
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mo_genus("B. fragilis") # "Bacteroides"
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mo_species("B. fragilis") # "fragilis"
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mo_aerobic("B. fragilis") # FALSE
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# Becker classification, see ?as.mo
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mo_fullname("S. epidermidis") # "Staphylococcus epidermidis"
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mo_fullname("S. epidermidis", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
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# Lancefield classification, see ?as.mo
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mo_fullname("S. pyogenes") # "Streptococcus pyogenes"
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mo_fullname("S. pyogenes", Lancefield = TRUE) # "Streptococcus group A"
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}
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\seealso{
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\code{\link{microorganisms}}
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}
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