mirror of https://github.com/msberends/AMR.git
89 lines
2.3 KiB
R
89 lines
2.3 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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\alias{mo_type_nl}
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\alias{mo_gramstain_nl}
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\title{Property of a microorganism}
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\usage{
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mo_property(x, property = "fullname")
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mo_family(x)
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mo_genus(x)
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mo_species(x)
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mo_subspecies(x)
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mo_fullname(x)
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mo_type(x)
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mo_gramstain(x)
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mo_aerobic(x)
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mo_type_nl(x)
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mo_gramstain_nl(x)
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}
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\arguments{
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\item{x}{a (vector of a) valid \code{\link{bactid}} or any text that can be coerced to a valid bactid with \code{\link{as.bactid}}}
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\item{property}{one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"bactid"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}}
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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, based on their \code{bactid}. Get such an ID with \code{\link{as.bactid}}.
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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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mo_type_nl("E. coli") # Bacterie
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mo_gramstain_nl("E. coli") # Negatieve staven
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# Abbreviations known in the field
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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("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("doylei") # Campylobacter
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mo_species("doylei") # jejuni
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mo_fullname("doylei") # Campylobacter jejuni (doylei)
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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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}
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\seealso{
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\code{\link{microorganisms}}
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}
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