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369 lines
20 KiB
R
369 lines
20 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_name}
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\alias{mo_fullname}
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\alias{mo_shortname}
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\alias{mo_subspecies}
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\alias{mo_species}
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\alias{mo_genus}
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\alias{mo_family}
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\alias{mo_order}
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\alias{mo_class}
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\alias{mo_phylum}
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\alias{mo_kingdom}
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\alias{mo_domain}
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\alias{mo_type}
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\alias{mo_status}
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\alias{mo_pathogenicity}
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\alias{mo_gramstain}
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\alias{mo_is_gram_negative}
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\alias{mo_is_gram_positive}
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\alias{mo_is_yeast}
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\alias{mo_is_intrinsic_resistant}
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\alias{mo_oxygen_tolerance}
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\alias{mo_is_anaerobic}
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\alias{mo_snomed}
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\alias{mo_ref}
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\alias{mo_authors}
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\alias{mo_year}
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\alias{mo_lpsn}
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\alias{mo_mycobank}
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\alias{mo_gbif}
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\alias{mo_rank}
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\alias{mo_taxonomy}
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\alias{mo_synonyms}
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\alias{mo_current}
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\alias{mo_group_members}
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\alias{mo_info}
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\alias{mo_url}
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\title{Get Properties of a Microorganism}
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\usage{
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mo_name(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_fullname(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_shortname(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_subspecies(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_species(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_genus(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_family(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_order(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_class(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_phylum(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_kingdom(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_domain(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_type(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_status(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_pathogenicity(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_gramstain(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_is_gram_negative(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_is_gram_positive(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_is_yeast(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_is_intrinsic_resistant(x, ab, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_oxygen_tolerance(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_is_anaerobic(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_snomed(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_ref(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_authors(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_year(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_lpsn(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_mycobank(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_gbif(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_rank(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_taxonomy(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_synonyms(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_current(x, language = get_AMR_locale(), ...)
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mo_group_members(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_info(x, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_url(x, open = FALSE, language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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mo_property(x, property = "fullname", language = get_AMR_locale(),
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keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...)
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}
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\arguments{
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\item{x}{Any \link{character} (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see \emph{Examples}.}
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\item{language}{Language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}).}
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\item{keep_synonyms}{A \link{logical} to indicate if outdated, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. Do note that the term "synonym" is in this case jargon from the field of microbial taxonomy - it is not in place to denote that e.g. "Streptococcus Group A" is a synonym of \emph{S. pyogenes}. Though this is practically the case, taxonomically it is not as "Streptococcus Group A" is not even a valid taxonomic name.
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The default is \code{FALSE}, which will return a note if outdated taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
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\item{...}{Other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'.}
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\item{ab}{Any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}.}
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\item{open}{Browse the URL using \code{\link[utils:browseURL]{browseURL()}}.}
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\item{property}{One of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be \code{"shortname"}.}
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}
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\value{
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\itemize{
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\item An \link{integer} in case of \code{\link[=mo_year]{mo_year()}}
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\item An \link[=factor]{ordered factor} in case of \code{\link[=mo_pathogenicity]{mo_pathogenicity()}}
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\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}}, \code{\link[=mo_synonyms]{mo_synonyms()}}, \code{\link[=mo_snomed]{mo_snomed()}}, and \code{\link[=mo_info]{mo_info()}}
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\item A \link{logical} in case of \code{\link[=mo_is_anaerobic]{mo_is_anaerobic()}}, \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}}, \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}}, \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}, and \code{\link[=mo_is_yeast]{mo_is_yeast()}}
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\item A named \link{character} in case of \code{\link[=mo_synonyms]{mo_synonyms()}} and \code{\link[=mo_url]{mo_url()}}
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\item A \link{character} in all other cases
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}
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}
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\description{
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Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with \code{\link[=as.mo]{as.mo()}}, which makes it possible to use microbial abbreviations, codes and names as input. See \emph{Examples}.
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}
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\details{
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All functions will, at default, \strong{not} keep old taxonomic properties, as synonyms are automatically replaced with the current taxonomy. Take for example \emph{Enterobacter aerogenes}, which was initially named in 1960 but renamed to \emph{Klebsiella aerogenes} in 2017:
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\itemize{
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\item \code{mo_genus("Enterobacter aerogenes")} will return \code{"Klebsiella"} (with a note about the renaming)
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\item \code{mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)} will return \code{"Enterobacter"} (with a once-per-session warning that the name is outdated)
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\item \code{mo_ref("Enterobacter aerogenes")} will return \code{"Tindall et al., 2017"} (with a note about the renaming)
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\item \code{mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)} will return \code{"Hormaeche et al., 1960"} (with a once-per-session warning that the name is outdated)
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}
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The short name (\code{\link[=mo_shortname]{mo_shortname()}}) returns the first character of the genus and the full species, such as \code{"E. coli"}, for species and subspecies. Exceptions are abbreviations of staphylococci (such as \emph{"CoNS"}, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as \emph{"GBS"}, Group B Streptococci). Please bear in mind that e.g. \emph{E. coli} could mean \emph{Escherichia coli} (kingdom of Bacteria) as well as \emph{Entamoeba coli} (kingdom of Protozoa). Returning to the full name will be done using \code{\link[=as.mo]{as.mo()}} internally, giving priority to bacteria and human pathogens, i.e. \code{"E. coli"} will be considered \emph{Escherichia coli}. As a result, \code{mo_fullname(mo_shortname("Entamoeba coli"))} returns \code{"Escherichia coli"}.
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Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions \code{\link[=mo_kingdom]{mo_kingdom()}} and \code{\link[=mo_domain]{mo_domain()}} return the exact same results.
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Determination of human pathogenicity (\code{\link[=mo_pathogenicity]{mo_pathogenicity()}}) is strongly based on Bartlett \emph{et al.} (2022, \doi{10.1099/mic.0.001269}). This function returns a \link{factor} with the levels \emph{Pathogenic}, \emph{Potentially pathogenic}, \emph{Non-pathogenic}, and \emph{Unknown}.
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Determination of the Gram stain (\code{\link[=mo_gramstain]{mo_gramstain()}}) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318/}{PMID 11837318}), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, \href{https://pubmed.ncbi.nlm.nih.gov/34694987/}{PMID 34694987}). Bacteria in these phyla are considered Gram-positive in this \code{AMR} package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria.
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Determination of yeasts (\code{\link[=mo_is_yeast]{mo_is_yeast()}}) will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. \emph{True yeasts} quite specifically refers to yeasts in the underlying order Saccharomycetales (such as \emph{Saccharomyces cerevisiae}). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}).
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Determination of intrinsic resistance (\code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}) will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antimicrobials).
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Determination of bacterial oxygen tolerance (\code{\link[=mo_oxygen_tolerance]{mo_oxygen_tolerance()}}) will be based on BacDive, see \emph{Source}. The function \code{\link[=mo_is_anaerobic]{mo_is_anaerobic()}} only returns \code{TRUE} if the oxygen tolerance is \code{"anaerobe"}, indicting an obligate anaerobic species or genus. It always returns \code{FALSE} for species outside the taxonomic kingdom of Bacteria.
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The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. \href{https://www.mycobank.org}{This MycoBank URL} will be used for fungi wherever available , \href{https://www.mycobank.org}{this LPSN URL} for bacteria wherever available, and \href{https://www.gbif.org}{this GBIF link} otherwise.
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SNOMED codes (\code{\link[=mo_snomed]{mo_snomed()}}) was last updated on July 16th, 2024. See \emph{Source} and the \link{microorganisms} data set for more info.
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Old taxonomic names (so-called 'synonyms') can be retrieved with \code{\link[=mo_synonyms]{mo_synonyms()}} (which will have the scientific reference as \link[base:names]{name}), the current taxonomic name can be retrieved with \code{\link[=mo_current]{mo_current()}}. Both functions return full names.
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All output \link[=translate]{will be translated} where possible.
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}
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\section{Matching Score for Microorganisms}{
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This function uses \code{\link[=as.mo]{as.mo()}} internally, which uses an advanced algorithm to translate arbitrary user input to valid taxonomy using a so-called matching score. You can read about this public algorithm on the \link[=mo_matching_score]{MO matching score page}.
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}
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\section{Source}{
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\itemize{
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\item Berends MS \emph{et al.} (2022). \strong{AMR: An R Package for Working with Antimicrobial Resistance Data}. \emph{Journal of Statistical Software}, 104(3), 1-31; \doi{10.18637/jss.v104.i03}
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\item Parte, AC \emph{et al.} (2020). \strong{List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.} International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}. Accessed from \url{https://lpsn.dsmz.de} on June 24th, 2024.
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\item Vincent, R \emph{et al} (2013). \strong{MycoBank gearing up for new horizons.} IMA Fungus, 4(2), 371-9; \doi{10.5598/imafungus.2013.04.02.16}. Accessed from \url{https://www.mycobank.org} on June 24th, 2024.
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\item GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset \doi{10.15468/39omei}. Accessed from \url{https://www.gbif.org} on June 24th, 2024.
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\item Reimer, LC \emph{et al.} (2022). \strong{\emph{BacDive} in 2022: the knowledge base for standardized bacterial and archaeal data.} Nucleic Acids Res., 50(D1):D741-D74; \doi{10.1093/nar/gkab961}. Accessed from \url{https://bacdive.dsmz.de} on July 16th, 2024.
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\item Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: \url{https://www.cdc.gov/phin/php/phinvads/}
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\item Bartlett A \emph{et al.} (2022). \strong{A comprehensive list of bacterial pathogens infecting humans} \emph{Microbiology} 168:001269; \doi{10.1099/mic.0.001269}
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}
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}
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\section{Download Our Reference Data}{
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All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
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For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
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Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw/datasets}{our GitHub repository}.
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}
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\examples{
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# taxonomic tree -----------------------------------------------------------
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mo_kingdom("Klebsiella pneumoniae")
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mo_phylum("Klebsiella pneumoniae")
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mo_class("Klebsiella pneumoniae")
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mo_order("Klebsiella pneumoniae")
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mo_family("Klebsiella pneumoniae")
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mo_genus("Klebsiella pneumoniae")
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mo_species("Klebsiella pneumoniae")
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mo_subspecies("Klebsiella pneumoniae")
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# full names and short names -----------------------------------------------
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mo_name("Klebsiella pneumoniae")
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mo_fullname("Klebsiella pneumoniae")
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mo_shortname("Klebsiella pneumoniae")
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# other properties ---------------------------------------------------------
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mo_pathogenicity("Klebsiella pneumoniae")
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mo_gramstain("Klebsiella pneumoniae")
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mo_snomed("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae")
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mo_rank("Klebsiella pneumoniae")
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mo_url("Klebsiella pneumoniae")
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mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
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mo_group_members(c(
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"Streptococcus group A",
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"Streptococcus group C",
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"Streptococcus group G",
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"Streptococcus group L"
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))
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# scientific reference -----------------------------------------------------
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mo_ref("Klebsiella aerogenes")
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mo_authors("Klebsiella aerogenes")
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mo_year("Klebsiella aerogenes")
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mo_synonyms("Klebsiella aerogenes")
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mo_lpsn("Klebsiella aerogenes")
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mo_gbif("Klebsiella aerogenes")
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mo_mycobank("Candida albicans")
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mo_mycobank("Candida krusei")
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mo_mycobank("Candida krusei", keep_synonyms = TRUE)
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# abbreviations known in the field -----------------------------------------
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mo_genus("MRSA")
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mo_species("MRSA")
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mo_shortname("VISA")
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mo_gramstain("VISA")
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mo_genus("EHEC")
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mo_species("EIEC")
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mo_name("UPEC")
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# known subspecies ---------------------------------------------------------
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mo_fullname("K. pneu rh")
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mo_shortname("K. pneu rh")
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\donttest{
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# Becker classification, see ?as.mo ----------------------------------------
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mo_fullname("Staph epidermidis")
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mo_fullname("Staph epidermidis", Becker = TRUE)
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mo_shortname("Staph epidermidis")
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mo_shortname("Staph epidermidis", Becker = TRUE)
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# Lancefield classification, see ?as.mo ------------------------------------
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mo_fullname("Strep agalactiae")
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mo_fullname("Strep agalactiae", Lancefield = TRUE)
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mo_shortname("Strep agalactiae")
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mo_shortname("Strep agalactiae", Lancefield = TRUE)
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# language support --------------------------------------------------------
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mo_gramstain("Klebsiella pneumoniae", language = "de") # German
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mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch
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mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish
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mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek
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mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian
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# mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated
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mo_kingdom("Klebsiella pneumoniae")
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mo_type("Klebsiella pneumoniae")
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mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect
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mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated
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mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de")
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|
mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk")
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# other --------------------------------------------------------------------
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# gram stains and intrinsic resistance can be used as a filter in dplyr verbs
|
|
if (require("dplyr")) {
|
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example_isolates \%>\%
|
|
filter(mo_is_gram_positive()) \%>\%
|
|
count(mo_genus(), sort = TRUE)
|
|
}
|
|
if (require("dplyr")) {
|
|
example_isolates \%>\%
|
|
filter(mo_is_intrinsic_resistant(ab = "vanco")) \%>\%
|
|
count(mo_genus(), sort = TRUE)
|
|
}
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|
|
|
# get a list with the complete taxonomy (from kingdom to subspecies)
|
|
mo_taxonomy("Klebsiella pneumoniae")
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|
|
|
# get a list with the taxonomy, the authors, Gram-stain,
|
|
# SNOMED codes, and URL to the online database
|
|
mo_info("Klebsiella pneumoniae")
|
|
}
|
|
}
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\seealso{
|
|
Data set \link{microorganisms}
|
|
}
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