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R/mo_property.R
113
R/mo_property.R
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#' Get Properties of a Microorganism
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#'
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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 [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. See *Examples*.
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#' @inheritSection lifecycle Stable Lifecycle
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#' @param x any [character] (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see *Examples*.
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#' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`, or must be `"shortname"`
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#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
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@ -67,93 +66,91 @@
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#' @export
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#' @seealso Data set [microorganisms]
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#' @inheritSection AMR Reference Data Publicly Available
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#' @inheritSection AMR Read more on Our Website!
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#' @examples
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#' # taxonomic tree -----------------------------------------------------------
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#' mo_kingdom("E. coli") # "Bacteria"
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#' mo_phylum("E. coli") # "Proteobacteria"
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#' mo_class("E. coli") # "Gammaproteobacteria"
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#' mo_order("E. coli") # "Enterobacterales"
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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") # ""
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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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#'
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#' # colloquial properties ----------------------------------------------------
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#' mo_name("E. coli") # "Escherichia coli"
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#' mo_fullname("E. coli") # "Escherichia coli" - same as mo_name()
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#' mo_shortname("E. coli") # "E. coli"
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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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#'
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#' # other properties ---------------------------------------------------------
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#' mo_gramstain("E. coli") # "Gram-negative"
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#' mo_snomed("E. coli") # 112283007, 116395006, ... (SNOMED codes)
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#' mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
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#' mo_rank("E. coli") # "species"
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#' mo_url("E. coli") # get the direct url to the online database entry
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#' mo_synonyms("E. coli") # get previously accepted taxonomic names
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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_synonyms("Klebsiella pneumoniae")
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#'
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#' # scientific reference -----------------------------------------------------
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#' mo_ref("E. coli") # "Castellani et al., 1919"
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#' mo_authors("E. coli") # "Castellani et al."
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#' mo_year("E. coli") # 1919
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#' mo_lpsn("E. coli") # 776057 (LPSN record ID)
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#' mo_ref("Klebsiella pneumoniae")
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#' mo_authors("Klebsiella pneumoniae")
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#' mo_year("Klebsiella pneumoniae")
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#' mo_lpsn("Klebsiella pneumoniae")
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#'
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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_shortname("VISA") # "S. aureus"
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#' mo_gramstain("VISA") # "Gram-positive"
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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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#'
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#' mo_genus("EHEC") # "Escherichia"
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#' mo_species("EHEC") # "coli"
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#' mo_genus("EHEC")
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#' mo_species("EHEC")
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#'
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#' # known subspecies ---------------------------------------------------------
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#' mo_name("doylei") # "Campylobacter jejuni doylei"
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#' mo_genus("doylei") # "Campylobacter"
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#' mo_species("doylei") # "jejuni"
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#' mo_subspecies("doylei") # "doylei"
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#' mo_name("doylei")
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#' mo_genus("doylei")
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#' mo_species("doylei")
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#' mo_subspecies("doylei")
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#'
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#' mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
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#' mo_shortname("K. pneu rh") # "K. pneumoniae"
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#' mo_fullname("K. pneu rh")
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#' mo_shortname("K. pneu rh")
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#'
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#' \donttest{
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#' # Becker classification, see ?as.mo ----------------------------------------
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#' mo_fullname("S. epi") # "Staphylococcus epidermidis"
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#' mo_fullname("S. epi", Becker = TRUE) # "Coagulase-negative Staphylococcus (CoNS)"
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#' mo_shortname("S. epi") # "S. epidermidis"
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#' mo_shortname("S. epi", Becker = TRUE) # "CoNS"
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#' mo_fullname("S. epi")
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#' mo_fullname("S. epi", Becker = TRUE)
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#' mo_shortname("S. epi")
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#' mo_shortname("S. epi", Becker = TRUE)
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#'
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#' # Lancefield classification, see ?as.mo ------------------------------------
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#' mo_fullname("S. pyo") # "Streptococcus pyogenes"
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#' mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
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#' mo_shortname("S. pyo") # "S. pyogenes"
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#' mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" (='Group A Streptococci')
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#' mo_fullname("S. pyo")
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#' mo_fullname("S. pyo", Lancefield = TRUE)
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#' mo_shortname("S. pyo")
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#' mo_shortname("S. pyo", Lancefield = TRUE)
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#'
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#'
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#' # language support --------------------------------------------------------
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#' mo_gramstain("E. coli", language = "de") # "Gramnegativ"
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#' mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
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#' mo_gramstain("E. coli", language = "es") # "Gram negativo"
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#' mo_gramstain("Klebsiella pneumoniae", language = "de")
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#' mo_gramstain("Klebsiella pneumoniae", language = "nl")
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#' mo_gramstain("Klebsiella pneumoniae", language = "es")
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#'
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#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official
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#' mo_kingdom("E. coli") # "Bacteria" on a German system
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#' mo_type("E. coli") # "Bakterien" on a German system
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#' mo_type("E. coli") # "Bacteria" on an English system
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#' mo_kingdom("Klebsiella pneumoniae")
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#' mo_type("Klebsiella pneumoniae")
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#' mo_type("Klebsiella pneumoniae")
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#'
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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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#' language = "de") # "Streptococcus Gruppe A"
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#' language = "de")
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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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#' language = "nl") # "Streptococcus groep A"
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#' language = "nl")
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#'
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#'
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#' # other --------------------------------------------------------------------
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#'
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#' mo_is_yeast(c("Candida", "E. coli")) # TRUE, FALSE
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#' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
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#'
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#' # gram stains and intrinsic resistance can also be used as a filter in dplyr verbs
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#' \donttest{
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#' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs
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#' if (require("dplyr")) {
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#' example_isolates %>%
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#' filter(mo_is_gram_positive())
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#'
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#'
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#' # get a list with the complete taxonomy (from kingdom to subspecies)
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#' mo_taxonomy("E. coli")
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#' mo_taxonomy("Klebsiella pneumoniae")
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#'
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#' # get a list with the taxonomy, the authors, Gram-stain,
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#' # SNOMED codes, and URL to the online database
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#' mo_info("E. coli")
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#' }
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#' # SNOMED codes, and URL to the online database
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#' mo_info("Klebsiella pneumoniae")
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#' }
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mo_name <- function(x, language = get_AMR_locale(), ...) {
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if (missing(x)) {
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