mirror of https://github.com/msberends/AMR.git
140 lines
4.5 KiB
R
140 lines
4.5 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' Property of a microorganism
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#'
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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{mo}. Get such an ID with \code{\link{as.mo}}.
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#' @param x a (vector of a) valid \code{\link{mo}} or any text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
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#' @param 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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#' @rdname mo_property
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#' @export
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#' @importFrom dplyr %>% left_join pull
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#' @seealso \code{\link{microorganisms}}
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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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#'
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#'
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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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#'
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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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#'
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#' mo_genus("VISA") # Staphylococcus
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#' mo_species("VISA") # aureus
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#'
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#'
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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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#'
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#'
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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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mo_property <- function(x, property = 'fullname') {
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property <- property[1]
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if (!property %in% colnames(microorganisms)) {
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stop("invalid property: ", property, " - use a column name of `microorganisms`")
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}
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if (!is.mo(x)) {
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x <- as.mo(x) # this will give a warning if x cannot be coerced
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}
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suppressWarnings(
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data.frame(mo = x, stringsAsFactors = FALSE) %>%
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left_join(AMR::microorganisms, by = "mo") %>%
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pull(property)
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)
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}
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#' @rdname mo_property
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#' @export
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mo_family <- function(x) {
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mo_property(x, "family")
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}
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#' @rdname mo_property
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#' @export
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mo_genus <- function(x) {
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mo_property(x, "genus")
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}
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#' @rdname mo_property
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#' @export
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mo_species <- function(x) {
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mo_property(x, "species")
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}
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#' @rdname mo_property
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#' @export
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mo_subspecies <- function(x) {
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mo_property(x, "subspecies")
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}
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#' @rdname mo_property
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#' @export
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mo_fullname <- function(x) {
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mo_property(x, "fullname")
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}
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#' @rdname mo_property
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#' @export
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mo_type <- function(x) {
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mo_property(x, "type")
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}
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#' @rdname mo_property
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#' @export
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mo_gramstain <- function(x) {
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mo_property(x, "gramstain")
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}
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#' @rdname mo_property
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#' @export
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mo_aerobic <- function(x) {
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mo_property(x, "aerobic")
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}
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#' @rdname mo_property
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#' @export
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mo_type_nl <- function(x) {
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mo_property(x, "type_nl")
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}
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#' @rdname mo_property
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#' @export
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mo_gramstain_nl <- function(x) {
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mo_property(x, "gramstain_nl")
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}
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