AMR/R/mo_property.R

140 lines
4.5 KiB
R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' Property of a microorganism
#'
#' 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}}.
#' @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}}
#' @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"}
#' @rdname mo_property
#' @export
#' @importFrom dplyr %>% left_join pull
#' @seealso \code{\link{microorganisms}}
#' @examples
#' # All properties
#' mo_family("E. coli") # Enterobacteriaceae
#' mo_genus("E. coli") # Escherichia
#' mo_species("E. coli") # coli
#' mo_subspecies("E. coli") # <NA>
#' mo_fullname("E. coli") # Escherichia coli
#' mo_type("E. coli") # Bacteria
#' mo_gramstain("E. coli") # Negative rods
#' mo_aerobic("E. coli") # TRUE
#' mo_type_nl("E. coli") # Bacterie
#' mo_gramstain_nl("E. coli") # Negatieve staven
#'
#'
#' # Abbreviations known in the field
#' mo_genus("EHEC") # Escherichia
#' mo_species("EHEC") # coli
#' mo_subspecies("EHEC") # EHEC
#' mo_fullname("EHEC") # Escherichia coli (EHEC)
#'
#' mo_genus("MRSA") # Staphylococcus
#' mo_species("MRSA") # aureus
#' mo_gramstain("MRSA") # Positive cocci
#'
#' mo_genus("VISA") # Staphylococcus
#' mo_species("VISA") # aureus
#'
#'
#' # Known subspecies
#' mo_genus("doylei") # Campylobacter
#' mo_species("doylei") # jejuni
#' mo_fullname("doylei") # Campylobacter jejuni (doylei)
#'
#'
#' # Anaerobic bacteria
#' mo_genus("B. fragilis") # Bacteroides
#' mo_species("B. fragilis") # fragilis
#' mo_aerobic("B. fragilis") # FALSE
mo_property <- function(x, property = 'fullname') {
property <- property[1]
if (!property %in% colnames(microorganisms)) {
stop("invalid property: ", property, " - use a column name of `microorganisms`")
}
if (!is.mo(x)) {
x <- as.mo(x) # this will give a warning if x cannot be coerced
}
suppressWarnings(
data.frame(mo = x, stringsAsFactors = FALSE) %>%
left_join(AMR::microorganisms, by = "mo") %>%
pull(property)
)
}
#' @rdname mo_property
#' @export
mo_family <- function(x) {
mo_property(x, "family")
}
#' @rdname mo_property
#' @export
mo_genus <- function(x) {
mo_property(x, "genus")
}
#' @rdname mo_property
#' @export
mo_species <- function(x) {
mo_property(x, "species")
}
#' @rdname mo_property
#' @export
mo_subspecies <- function(x) {
mo_property(x, "subspecies")
}
#' @rdname mo_property
#' @export
mo_fullname <- function(x) {
mo_property(x, "fullname")
}
#' @rdname mo_property
#' @export
mo_type <- function(x) {
mo_property(x, "type")
}
#' @rdname mo_property
#' @export
mo_gramstain <- function(x) {
mo_property(x, "gramstain")
}
#' @rdname mo_property
#' @export
mo_aerobic <- function(x) {
mo_property(x, "aerobic")
}
#' @rdname mo_property
#' @export
mo_type_nl <- function(x) {
mo_property(x, "type_nl")
}
#' @rdname mo_property
#' @export
mo_gramstain_nl <- function(x) {
mo_property(x, "gramstain_nl")
}