mirror of https://github.com/msberends/AMR.git
392 lines
18 KiB
R
392 lines
18 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. All input values will be evaluated internally with \code{\link{as.mo}}.
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#' @param x any (vector of) 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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#' @inheritParams as.mo
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#' @param language language of the returned text, defaults to the systems language. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).
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#' @source
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#' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
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#'
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#' [2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
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#'
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#' [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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#' @rdname mo_property
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#' @name mo_property
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#' @return A logical (in case of \code{mo_aerobic}), a list (in case of \code{mo_taxonomy}), a character otherwise
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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_phylum("E. coli") # "Proteobacteria"
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#' mo_class("E. coli") # "Gammaproteobacteria"
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#' mo_order("E. coli") # "Enterobacteriales"
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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_fullname("E. coli") # "Escherichia coli"
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#' mo_shortname("E. coli") # "E. 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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#'
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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("MRSA") # "S. 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("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_shortname("EHEC") # "E. coli"
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#'
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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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#' mo_fullname("K. pneu rh") # "Klebsiella pneumoniae (rhinoscleromatis)"
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#' mo_shortname("K. pneu rh") # "K. pneumoniae"
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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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#'
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#'
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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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#'
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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"
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#'
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#'
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#' # Language support for German, Dutch, Spanish and Portuguese
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#' mo_type("E. coli", language = "de") # "Bakterium"
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#' mo_type("E. coli", language = "nl") # "Bacterie"
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#' mo_type("E. coli", language = "es") # "Bakteria"
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#' mo_gramstain("E. coli", language = "de") # "Negative Staebchen"
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#' mo_gramstain("E. coli", language = "nl") # "Negatieve staven"
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#' mo_gramstain("E. coli", language = "es") # "Bacilos negativos"
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#' mo_gramstain("Giardia", language = "pt") # "Parasitas"
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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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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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#' language = "nl") # "Streptococcus groep A"
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#'
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#'
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#' # Complete taxonomy up to Phylum, returns a list
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#' mo_taxonomy("E. coli")
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mo_fullname <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
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mo_property(x, "fullname", Becker = Becker, Lancefield = Lancefield, language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
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if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
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res1 <- as.mo(x)
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res2 <- suppressWarnings(as.mo(x, Becker = Becker, Lancefield = Lancefield))
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res2_fullname <- mo_fullname(res2)
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res2_fullname[res2_fullname %like% "\\(CoNS\\)"] <- "CoNS"
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res2_fullname[res2_fullname %like% "\\(CoPS\\)"] <- "CoPS"
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res2_fullname <- gsub("Streptococcus (group|Gruppe|gruppe|groep|grupo|gruppo|groupe) (.)",
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"G\\2S",
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res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
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res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(x)]
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res2_fullname[res2_fullname == mo_fullname(x)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
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". ",
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suppressWarnings(mo_species(res2_fullname_vector)))
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if (sum(res1 == res2, na.rm = TRUE) > 0) {
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res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
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". ",
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suppressWarnings(mo_species(res1[res1 == res2])))
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}
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res1[res1 != res2] <- res2_fullname
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result <- as.character(res1)
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} else {
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# return G. species
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result <- paste0(substr(mo_genus(x), 1, 1), ". ", suppressWarnings(mo_species(x)))
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}
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result[result %in% c(". ", "(. ")] <- ""
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mo_translate(result, language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_subspecies <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
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mo_property(x, "subspecies", Becker = Becker, Lancefield = Lancefield, language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_species <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
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mo_property(x, "species", Becker = Becker, Lancefield = Lancefield, language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_genus <- function(x, language = NULL) {
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mo_property(x, "genus", language = language)
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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_order <- function(x) {
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mo_property(x, "order")
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}
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#' @rdname mo_property
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#' @export
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mo_class <- function(x) {
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mo_property(x, "class")
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}
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#' @rdname mo_property
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#' @export
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mo_phylum <- function(x) {
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mo_property(x, "phylum")
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}
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#' @rdname mo_property
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#' @export
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mo_type <- function(x, language = NULL) {
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mo_property(x, "type", language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_gramstain <- function(x, language = NULL) {
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mo_property(x, "gramstain", language = language)
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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_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE, language = NULL) {
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property <- tolower(property[1])
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if (!property %in% colnames(AMR::microorganisms)) {
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stop("invalid property: ", property, " - use a column name of the `microorganisms` data set")
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}
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result1 <- as.mo(x = x, Becker = Becker, Lancefield = Lancefield) # this will give a warning if x cannot be coerced
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result2 <- suppressWarnings(
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data.frame(mo = result1, 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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if (property != "aerobic") {
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# will else not retain `logical` class
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result2[x %in% c("", NA) | result2 %in% c("", NA, "(no MO)")] <- ""
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result2 <- mo_translate(result2, language = language)
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}
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result2
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}
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#' @rdname mo_property
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#' @export
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mo_taxonomy <- function(x) {
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x <- as.mo(x)
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base::list(phylum = mo_phylum(x),
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class = mo_class(x),
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order = mo_order(x),
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family = mo_family(x),
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genus = mo_genus(x),
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species = mo_species(x),
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subspecies = mo_subspecies(x))
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}
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#' @importFrom dplyr %>% case_when
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mo_translate <- function(x, language) {
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if (is.null(language)) {
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language <- Sys.locale()
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} else {
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language <- tolower(language[1])
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}
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if (language %in% c("en", "")) {
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return(x)
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}
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supported <- c("en", "de", "nl", "es", "pt", "it", "fr")
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if (!language %in% supported) {
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stop("Unsupported language: '", language, "' - use one of: ", paste0("'", sort(supported), "'", collapse = ", "), call. = FALSE)
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}
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case_when(
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# German
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language == "de" ~ x %>%
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gsub("Coagulase Negative Staphylococcus","Koagulase-negative Staphylococcus", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Koagulase-positive Staphylococcus", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Beta-h\u00e4molytischer Streptococcus", ., fixed = TRUE) %>%
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gsub("(no MO)", "(kein MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Negative St\u00e4bchen", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Negative Kokken", ., fixed = TRUE) %>%
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gsub("Positive rods", "Positive St\u00e4bchen", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Positive Kokken", ., fixed = TRUE) %>%
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gsub("Parasites", "Parasiten", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Pilze und Hefen", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bakterium", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Pilz/Hefe", ., fixed = TRUE) %>%
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gsub("Parasite", "Parasit", ., fixed = TRUE) %>%
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gsub("biogroup", "Biogruppe", ., fixed = TRUE) %>%
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gsub("biotype", "Biotyp", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativ", ., fixed = TRUE) %>%
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gsub("([([ ]*?)group", "\\1Gruppe", .) %>%
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gsub("([([ ]*?)Group", "\\1Gruppe", .),
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# Dutch
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language == "nl" ~ x %>%
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gsub("Coagulase Negative Staphylococcus","Coagulase-negatieve Staphylococcus", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Coagulase-positieve Staphylococcus", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Beta-hemolytische Streptococcus", ., fixed = TRUE) %>%
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gsub("(no MO)", "(geen MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Negatieve staven", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Negatieve kokken", ., fixed = TRUE) %>%
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gsub("Positive rods", "Positieve staven", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Positieve kokken", ., fixed = TRUE) %>%
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gsub("Parasites", "Parasieten", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Schimmels en gisten", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bacterie", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Schimmel/gist", ., fixed = TRUE) %>%
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gsub("Parasite", "Parasiet", ., fixed = TRUE) %>%
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gsub("biogroup", "biogroep", ., fixed = TRUE) %>%
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# gsub("biotype", "biotype", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetatief", ., fixed = TRUE) %>%
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gsub("([([ ]*?)group", "\\1groep", .) %>%
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gsub("([([ ]*?)Group", "\\1Groep", .),
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# Spanish
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language == "es" ~ x %>%
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gsub("Coagulase Negative Staphylococcus","Staphylococcus coagulasa negativo", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Staphylococcus coagulasa positivo", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
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gsub("(no MO)", "(sin MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Bacilos negativos", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Cocos negativos", ., fixed = TRUE) %>%
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gsub("Positive rods", "Bacilos positivos", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Cocos positivos", ., fixed = TRUE) %>%
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gsub("Parasites", "Par\u00e1sitos", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Hongos y levaduras", ., fixed = TRUE) %>%
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# gsub("Bacteria", "Bacteria", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Hongo/levadura", ., fixed = TRUE) %>%
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gsub("Parasite", "Par\u00e1sito", ., fixed = TRUE) %>%
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gsub("biogroup", "biogrupo", ., fixed = TRUE) %>%
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gsub("biotype", "biotipo", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
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gsub("([([ ]*?)group", "\\1grupo", .) %>%
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gsub("([([ ]*?)Group", "\\1Grupo", .),
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# Portuguese
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language == "pt" ~ x %>%
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gsub("Coagulase Negative Staphylococcus","Staphylococcus coagulase negativo", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Staphylococcus coagulase positivo", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
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gsub("(no MO)", "(sem MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Bacilos negativos", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Cocos negativos", ., fixed = TRUE) %>%
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gsub("Positive rods", "Bacilos positivos", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Cocos positivos", ., fixed = TRUE) %>%
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gsub("Parasites", "Parasitas", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Cogumelos e leveduras", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bact\u00e9ria", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Cogumelo/levedura", ., fixed = TRUE) %>%
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gsub("Parasite", "Parasita", ., fixed = TRUE) %>%
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gsub("biogroup", "biogrupo", ., fixed = TRUE) %>%
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gsub("biotype", "bi\u00f3tipo", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
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gsub("([([ ]*?)group", "\\1grupo", .) %>%
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gsub("([([ ]*?)Group", "\\1Grupo", .),
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# Italian
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language == "it" ~ x %>%
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gsub("Coagulase Negative Staphylococcus","Staphylococcus negativo coagulasi", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Staphylococcus positivo coagulasi", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-emolitico", ., fixed = TRUE) %>%
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gsub("(no MO)", "(non MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Bastoncini Gram-negativi", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Cocchi Gram-negativi", ., fixed = TRUE) %>%
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gsub("Positive rods", "Bastoncini Gram-positivi", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Cocchi Gram-positivi", ., fixed = TRUE) %>%
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gsub("Parasites", "Parassiti", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Funghi e lieviti", ., fixed = TRUE) %>%
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gsub("Bacteria", "Batterio", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Fungo/lievito", ., fixed = TRUE) %>%
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gsub("Parasite", "Parassita", ., fixed = TRUE) %>%
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gsub("biogroup", "biogruppo", ., fixed = TRUE) %>%
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gsub("biotype", "biotipo", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
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gsub("([([ ]*?)group", "\\1gruppo", .) %>%
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gsub("([([ ]*?)Group", "\\1Gruppo", .),
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# French
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language == "fr" ~ x %>%
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gsub("Coagulase Negative Staphylococcus","Staphylococcus \u00e0 coagulase n\u00e9gative", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Staphylococcus \u00e0 coagulase positif", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Streptococcus B\u00eata-h\u00e9molytique", ., fixed = TRUE) %>%
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gsub("(no MO)", "(pas MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Bacilles n\u00e9gatif", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Cocci n\u00e9gatif", ., fixed = TRUE) %>%
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gsub("Positive rods", "Bacilles positif", ., fixed = TRUE) %>%
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||
gsub("Positive cocci", "Cocci positif", ., fixed = TRUE) %>%
|
||
# gsub("Parasites", "Parasites", ., fixed = TRUE) %>%
|
||
gsub("Fungi and yeasts", "Champignons et levures", ., fixed = TRUE) %>%
|
||
gsub("Bacteria", "Bact\u00e9rie", ., fixed = TRUE) %>%
|
||
gsub("Fungus/yeast", "Champignon/levure", ., fixed = TRUE) %>%
|
||
# gsub("Parasite", "Parasite", ., fixed = TRUE) %>%
|
||
gsub("biogroup", "biogroupe", ., fixed = TRUE) %>%
|
||
# gsub("biotype", "biotype", ., fixed = TRUE) %>%
|
||
gsub("vegetative", "v\u00e9g\u00e9tatif", ., fixed = TRUE) %>%
|
||
gsub("([([ ]*?)group", "\\1groupe", .) %>%
|
||
gsub("([([ ]*?)Group", "\\1Groupe", .)
|
||
|
||
)
|
||
|
||
}
|