# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # # https://gitlab.com/msberends/AMR # # # # LICENCE # # (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # # # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # # Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Property of a microorganism #' #' 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}}. #' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}} #' @param property one of the column names of the \code{\link{microorganisms}} data set or \code{"shortname"} #' @param language language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation. #' @param ... other parameters passed on to \code{\link{as.mo}} #' @param open browse the URL using \code{\link[utils]{browseURL}()} #' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results: #' \itemize{ #' \item{\code{mo_name("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)} #' \item{\code{mo_ref("Chlamydia psittaci")} will return \code{"Page, 1968"} (with a warning about the renaming)} #' \item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)} #' } #' #' The Gram stain - \code{mo_gramstain()} - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value \code{NA}. #' #' All output will be \link{translate}d where possible. #' #' The function \code{mo_url()} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. #' @inheritSection catalogue_of_life Catalogue of Life #' @inheritSection as.mo Source #' @rdname mo_property #' @name mo_property #' @return \itemize{ #' \item{An \code{integer} in case of \code{mo_year}} #' \item{A \code{list} in case of \code{mo_taxonomy}} #' \item{A named \code{character} in case of \code{mo_url}} #' \item{A \code{character} in all other cases} #' } #' @export #' @seealso \code{\link{microorganisms}} #' @inheritSection AMR Read more on our website! #' @examples #' ## taxonomic tree #' mo_kingdom("E. coli") # "Bacteria" #' mo_phylum("E. coli") # "Proteobacteria" #' mo_class("E. coli") # "Gammaproteobacteria" #' mo_order("E. coli") # "Enterobacteriales" #' mo_family("E. coli") # "Enterobacteriaceae" #' mo_genus("E. coli") # "Escherichia" #' mo_species("E. coli") # "coli" #' mo_subspecies("E. coli") # "" #' #' ## colloquial properties #' mo_name("E. coli") # "Escherichia coli" #' mo_fullname("E. coli") # "Escherichia coli", same as mo_name() #' mo_shortname("E. coli") # "E. coli" #' #' ## other properties #' mo_gramstain("E. coli") # "Gram negative" #' mo_type("E. coli") # "Bacteria" (equal to kingdom) #' mo_rank("E. coli") # "species" #' mo_url("E. coli") # get the direct url to the online database entry #' #' ## scientific reference #' mo_ref("E. coli") # "Castellani et al., 1919" #' mo_authors("E. coli") # "Castellani et al." #' mo_year("E. coli") # 1919 #' #' #' # Abbreviations known in the field #' mo_genus("MRSA") # "Staphylococcus" #' mo_species("MRSA") # "aureus" #' mo_shortname("MRSA") # "S. aureus" #' mo_gramstain("MRSA") # "Gram positive" #' #' mo_genus("VISA") # "Staphylococcus" #' mo_species("VISA") # "aureus" #' #' #' # Known subspecies #' mo_name("doylei") # "Campylobacter jejuni doylei" #' mo_genus("doylei") # "Campylobacter" #' mo_species("doylei") # "jejuni" #' mo_subspecies("doylei") # "doylei" #' #' mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis" #' mo_shortname("K. pneu rh") # "K. pneumoniae" #' #' #' # Becker classification, see ?as.mo #' mo_fullname("S. epi") # "Staphylococcus epidermidis" #' mo_fullname("S. epi", Becker = TRUE) # "Coagulase-negative Staphylococcus (CoNS)" #' mo_shortname("S. epi") # "S. epidermidis" #' mo_shortname("S. epi", Becker = TRUE) # "CoNS" #' #' # Lancefield classification, see ?as.mo #' mo_fullname("S. pyo") # "Streptococcus pyogenes" #' mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A" #' mo_shortname("S. pyo") # "S. pyogenes" #' mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" ('Group A streptococci') #' #' #' # language support for German, Dutch, Spanish, Portuguese, Italian and French #' mo_gramstain("E. coli", language = "de") # "Gramnegativ" #' mo_gramstain("E. coli", language = "nl") # "Gram-negatief" #' mo_gramstain("E. coli", language = "es") # "Gram negativo" #' #' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official #' mo_kingdom("E. coli") # "Bacteria" on a German system #' mo_type("E. coli") # "Bakterien" on a German system #' mo_type("E. coli") # "Bacteria" on an English system #' #' mo_fullname("S. pyogenes", #' Lancefield = TRUE, #' language = "de") # "Streptococcus Gruppe A" #' mo_fullname("S. pyogenes", #' Lancefield = TRUE, #' language = "nl") # "Streptococcus groep A" #' #' #' # get a list with the complete taxonomy (from kingdom to subspecies) #' mo_taxonomy("E. coli") mo_name <- function(x, language = get_locale(), ...) { mo_fullname(x = x, language = language, ... = ...) } #' @rdname mo_property #' @export mo_fullname <- function(x, language = get_locale(), ...) { t(mo_validate(x = x, property = "fullname", ...), language = language) } #' @rdname mo_property #' @importFrom dplyr %>% mutate pull #' @export mo_shortname <- function(x, language = get_locale(), ...) { dots <- list(...) Becker <- dots$Becker if (is.null(Becker)) { Becker <- FALSE } Lancefield <- dots$Lancefield if (is.null(Lancefield)) { Lancefield <- FALSE } # get result without transformations res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df) # and result with transformations res2 <- suppressWarnings(AMR::as.mo(res1, ...)) res2_fullname <- mo_fullname(res2, language = language) res2_fullname[res2_fullname %like% " \\(CoNS\\)"] <- "CoNS" res2_fullname[res2_fullname %like% " \\(CoPS\\)"] <- "CoPS" res2_fullname[res2_fullname %like% " \\(KNS\\)"] <- "KNS" res2_fullname[res2_fullname %like% " \\(KPS\\)"] <- "KPS" res2_fullname[res2_fullname %like% " \\(CNS\\)"] <- "CNS" res2_fullname[res2_fullname %like% " \\(CPS\\)"] <- "CPS" res2_fullname[res2_fullname %like% " \\(SCN\\)"] <- "SCN" res2_fullname <- gsub("Streptococcus (group|Gruppe|gruppe|groep|grupo|gruppo|groupe) (.)", "G\\2S", res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS" res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(res1)] res2_fullname[res2_fullname == mo_fullname(res1)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1), ". ", suppressWarnings(mo_species(res2_fullname_vector))) if (sum(res1 == res2, na.rm = TRUE) > 0) { res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1), ". ", suppressWarnings(mo_species(res1[res1 == res2]))) } res1[res1 != res2] <- res2_fullname result <- as.character(res1) t(result, language = language) } #' @rdname mo_property #' @export mo_subspecies <- function(x, language = get_locale(), ...) { t(mo_validate(x = x, property = "subspecies", ...), language = language) } #' @rdname mo_property #' @export mo_species <- function(x, language = get_locale(), ...) { t(mo_validate(x = x, property = "species", ...), language = language) } #' @rdname mo_property #' @export mo_genus <- function(x, language = get_locale(), ...) { t(mo_validate(x = x, property = "genus", ...), language = language) } #' @rdname mo_property #' @export mo_family <- function(x, language = get_locale(), ...) { t(mo_validate(x = x, property = "family", ...), language = language) } #' @rdname mo_property #' @export mo_order <- function(x, language = get_locale(), ...) { t(mo_validate(x = x, property = "order", ...), language = language) } #' @rdname mo_property #' @export mo_class <- function(x, language = get_locale(), ...) { t(mo_validate(x = x, property = "class", ...), language = language) } #' @rdname mo_property #' @export mo_phylum <- function(x, language = get_locale(), ...) { t(mo_validate(x = x, property = "phylum", ...), language = language) } #' @rdname mo_property #' @export mo_kingdom <- function(x, language = get_locale(), ...) { if (all(x %in% AMR::microorganisms$kingdom)) { return(x) } x <- as.mo(x, ...) kngdm <- mo_validate(x = x, property = "kingdom", ...) if (language != "en") { # translate only unknown, so "Bacteria" (the official taxonomic name) would not change kngdm[identical(x, "UNKNOWN")] <- t(kngdm[identical(x, "UNKNOWN")], language = language) } kngdm } #' @rdname mo_property #' @export mo_type <- function(x, language = get_locale(), ...) { t(mo_validate(x = x, property = "kingdom", ...), language = language) } #' @rdname mo_property #' @export mo_gramstain <- function(x, language = get_locale(), ...) { x.mo <- as.mo(x, ...) x.phylum <- mo_phylum(x.mo, language = "en") x[x.phylum %in% c("Actinobacteria", "Chloroflexi", "Firmicutes", "Tenericutes")] <- "Gram positive" x[x != "Gram positive"] <- "Gram negative" x[mo_kingdom(x.mo, language = "en") != "Bacteria"] <- NA_character_ x[x.mo == "B_GRAMP"] <- "Gram positive" x[x.mo == "B_GRAMN"] <- "Gram negative" t(x, language = language) } #' @rdname mo_property #' @export mo_ref <- function(x, ...) { mo_validate(x = x, property = "ref", ...) } #' @rdname mo_property #' @export mo_authors <- function(x, ...) { x <- mo_validate(x = x, property = "ref", ...) # remove last 4 digits and presumably the comma and space that preceeds them x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)]) suppressWarnings(x) } #' @rdname mo_property #' @export mo_year <- function(x, ...) { x <- mo_validate(x = x, property = "ref", ...) # get last 4 digits x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)]) suppressWarnings(as.integer(x)) } #' @rdname mo_property #' @export mo_rank <- function(x, ...) { mo_validate(x = x, property = "rank", ...) } #' @rdname mo_property #' @export mo_taxonomy <- function(x, language = get_locale(), ...) { x <- AMR::as.mo(x, ...) base::list(kingdom = mo_kingdom(x, language = language), phylum = mo_phylum(x, language = language), class = mo_class(x, language = language), order = mo_order(x, language = language), family = mo_family(x, language = language), genus = mo_genus(x, language = language), species = mo_species(x, language = language), subspecies = mo_subspecies(x, language = language)) } #' @rdname mo_property #' @importFrom utils browseURL #' @importFrom dplyr %>% left_join select mutate case_when #' @export mo_url <- function(x, open = FALSE, ...) { mo <- AMR::as.mo(x = x, ... = ...) df <- data.frame(mo, stringsAsFactors = FALSE) %>% left_join(select(AMR::microorganisms, mo, source, species_id), by = "mo") %>% mutate(url = case_when(source == "CoL" ~ paste0(gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE), "details/species/id/", species_id), source == "DSMZ" ~ paste0(catalogue_of_life$url_DSMZ, "?bnu_no=", species_id, "#", species_id), TRUE ~ NA_character_)) u <- df$url names(u) <- mo_fullname(mo) if (open == TRUE) { if (length(u) > 1) { warning("only the first URL will be opened, as `browseURL()` only suports one string.") } browseURL(u[1L]) } u } #' @rdname mo_property #' @importFrom data.table data.table as.data.table setkey #' @export mo_property <- function(x, property = 'fullname', language = get_locale(), ...) { if (length(property) != 1L) { stop("'property' must be of length 1.") } if (!property %in% colnames(AMR::microorganisms)) { stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set") } t(mo_validate(x = x, property = property, ...), language = language) } mo_validate <- function(x, property, ...) { dots <- list(...) Becker <- dots$Becker if (is.null(Becker)) { Becker <- FALSE } Lancefield <- dots$Lancefield if (is.null(Lancefield)) { Lancefield <- FALSE } if (!"AMR" %in% base::.packages()) { require("AMR") # check onLoad() in R/zzz.R: data tables are created there. } # try to catch an error when inputting an invalid parameter # so the 'call.' can be set to FALSE tryCatch(x[1L] %in% AMR::microorganisms[1, property], error = function(e) stop(e$message, call. = FALSE)) if (!all(x %in% pull(AMR::microorganisms, property)) | Becker %in% c(TRUE, "all") | Lancefield %in% c(TRUE, "all")) { exec_as.mo(x, property = property, ...) } else { if (property == "mo") { return(structure(x, class = "mo")) } else { return(x) } } }