# ==================================================================== # # 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. All input values will be evaluated internally with \code{\link{as.mo}}, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples. #' @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, but may be translated) #' mo_rank("E. coli") # "species" #' mo_url("E. coli") # get the direct url to the online database entry #' mo_synonyms("E. coli") # get previously accepted taxonomic names #' #' # 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("VISA") # "S. aureus" #' mo_gramstain("VISA") # "Gram-positive" #' #' mo_genus("EHEC") # "Escherichia" #' mo_species("EHEC") # "coli" #' #' # 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" #' #' \donttest{ #' # 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") #' # get a list with the taxonomy, the authors and the URL to the online database #' mo_info("E. coli") #' } mo_name <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "fullname", ...), language = language, only_unknown = FALSE) } #' @rdname mo_property #' @export mo_fullname <- mo_name #' @rdname mo_property #' @importFrom dplyr %>% mutate pull #' @export mo_shortname <- function(x, language = get_locale(), ...) { x.mo <- AMR::as.mo(x, ...) metadata <- get_mo_failures_uncertainties_renamed() replace_empty <- function(x) { x[x == ""] <- "spp." x } # get first char of genus and complete species in English shortnames <- paste0(substr(mo_genus(x.mo, language = NULL), 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL))) # exceptions for Staphylococci shortnames[shortnames == "S. coagulase-negative" ] <- "CoNS" shortnames[shortnames == "S. coagulase-positive" ] <- "CoPS" # exceptions for Streptococci: Streptococcus Group A -> GAS shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S") load_mo_failures_uncertainties_renamed(metadata) translate_AMR(shortnames, language = language, only_unknown = FALSE) } #' @rdname mo_property #' @export mo_subspecies <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "subspecies", ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_species <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "species", ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_genus <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "genus", ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_family <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "family", ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_order <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "order", ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_class <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "class", ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_phylum <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "phylum", ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_kingdom <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_type <- function(x, language = get_locale(), ...) { translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = FALSE) } #' @rdname mo_property #' @export mo_gramstain <- function(x, language = get_locale(), ...) { x.mo <- AMR::as.mo(x, ...) metadata <- get_mo_failures_uncertainties_renamed() x.phylum <- mo_phylum(x.mo) # DETERMINE GRAM STAIN FOR BACTERIA # Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 # It says this: # Kingdom Bacteria (Cavalier-Smith, 2002) # Subkingdom Posibacteria (Cavalier-Smith, 2002) # Direct Children: # Phylum Actinobacteria (Cavalier-Smith, 2002) # Phylum Chloroflexi (Garrity and Holt, 2002) # Phylum Firmicutes (corrig. Gibbons and Murray, 1978) # Phylum Tenericutes (Murray, 1984) x <- NA_character_ # make all bacteria Gram negative x[mo_kingdom(x.mo) == "Bacteria"] <- "Gram-negative" # overwrite these phyla with Gram positive x[x.phylum %in% c("Actinobacteria", "Chloroflexi", "Firmicutes", "Tenericutes") | x.mo == "B_GRAMP"] <- "Gram-positive" load_mo_failures_uncertainties_renamed(metadata) translate_AMR(x, language = language, only_unknown = FALSE) } #' @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 preceed 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})$", "\\1", x[!is.na(x)]) suppressWarnings(as.integer(x)) } #' @rdname mo_property #' @export mo_rank <- function(x, ...) { mo_validate(x = x, property = "rank", ...) } #' @rdname mo_property #' @export mo_taxonomy <- function(x, language = get_locale(), ...) { x <- AMR::as.mo(x, ...) metadata <- get_mo_failures_uncertainties_renamed() result <- base::list(kingdom = AMR::mo_kingdom(x, language = language), phylum = AMR::mo_phylum(x, language = language), class = AMR::mo_class(x, language = language), order = AMR::mo_order(x, language = language), family = AMR::mo_family(x, language = language), genus = AMR::mo_genus(x, language = language), species = AMR::mo_species(x, language = language), subspecies = AMR::mo_subspecies(x, language = language)) load_mo_failures_uncertainties_renamed(metadata) result } #' @rdname mo_property #' @export mo_synonyms <- function(x, ...) { x <- AMR::as.mo(x, ...) metadata <- get_mo_failures_uncertainties_renamed() IDs <- AMR::mo_property(x = x, property = "col_id", language = NULL) syns <- lapply(IDs, function(col_id) { res <- sort(AMR::microorganisms.old[which(AMR::microorganisms.old$col_id_new == col_id), "fullname"]) if (length(res) == 0) { NULL } else { res } }) if (length(syns) > 1) { names(syns) <- mo_fullname(x) result <- syns } else { result <- unlist(syns) } load_mo_failures_uncertainties_renamed(metadata) result } #' @rdname mo_property #' @export mo_info <- function(x, language = get_locale(), ...) { x <- AMR::as.mo(x, ...) metadata <- get_mo_failures_uncertainties_renamed() info <- lapply(x, function(y) c(mo_taxonomy(y, language = language), list(synonyms = mo_synonyms(y), url = unname(mo_url(y, open = FALSE)), ref = mo_ref(y)))) if (length(info) > 1) { names(info) <- mo_fullname(x) result <- info } else { result <- info[[1L]] } load_mo_failures_uncertainties_renamed(metadata) result } #' @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, ... = ...) metadata <- get_mo_failures_uncertainties_renamed() 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) <- AMR::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]) } load_mo_failures_uncertainties_renamed(metadata) 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") } translate_AMR(mo_validate(x = x, property = property, ...), language = language, only_unknown = TRUE) } 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")) { x <- exec_as.mo(x, property = property, ...) } if (property == "mo") { return(to_class_mo(x)) } else if (property == "col_id") { return(as.integer(x)) } else { return(x) } }