# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2020 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # 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. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR analysis: https://msberends.github.io/AMR/ # # ==================================================================== # #' Get properties of a microorganism #' #' Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. Please see *Examples*. #' @inheritSection lifecycle Stable lifecycle #' @param x any character (vector) that can be coerced to a valid microorganism code with [as.mo()] #' @param property one of the column names of the [microorganisms] data set or `"shortname"` #' @param language language of the returned text, defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation. #' @param ... other parameters passed on to [as.mo()], such as 'allow_uncertain' and 'ignore_pattern' #' @param open browse the URL using [utils::browseURL()] #' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for [mo_ref()], [mo_authors()] and [mo_year()]. Please refer to this example, knowing that *Escherichia blattae* was renamed to *Shimwellia blattae* in 2010: #' - `mo_name("Escherichia blattae")` will return `"Shimwellia blattae"` (with a message about the renaming) #' - `mo_ref("Escherichia blattae")` will return `"Burgess et al., 1973"` (with a message about the renaming) #' - `mo_ref("Shimwellia blattae")` will return `"Priest et al., 2010"` (without a message) #' #' The short name - [mo_shortname()] - almost always returns the first character of the genus and the full species, like `"E. coli"`. Exceptions are abbreviations of staphylococci (like *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (like *"GBS"*, Group B Streptococci). Please bear in mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning to the full name will be done using [as.mo()] internally, giving priority to bacteria and human pathogens, i.e. `"E. coli"` will be considered *Escherichia coli*. In other words, `mo_fullname(mo_shortname("Entamoeba coli"))` returns `"Escherichia coli"`. #' #' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results. #' #' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), 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 `NA`. Functions [is_gram_negative()] and [is_gram_positive()] always return `TRUE` or `FALSE`, even for species outside the kingdom of Bacteria. #' #' All output will be [translate]d where possible. #' #' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. #' @inheritSection mo_matching_score Matching score for microorganisms #' @inheritSection catalogue_of_life Catalogue of Life #' @inheritSection as.mo Source #' @rdname mo_property #' @name mo_property #' @return #' - An [integer] in case of [mo_year()] #' - A [list] in case of [mo_taxonomy()] and [mo_info()] #' - A named [character] in case of [mo_url()] #' - A [double] in case of [mo_snomed()] #' - A [character] in all other cases #' @export #' @seealso [microorganisms] #' @inheritSection AMR Reference data publicly available #' @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") # "Enterobacterales" #' 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_snomed("E. coli") # 112283007, 116395006, ... (SNOMED codes) #' 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, Gram-stain and URL to the online database #' mo_info("E. coli") #' } mo_name <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...), language = language, only_unknown = FALSE) } #' @rdname mo_property #' @export mo_fullname <- mo_name #' @rdname mo_property #' @export mo_shortname <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) x.mo <- as.mo(x, language = language, ...) metadata <- get_mo_failures_uncertainties_renamed() replace_empty <- function(x) { x[x == ""] <- "spp." x } # get first char of genus and complete species in English genera <- mo_genus(x.mo, language = NULL) shortnames <- paste0(substr(genera, 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL))) # exceptions for where no species is known shortnames[shortnames %like% ".[.] spp[.]"] <- genera[shortnames %like% ".[.] spp[.]"] # 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") # unknown species etc. shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")") 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(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_species <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_genus <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_family <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_order <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_class <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_phylum <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_kingdom <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_domain <- mo_kingdom #' @rdname mo_property #' @export mo_type <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = FALSE) } #' @rdname mo_property #' @export mo_gramstain <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) x.mo <- as.mo(x, language = language, ...) 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 is_gram_negative <- function(x, ...) { meet_criteria(x, allow_NA = TRUE) grams <- mo_gramstain(x, language = NULL, ...) "Gram-negative" == grams & !is.na(grams) } #' @rdname mo_property #' @export is_gram_positive <- function(x, ...) { meet_criteria(x, allow_NA = TRUE) grams <- mo_gramstain(x, language = NULL, ...) "Gram-positive" == grams & !is.na(grams) } #' @rdname mo_property #' @export mo_snomed <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) mo_validate(x = x, property = "snomed", language = language, ...) } #' @rdname mo_property #' @export mo_ref <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) mo_validate(x = x, property = "ref", language = language, ...) } #' @rdname mo_property #' @export mo_authors <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) x <- mo_validate(x = x, property = "ref", language = language, ...) # 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, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) x <- mo_validate(x = x, property = "ref", language = language, ...) # get last 4 digits x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)]) suppressWarnings(as.integer(x)) } #' @rdname mo_property #' @export mo_rank <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) mo_validate(x = x, property = "rank", language = language, ...) } #' @rdname mo_property #' @export mo_taxonomy <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) x <- as.mo(x, language = language, ...) metadata <- get_mo_failures_uncertainties_renamed() result <- list(kingdom = mo_kingdom(x, language = language), phylum = mo_phylum(x, language = language), class = mo_class(x, language = language), order = mo_order(x, language = language), family = mo_family(x, language = language), genus = mo_genus(x, language = language), species = mo_species(x, language = language), subspecies = mo_subspecies(x, language = language)) load_mo_failures_uncertainties_renamed(metadata) result } #' @rdname mo_property #' @export mo_synonyms <- function(x, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) x <- as.mo(x, language = language, ...) metadata <- get_mo_failures_uncertainties_renamed() IDs <- mo_name(x = x, language = NULL) syns <- lapply(IDs, function(newname) { res <- sort(microorganisms.old[which(microorganisms.old$fullname_new == newname), "fullname"]) if (length(res) == 0) { NULL } else { res } }) if (length(syns) > 1) { names(syns) <- mo_name(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(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) x <- as.mo(x, language = language, ...) metadata <- get_mo_failures_uncertainties_renamed() info <- lapply(x, function(y) c(mo_taxonomy(y, language = language), list(synonyms = mo_synonyms(y), gramstain = mo_gramstain(y, language = language), url = unname(mo_url(y, open = FALSE)), ref = mo_ref(y)))) if (length(info) > 1) { names(info) <- mo_name(x) result <- info } else { result <- info[[1L]] } load_mo_failures_uncertainties_renamed(metadata) result } #' @rdname mo_property #' @export mo_url <- function(x, open = FALSE, language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(open, allow_class = "logical", has_length = 1) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) mo <- as.mo(x = x, language = language, ... = ...) mo_names <- mo_name(mo) metadata <- get_mo_failures_uncertainties_renamed() df <- data.frame(mo, stringsAsFactors = FALSE) %pm>% pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo") df$url <- ifelse(df$source == "CoL", paste0(catalogue_of_life$url_CoL, "details/species/id/", df$species_id, "/"), ifelse(df$source == "DSMZ", paste0(catalogue_of_life$url_DSMZ, "/advanced_search?adv[taxon-name]=", gsub(" ", "+", mo_names), "/"), NA_character_)) u <- df$url names(u) <- mo_names if (open == TRUE) { if (length(u) > 1) { warning("only the first URL will be opened, as `browseURL()` only suports one string.") } utils::browseURL(u[1L]) } load_mo_failures_uncertainties_renamed(metadata) u } #' @rdname mo_property #' @export mo_property <- function(x, property = "fullname", language = get_locale(), ...) { meet_criteria(x, allow_NA = TRUE) meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms)) meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE) translate_AMR(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE) } mo_validate <- function(x, property, language, ...) { check_dataset_integrity() if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & length(list(...)) == 0, error = function(e) FALSE)) { # special case for mo_* functions where class is already return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]) } dots <- list(...) Becker <- dots$Becker if (is.null(Becker)) { Becker <- FALSE } Lancefield <- dots$Lancefield if (is.null(Lancefield)) { Lancefield <- FALSE } # try to catch an error when inputting an invalid parameter # so the 'call.' can be set to FALSE tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE], error = function(e) stop(e$message, call. = FALSE)) if (is.mo(x) & !Becker %in% c(TRUE, "all") & !Lancefield %in% c(TRUE, "all")) { # this will not reset mo_uncertainties and mo_failures # because it's already a valid MO x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...) } else if (!all(x %in% MO_lookup[, property, drop = TRUE]) | Becker %in% c(TRUE, "all") | Lancefield %in% c(TRUE, "all")) { x <- exec_as.mo(x, property = property, language = language, ...) } if (property == "mo") { return(to_class_mo(x)) } else if (property == "snomed") { return(as.double(eval(parse(text = x)))) } else { return(x) } }