# ==================================================================== # # TITLE: # # AMR: An R Package for Working with Antimicrobial Resistance Data # # # # SOURCE CODE: # # https://github.com/msberends/AMR # # # # PLEASE CITE THIS SOFTWARE AS: # # Berends MS, Luz CF, Friedrich AW, et al. (2022). # # AMR: An R Package for Working with Antimicrobial Resistance Data. # # Journal of Statistical Software, 104(3), 1-31. # # https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # # colleagues from around the world, see our website. # # # # 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 data 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. See *Examples*. #' @param x any [character] (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see *Examples*. #' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`, or must be `"shortname"` #' @inheritParams as.mo #' @param ... other arguments passed on to [as.mo()], such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input' #' @param ab any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()] #' @param open browse the URL using [`browseURL()`][utils::browseURL()] #' @details All functions will, at default, **not** keep old taxonomic properties, as synonyms are automatically replaced with the current taxonomy. Take for example *Enterobacter aerogenes*, which was initially named in 1960 but renamed to *Klebsiella aerogenes* in 2017: #' - `mo_genus("Enterobacter aerogenes")` will return `"Klebsiella"` (with a note about the renaming) #' - `mo_genus("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Enterobacter"` (with a once-per-session warning that the name is outdated) #' - `mo_ref("Enterobacter aerogenes")` will return `"Tindall et al., 2017"` (with a note about the renaming) #' - `mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)` will return `"Hormaeche et al., 1960"` (with a once-per-session warning that the name is outdated) #' #' The short name ([mo_shortname()]) returns the first character of the genus and the full species, such as `"E. coli"`, for species and subspecies. Exceptions are abbreviations of staphylococci (such as *"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as *"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*. As a result, `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. #' #' Determination of human pathogenicity ([mo_pathogenicity()]) is strongly based on Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}). This function returns a [factor] with the levels *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*. #' #' Determination of the Gram stain ([mo_gramstain()]) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. #' #' Determination of yeasts ([mo_is_yeast()]) will be based on the taxonomic kingdom and class. *Budding yeasts* are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. *True yeasts* quite specifically refers to yeasts in the underlying order Saccharomycetales (such as *Saccharomyces cerevisiae*). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`). #' #' Determination of intrinsic resistance ([mo_is_intrinsic_resistant()]) will be based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antibiotics). #' #' Determination of bacterial oxygen tolerance ([mo_oxygen_tolerance()]) will be based on BacDive, see *Source*. The function [mo_is_anaerobic()] only returns `TRUE` if the oxygen tolerance is `"anaerobe"`, indicting an obligate anaerobic species or genus. It always returns `FALSE` for species outside the taxonomic kingdom of Bacteria. #' #' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. [This MycoBank URL](`r TAXONOMY_VERSION$MycoBank$url`) will be used for fungi wherever available , [this LPSN URL](`r TAXONOMY_VERSION$MycoBank$url`) for bacteria wherever available, and [this GBIF link](`r TAXONOMY_VERSION$GBIF$url`) otherwise. #' #' SNOMED codes ([mo_snomed()]) was last updated on `r documentation_date(TAXONOMY_VERSION$SNOMED$accessed_date)`. See *Source* and the [microorganisms] data set for more info. #' #' Old taxonomic names (so-called 'synonyms') can be retrieved with [mo_synonyms()] (which will have the scientific reference as [name][base::names()]), the current taxonomic name can be retrieved with [mo_current()]. Both functions return full names. #' #' All output [will be translated][translate] where possible. #' @section Matching Score for Microorganisms: #' This function uses [as.mo()] internally, which uses an advanced algorithm to translate arbitrary user input to valid taxonomy using a so-called matching score. You can read about this public algorithm on the [MO matching score page][mo_matching_score()]. #' @inheritSection as.mo Source #' @rdname mo_property #' @name mo_property #' @return #' - An [integer] in case of [mo_year()] #' - An [ordered factor][factor] in case of [mo_pathogenicity()] #' - A [list] in case of [mo_taxonomy()], [mo_synonyms()], [mo_snomed()], and [mo_info()] #' - A [logical] in case of [mo_is_anaerobic()], [mo_is_gram_negative()], [mo_is_gram_positive()], [mo_is_intrinsic_resistant()], and [mo_is_yeast()] #' - A named [character] in case of [mo_synonyms()] and [mo_url()] #' - A [character] in all other cases #' @export #' @seealso Data set [microorganisms] #' @inheritSection AMR Reference Data Publicly Available #' @examples #' # taxonomic tree ----------------------------------------------------------- #' #' mo_kingdom("Klebsiella pneumoniae") #' mo_phylum("Klebsiella pneumoniae") #' mo_class("Klebsiella pneumoniae") #' mo_order("Klebsiella pneumoniae") #' mo_family("Klebsiella pneumoniae") #' mo_genus("Klebsiella pneumoniae") #' mo_species("Klebsiella pneumoniae") #' mo_subspecies("Klebsiella pneumoniae") #' #' #' # full names and short names ----------------------------------------------- #' #' mo_name("Klebsiella pneumoniae") #' mo_fullname("Klebsiella pneumoniae") #' mo_shortname("Klebsiella pneumoniae") #' #' #' # other properties --------------------------------------------------------- #' #' mo_pathogenicity("Klebsiella pneumoniae") #' mo_gramstain("Klebsiella pneumoniae") #' mo_snomed("Klebsiella pneumoniae") #' mo_type("Klebsiella pneumoniae") #' mo_rank("Klebsiella pneumoniae") #' mo_url("Klebsiella pneumoniae") #' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella")) #' #' mo_group_members(c("Streptococcus group A", #' "Streptococcus group C", #' "Streptococcus group G", #' "Streptococcus group L")) #' #' #' # scientific reference ----------------------------------------------------- #' #' mo_ref("Klebsiella aerogenes") #' mo_authors("Klebsiella aerogenes") #' mo_year("Klebsiella aerogenes") #' mo_synonyms("Klebsiella aerogenes") #' mo_lpsn("Klebsiella aerogenes") #' mo_gbif("Klebsiella aerogenes") #' mo_mycobank("Candida albicans") #' mo_mycobank("Candida krusei") #' mo_mycobank("Candida krusei", keep_synonyms = TRUE) #' #' #' # abbreviations known in the field ----------------------------------------- #' #' mo_genus("MRSA") #' mo_species("MRSA") #' mo_shortname("VISA") #' mo_gramstain("VISA") #' #' mo_genus("EHEC") #' mo_species("EIEC") #' mo_name("UPEC") #' #' #' # known subspecies --------------------------------------------------------- #' #' mo_fullname("K. pneu rh") #' mo_shortname("K. pneu rh") #' #' \donttest{ #' # Becker classification, see ?as.mo ---------------------------------------- #' #' mo_fullname("Staph epidermidis") #' mo_fullname("Staph epidermidis", Becker = TRUE) #' mo_shortname("Staph epidermidis") #' mo_shortname("Staph epidermidis", Becker = TRUE) #' #' #' # Lancefield classification, see ?as.mo ------------------------------------ #' #' mo_fullname("Strep agalactiae") #' mo_fullname("Strep agalactiae", Lancefield = TRUE) #' mo_shortname("Strep agalactiae") #' mo_shortname("Strep agalactiae", Lancefield = TRUE) #' #' #' # language support -------------------------------------------------------- #' #' mo_gramstain("Klebsiella pneumoniae", language = "de") # German #' mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch #' mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish #' mo_gramstain("Klebsiella pneumoniae", language = "el") # Greek #' mo_gramstain("Klebsiella pneumoniae", language = "uk") # Ukrainian #' #' # mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated #' mo_kingdom("Klebsiella pneumoniae") #' mo_type("Klebsiella pneumoniae") #' mo_kingdom("Klebsiella pneumoniae", language = "zh") # Chinese, no effect #' mo_type("Klebsiella pneumoniae", language = "zh") # Chinese, translated #' #' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "de") #' mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk") #' #' #' # other -------------------------------------------------------------------- #' #' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs #' if (require("dplyr")) { #' example_isolates %>% #' filter(mo_is_gram_positive()) %>% #' count(mo_genus(), sort = TRUE) #' } #' if (require("dplyr")) { #' example_isolates %>% #' filter(mo_is_intrinsic_resistant(ab = "vanco")) %>% #' count(mo_genus(), sort = TRUE) #' } #' #' # get a list with the complete taxonomy (from kingdom to subspecies) #' mo_taxonomy("Klebsiella pneumoniae") #' #' # get a list with the taxonomy, the authors, Gram-stain, #' # SNOMED codes, and URL to the online database #' mo_info("Klebsiella pneumoniae") #' } mo_name <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_name") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "fullname", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = FALSE, only_affect_mo_names = TRUE ) } #' @rdname mo_property #' @export mo_fullname <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_fullname") } mo_name(x = x, language = language, keep_synonyms = keep_synonyms, ...) } #' @rdname mo_property #' @export mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_shortname") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() 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, keep_synonyms = keep_synonyms) shortnames <- paste0(substr(genera, 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL, keep_synonyms = keep_synonyms))) # 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: Group A Streptococcus -> GAS shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"] <- paste0("G", gsub("S. Group ([ABCDFGHK])", "\\1", shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"], perl = TRUE), "S") # unknown species etc. shortnames[shortnames %like% "unknown"] <- paste0("(", trimws2(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")") shortnames[mo_rank(x.mo) %in% c("kingdom", "phylum", "class", "order", "family")] <- mo_name(x.mo[mo_rank(x.mo) %in% c("kingdom", "phylum", "class", "order", "family")], language = NULL, keep_synonyms = keep_synonyms) shortnames[is.na(x.mo)] <- NA_character_ load_mo_uncertainties(metadata) translate_into_language(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE) } #' @rdname mo_property #' @export mo_subspecies <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_subspecies") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "subspecies", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_species <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_species") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "species", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_genus <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_genus") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "genus", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_family <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_family") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "family", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_order <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_order") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "order", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_class <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_class") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "class", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_phylum <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_phylum") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "phylum", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_kingdom <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_kingdom") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "kingdom", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_domain <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_domain") } mo_kingdom(x = x, language = language, keep_synonyms = keep_synonyms, ...) } #' @rdname mo_property #' @export mo_type <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_type") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) out <- mo_kingdom(x.mo, language = NULL, keep_synonyms = keep_synonyms) out[which(mo_is_yeast(x.mo, keep_synonyms = keep_synonyms))] <- "Yeasts" translate_into_language(out, language = language, only_unknown = FALSE) } #' @rdname mo_property #' @export mo_status <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_status") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = "status", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } #' @rdname mo_property #' @export mo_pathogenicity <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_pathogenicity") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) add_MO_lookup_to_AMR_env() x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() prev <- AMR_env$MO_lookup$prevalence[match(x.mo, AMR_env$MO_lookup$mo)] kngd <- AMR_env$MO_lookup$kingdom[match(x.mo, AMR_env$MO_lookup$mo)] rank <- AMR_env$MO_lookup$rank[match(x.mo, AMR_env$MO_lookup$mo)] out <- factor(case_when_AMR(prev == 1 & kngd == "Bacteria" & rank != "genus" ~ "Pathogenic", (prev < 2 & kngd == "Fungi") ~ "Potentially pathogenic", prev == 2 & kngd == "Bacteria" ~ "Non-pathogenic", kngd == "Bacteria" ~ "Potentially pathogenic", TRUE ~ "Unknown"), levels = c("Pathogenic", "Potentially pathogenic", "Non-pathogenic", "Unknown"), ordered = TRUE ) load_mo_uncertainties(metadata) out } #' @rdname mo_property #' @export mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_gramstain") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() x <- rep(NA_character_, length(x)) # make all bacteria Gram negative x[mo_kingdom(x.mo, language = NULL, keep_synonyms = keep_synonyms) == "Bacteria"] <- "Gram-negative" # overwrite these 4 phyla with Gram-positives # Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 (Cavalier-Smith, 2002) x[(mo_phylum(x.mo, language = NULL, keep_synonyms = keep_synonyms) %in% c( # no longer in use, does not hurt to keep here: "Actinobacteria", "Chloroflexi", "Firmicutes", "Tenericutes", "Actinomycetota", # since 2021, old name was Actinobacteria "Chloroflexota", # since 2021, old name was Chloroflexi "Bacillota", # since 2021, old name was Firmicutes "Mycoplasmatota" # since 2021, old name was Tenericutes ) & # but class Negativicutes (of phylum Bacillota) are Gram-negative! mo_class(x.mo, language = NULL, keep_synonyms = keep_synonyms) != "Negativicutes") # and of course our own ID for Gram-positives | x.mo %in% c("B_GRAMP", "B_ANAER-POS")] <- "Gram-positive" load_mo_uncertainties(metadata) translate_into_language(x, language = language, only_unknown = FALSE) } #' @rdname mo_property #' @export mo_is_gram_negative <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_is_gram_negative") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() grams <- mo_gramstain(x.mo, language = NULL, keep_synonyms = keep_synonyms) load_mo_uncertainties(metadata) out <- grams == "Gram-negative" & !is.na(grams) out[x.mo %in% c(NA_character_, "UNKNOWN")] <- NA out } #' @rdname mo_property #' @export mo_is_gram_positive <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_is_gram_positive") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() grams <- mo_gramstain(x.mo, language = NULL, keep_synonyms = keep_synonyms) load_mo_uncertainties(metadata) out <- grams == "Gram-positive" & !is.na(grams) out[x.mo %in% c(NA_character_, "UNKNOWN")] <- NA out } #' @rdname mo_property #' @export mo_is_yeast <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_is_yeast") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() x.kingdom <- mo_kingdom(x.mo, language = NULL, keep_synonyms = keep_synonyms) x.class <- mo_class(x.mo, language = NULL, keep_synonyms = keep_synonyms) load_mo_uncertainties(metadata) out <- x.mo == "F_YEAST" | (x.kingdom == "Fungi" & x.class %in% c("Saccharomycetes", "Pichiomycetes")) out[x.mo %in% c(NA_character_, "UNKNOWN")] <- NA out } #' @rdname mo_property #' @export mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_is_intrinsic_resistant") } meet_criteria(x, allow_NA = TRUE) meet_criteria(ab, allow_NA = FALSE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) ab <- as.ab(ab, language = NULL, flag_multiple_results = FALSE, info = FALSE) if (length(x) == 1 & length(ab) > 1) { x <- rep(x, length(ab)) } else if (length(ab) == 1 & length(x) > 1) { ab <- rep(ab, length(x)) } if (length(x) != length(ab)) { stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.") } # show used version number once per session (AMR_env will reload every session) if (message_not_thrown_before("mo_is_intrinsic_resistant", "version.mo", entire_session = TRUE)) { message_( "Determining intrinsic resistance based on ", format_eucast_version_nr(3.3, markdown = FALSE), ". ", font_red("This note will be shown once per session.") ) } # runs against internal vector: intrinsic_resistant (see zzz.R) add_intrinsic_resistance_to_AMR_env() paste(x, ab) %in% AMR_env$intrinsic_resistant } #' @rdname mo_property #' @export mo_oxygen_tolerance <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_oxygen_tolerance") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) mo_validate(x = x, property = "oxygen_tolerance", language = language, keep_synonyms = keep_synonyms, ...) } #' @rdname mo_property #' @export mo_is_anaerobic <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_is_anaerobic") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() oxygen <- mo_oxygen_tolerance(x.mo, language = NULL, keep_synonyms = keep_synonyms) load_mo_uncertainties(metadata) out <- oxygen == "anaerobe" & !is.na(oxygen) out[x.mo %in% c(NA_character_, "UNKNOWN")] <- NA out } #' @rdname mo_property #' @export mo_snomed <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_snomed") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) mo_validate(x = x, property = "snomed", language = language, keep_synonyms = keep_synonyms, ...) } #' @rdname mo_property #' @export mo_ref <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_ref") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) mo_validate(x = x, property = "ref", language = language, keep_synonyms = keep_synonyms, ...) } #' @rdname mo_property #' @export mo_authors <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_authors") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x <- mo_validate(x = x, property = "ref", language = language, keep_synonyms = keep_synonyms, ...) # 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)], perl = TRUE) suppressWarnings(x) } #' @rdname mo_property #' @export mo_year <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_year") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x <- mo_validate(x = x, property = "ref", language = language, keep_synonyms = keep_synonyms, ...) # get last 4 digits x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)], perl = TRUE) suppressWarnings(as.integer(x)) } #' @rdname mo_property #' @export mo_lpsn <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_lpsn") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) mo_validate(x = x, property = "lpsn", language = language, keep_synonyms = keep_synonyms, ...) } #' @rdname mo_property #' @export mo_mycobank <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_mycobank") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) mo_validate(x = x, property = "mycobank", language = language, keep_synonyms = keep_synonyms, ...) } #' @rdname mo_property #' @export mo_gbif <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_gbif") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) mo_validate(x = x, property = "gbif", language = language, keep_synonyms = keep_synonyms, ...) } #' @rdname mo_property #' @export mo_rank <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_rank") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) mo_validate(x = x, property = "rank", language = language, keep_synonyms = keep_synonyms, ...) } #' @rdname mo_property #' @export mo_taxonomy <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_taxonomy") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() out <- list( kingdom = mo_kingdom(x, language = language, keep_synonyms = keep_synonyms), phylum = mo_phylum(x, language = language, keep_synonyms = keep_synonyms), class = mo_class(x, language = language, keep_synonyms = keep_synonyms), order = mo_order(x, language = language, keep_synonyms = keep_synonyms), family = mo_family(x, language = language, keep_synonyms = keep_synonyms), genus = mo_genus(x, language = language, keep_synonyms = keep_synonyms), species = mo_species(x, language = language, keep_synonyms = keep_synonyms), subspecies = mo_subspecies(x, language = language, keep_synonyms = keep_synonyms) ) load_mo_uncertainties(metadata) out } #' @rdname mo_property #' @export mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_synonyms") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) add_MO_lookup_to_AMR_env() x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() syns <- lapply(x.mo, function(y) { gbif <- AMR_env$MO_lookup$gbif[match(y, AMR_env$MO_lookup$mo)] lpsn <- AMR_env$MO_lookup$lpsn[match(y, AMR_env$MO_lookup$mo)] fullname <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$lpsn_renamed_to == lpsn | AMR_env$MO_lookup$gbif_renamed_to == gbif), "fullname", drop = TRUE] if (length(fullname) == 0) { NULL } else { ref <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$lpsn_renamed_to == lpsn | AMR_env$MO_lookup$gbif_renamed_to == gbif), "ref", drop = TRUE] names(fullname) <- ref fullname } }) if (length(syns) == 1) { syns <- unlist(syns) } load_mo_uncertainties(metadata) syns } #' @rdname mo_property #' @export mo_current <- function(x, language = get_AMR_locale(), ...) { meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) x.mo <- suppressWarnings(as.mo(x, keep_synonyms = TRUE, info = FALSE, ...)) out <- synonym_mo_to_accepted_mo(x.mo, fill_in_accepted = TRUE) mo_name(out, language = language) } #' @rdname mo_property #' @export mo_group_members <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_synonyms") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) add_MO_lookup_to_AMR_env() x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() members <- lapply(x.mo, function(y) { AMR::microorganisms.groups$mo_name[which(AMR::microorganisms.groups$mo_group == y)] }) names(members) <- mo_name(x, keep_synonyms = TRUE, language = language) if (length(members) == 1) { members <- unname(unlist(members)) } load_mo_uncertainties(metadata) members } #' @rdname mo_property #' @export mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_info") } meet_criteria(x, allow_NA = TRUE) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) metadata <- get_mo_uncertainties() info <- lapply(x, function(y) { c( list(mo = as.character(y), rank = mo_rank(y, language = language, keep_synonyms = keep_synonyms)), mo_taxonomy(y, language = language, keep_synonyms = keep_synonyms), list( status = mo_status(y, language = language, keep_synonyms = keep_synonyms), synonyms = mo_synonyms(y, keep_synonyms = keep_synonyms), gramstain = mo_gramstain(y, language = language, keep_synonyms = keep_synonyms), oxygen_tolerance = mo_oxygen_tolerance(y, language = language, keep_synonyms = keep_synonyms), url = unname(mo_url(y, open = FALSE, keep_synonyms = keep_synonyms)), ref = mo_ref(y, keep_synonyms = keep_synonyms), snomed = unlist(mo_snomed(y, keep_synonyms = keep_synonyms)), lpsn = mo_lpsn(y, language = language, keep_synonyms = keep_synonyms), mycobank = mo_mycobank(y, language = language, keep_synonyms = keep_synonyms), gbif = mo_gbif(y, language = language, keep_synonyms = keep_synonyms), group_members = mo_group_members(y, language = language, keep_synonyms = keep_synonyms) ) ) }) if (length(info) > 1) { names(info) <- mo_name(x) result <- info } else { result <- info[[1L]] } load_mo_uncertainties(metadata) result } #' @rdname mo_property #' @export mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_url") } meet_criteria(x, allow_NA = TRUE) meet_criteria(open, allow_class = "logical", has_length = 1) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) add_MO_lookup_to_AMR_env() x.mo <- as.mo(x = x, language = language, keep_synonyms = keep_synonyms, ... = ...) metadata <- get_mo_uncertainties() x.rank <- AMR_env$MO_lookup$rank[match(x.mo, AMR_env$MO_lookup$mo)] x.name <- AMR_env$MO_lookup$fullname[match(x.mo, AMR_env$MO_lookup$mo)] x.lpsn <- AMR_env$MO_lookup$lpsn[match(x.mo, AMR_env$MO_lookup$mo)] x.mycobank <- AMR_env$MO_lookup$mycobank[match(x.mo, AMR_env$MO_lookup$mo)] x.gbif <- AMR_env$MO_lookup$gbif[match(x.mo, AMR_env$MO_lookup$mo)] u <- character(length(x)) u[!is.na(x.gbif)] <- paste0(TAXONOMY_VERSION$GBIF$url, "/species/", x.gbif[!is.na(x.gbif)]) # overwrite with LPSN: u[!is.na(x.lpsn)] <- paste0(TAXONOMY_VERSION$LPSN$url, "/", x.rank[!is.na(x.lpsn)], "/", gsub(" ", "-", tolower(x.name[!is.na(x.lpsn)]), fixed = TRUE)) # overwrite with MycoBank (bacteria from LPSN will not be overwritten since MycoBank has no bacteria) u[!is.na(x.mycobank)] <- paste0(TAXONOMY_VERSION$MycoBank$url, "/mb/", gsub(" ", "%20", tolower(x.mycobank[!is.na(x.mycobank)]), fixed = TRUE)) names(u) <- x.name if (isTRUE(open)) { if (length(u) > 1) { warning_("in `mo_url()`: only the first URL will be opened, as R's built-in function `browseURL()` only suports one string.") } utils::browseURL(u[1L]) } load_mo_uncertainties(metadata) u } #' @rdname mo_property #' @export mo_property <- function(x, property = "fullname", language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_property") } meet_criteria(x, allow_NA = TRUE) meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR::microorganisms)) language <- validate_language(language) meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) translate_into_language(mo_validate(x = x, property = property, language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ...) { add_MO_lookup_to_AMR_env() # try to catch an error when inputting an invalid argument # so the 'call.' can be set to FALSE tryCatch(x[1L] %in% unlist(AMR_env$MO_lookup[1, property, drop = TRUE]), error = function(e) stop(e$message, call. = FALSE) ) dots <- list(...) Becker <- dots$Becker if (is.null(Becker) || property %in% c("kingdom", "phylum", "class", "order", "family", "genus")) { Becker <- FALSE } Lancefield <- dots$Lancefield if (is.null(Lancefield) || property %in% c("kingdom", "phylum", "class", "order", "family", "genus")) { Lancefield <- FALSE } has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") || Lancefield %in% c(TRUE, "all") if (isFALSE(has_Becker_or_Lancefield) && isTRUE(keep_synonyms) && all(x %in% c(AMR_env$MO_lookup$mo, NA))) { # fastest way to get properties if (property == "snomed") { x <- lapply(x, function(y) unlist(AMR_env$MO_lookup$snomed[match(y, AMR_env$MO_lookup$mo)])) } else { x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)] } } else { # get microorganisms data set, but remove synonyms if keep_synonyms is FALSE mo_data_check <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$status %in% if (isTRUE(keep_synonyms)) c("synonym", "accepted") else "accepted"), , drop = FALSE] if (all(x %in% c(mo_data_check$mo, NA)) && !has_Becker_or_Lancefield) { # do nothing, just don't run the other if-else's } else if (all(x %in% c(unlist(mo_data_check[[property]]), NA)) && !has_Becker_or_Lancefield) { # no need to do anything, just return it return(x) } else { # we need to get MO codes now x <- replace_old_mo_codes(x, property = property) x <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) } # get property reeaaally fast using match() if (property == "snomed") { x <- lapply(x, function(y) unlist(AMR_env$MO_lookup$snomed[match(y, AMR_env$MO_lookup$mo)])) } else { x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)] } } if (property == "mo") { return(set_clean_class(x, new_class = c("mo", "character"))) } else if (property == "snomed") { return(x) } else if (property == "prevalence") { return(as.double(x)) } else { # everything else as character return(as.character(x)) } } find_mo_col <- function(fn) { # this function tries to find an mo column in the data the function was called in, # which is useful when functions are used within dplyr verbs df <- get_current_data(arg_name = "x", call = -3) # will return an error if not found mo <- NULL try( { mo <- suppressMessages(search_type_in_df(df, "mo")) }, silent = TRUE ) if (!is.null(df) && !is.null(mo) && is.data.frame(df)) { if (message_not_thrown_before(fn = fn)) { message_("Using column '", font_bold(mo), "' as input for `", fn, "()`") } return(df[, mo, drop = TRUE]) } else { stop_("argument `x` is missing and no column with info about microorganisms could be found.", call = -2) } }