mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 19:26:13 +01:00
446 lines
18 KiB
R
Executable File
446 lines
18 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
|
# #
|
|
# 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 more info: https://msberends.github.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 [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 (vector of) text 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 also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
|
|
#' @param ... other parameters passed on to [as.mo()]
|
|
#' @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`.
|
|
#'
|
|
#' 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 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 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(), ...) {
|
|
translate_AMR(mo_validate(x = x, property = "fullname", ...), language = language, only_unknown = FALSE)
|
|
}
|
|
|
|
#' @rdname mo_property
|
|
#' @export
|
|
mo_fullname <- mo_name
|
|
|
|
#' @rdname mo_property
|
|
#' @export
|
|
mo_shortname <- function(x, language = get_locale(), ...) {
|
|
x.mo <- 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_domain <- mo_kingdom
|
|
|
|
#' @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 <- 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_snomed <- function(x, ...) {
|
|
mo_validate(x = x, property = "snomed", ...)
|
|
}
|
|
|
|
#' @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})$", "\\1", x[!is.na(x)])
|
|
suppressWarnings(as.integer(x))
|
|
}
|
|
|
|
#' @rdname mo_property
|
|
#' @export
|
|
mo_rank <- function(x, ...) {
|
|
mo_validate(x = x, property = "rank", ...)
|
|
}
|
|
|
|
#' @rdname mo_property
|
|
#' @export
|
|
mo_taxonomy <- function(x, language = get_locale(), ...) {
|
|
x <- as.mo(x, ...)
|
|
metadata <- get_mo_failures_uncertainties_renamed()
|
|
|
|
result <- base::list(kingdom = mo_kingdom(x, language = language),
|
|
phylum = mo_phylum(x, language = language),
|
|
class = mo_class(x, language = language),
|
|
order = mo_order(x, language = language),
|
|
family = mo_family(x, language = language),
|
|
genus = mo_genus(x, language = language),
|
|
species = mo_species(x, language = language),
|
|
subspecies = mo_subspecies(x, language = language))
|
|
|
|
load_mo_failures_uncertainties_renamed(metadata)
|
|
result
|
|
}
|
|
|
|
#' @rdname mo_property
|
|
#' @export
|
|
mo_synonyms <- function(x, ...) {
|
|
x <- as.mo(x, ...)
|
|
metadata <- get_mo_failures_uncertainties_renamed()
|
|
|
|
IDs <- mo_name(x = x, language = NULL)
|
|
syns <- lapply(IDs, function(newname) {
|
|
res <- sort(microorganisms.old[which(microorganisms.old$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(), ...) {
|
|
x <- 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),
|
|
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, ...) {
|
|
mo <- as.mo(x = x, ... = ...)
|
|
mo_names <- mo_name(mo)
|
|
metadata <- get_mo_failures_uncertainties_renamed()
|
|
|
|
df <- data.frame(mo, stringsAsFactors = FALSE) %>%
|
|
left_join(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$url
|
|
names(u) <- mo_names
|
|
|
|
if (open == TRUE) {
|
|
if (length(u) > 1) {
|
|
warning("only the first URL will be opened, as `browseURL()` only suports one string.")
|
|
}
|
|
utils::browseURL(u[1L])
|
|
}
|
|
|
|
load_mo_failures_uncertainties_renamed(metadata)
|
|
u
|
|
}
|
|
|
|
|
|
#' @rdname mo_property
|
|
#' @export
|
|
mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
|
|
stop_ifnot(length(property) == 1L, "'property' must be of length 1")
|
|
stop_ifnot(property %in% colnames(microorganisms),
|
|
"invalid property: '", property, "' - use a column name of the `microorganisms` data set")
|
|
|
|
translate_AMR(mo_validate(x = x, property = property, ...), language = language, only_unknown = TRUE)
|
|
}
|
|
|
|
mo_validate <- function(x, property, ...) {
|
|
|
|
check_dataset_integrity()
|
|
|
|
dots <- list(...)
|
|
Becker <- dots$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, ...)
|
|
} 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, ...)
|
|
}
|
|
|
|
if (property == "mo") {
|
|
return(to_class_mo(x))
|
|
} else if (property == "snomed") {
|
|
return(as.double(eval(parse(text = x))))
|
|
} else {
|
|
return(x)
|
|
}
|
|
}
|