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AMR/R/mo_property.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This R package is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License version 2.0 for more details. #
# ==================================================================== #
#' Property of a microorganism
#'
#' Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
#' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
#' @param property one of the column names of one 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}}
#' @details All functions will return the most recently known taxonomic property according to ITIS, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
#' \itemize{
#' \item{\code{mo_fullname("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)}
#' }
#' @inheritSection get_locale Supported languages
#' @inheritSection as.mo ITIS
#' @inheritSection as.mo Source
#' @rdname mo_property
#' @name mo_property
#' @return \itemize{
#' \item{An \code{integer} in case of \code{mo_TSN} and \code{mo_year}}
#' \item{A \code{list} in case of \code{mo_taxonomy}}
#' \item{A \code{character} in all other cases}
#' }
#' @export
#' @seealso \code{\link{microorganisms}}
#' @examples
#' # All properties of Escherichia coli
#' ## taxonomic properties
#' mo_kingdom("E. coli") # "Bacteria"
#' mo_subkingdom("E. coli") # "Negibacteria"
#' 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") # NA
#' mo_TSN("E. coli") # 285 (Taxonomic Serial Number)
#'
#' ## colloquial properties
#' mo_fullname("E. coli") # "Escherichia coli"
#' mo_shortname("E. coli") # "E. coli"
#'
#' ## other properties
#' mo_gramstain("E. coli") # "Gram negative"
#' mo_type("E. coli") # "Bacteria" (equal to kingdom)
#'
#' ## scientific reference
#' mo_ref("E. coli") # "Castellani and Chalmers, 1919"
#' mo_authors("E. coli") # "Castellani and Chalmers"
#' mo_year("E. coli") # 1919
#'
#'
#' # Abbreviations known in the field
#' mo_genus("MRSA") # "Staphylococcus"
#' mo_species("MRSA") # "aureus"
#' mo_shortname("MRSA") # "S. aureus"
#' mo_gramstain("MRSA") # "Gram positive"
#'
#' mo_genus("VISA") # "Staphylococcus"
#' mo_species("VISA") # "aureus"
#'
#'
#' # Known subspecies
#' mo_genus("doylei") # "Campylobacter"
#' mo_species("doylei") # "jejuni"
#' mo_fullname("doylei") # "Campylobacter jejuni doylei"
#'
#' mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
#' mo_shortname("K. pneu rh") # "K. pneumoniae"
#'
#'
#' # Becker classification, see ?as.mo
#' mo_fullname("S. epi") # "Staphylococcus epidermidis"
#' mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
#' mo_shortname("S. epi") # "S. epidermidis"
#' mo_shortname("S. epi", Becker = TRUE) # "CoNS"
#'
#' # Lancefield classification, see ?as.mo
#' mo_fullname("S. pyo") # "Streptococcus pyogenes"
#' mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
#' mo_shortname("S. pyo") # "S. pyogenes"
#' mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" ('Group A streptococci')
#'
#'
#' # Language support for German, Dutch, Spanish, Portuguese, Italian and French
#' mo_gramstain("E. coli", language = "de") # "Gramnegativ"
#' mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
#' mo_gramstain("E. coli", language = "es") # "Gram negativo"
#'
#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official
#' mo_kingdom("E. coli") # "Bacteria" on a German system
#' mo_type("E. coli") # "Bakterien" on a German system
#' mo_type("E. coli") # "Bacteria" on an English system
#'
#' mo_fullname("S. pyogenes",
#' Lancefield = TRUE,
#' language = "de") # "Streptococcus Gruppe A"
#' mo_fullname("S. pyogenes",
#' Lancefield = TRUE,
#' language = "nl") # "Streptococcus groep A"
#'
#'
#' # Get a list with the complete taxonomy (subkingdom to subspecies)
#' mo_taxonomy("E. coli")
mo_fullname <- function(x, language = get_locale(), ...) {
x <- mo_validate(x = x, property = "fullname", ...)
mo_translate(x, language = language)
}
#' @rdname mo_property
#' @importFrom dplyr %>% left_join mutate pull
#' @export
mo_shortname <- function(x, language = get_locale(), ...) {
dots <- list(...)
Becker <- dots$Becker
if (is.null(Becker)) {
Becker <- FALSE
}
Lancefield <- dots$Lancefield
if (is.null(Lancefield)) {
Lancefield <- FALSE
}
if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df)
res2 <- suppressWarnings(AMR::as.mo(res1, ...))
res2_fullname <- mo_fullname(res2, language = language)
res2_fullname[res2_fullname %like% " \\(CoNS\\)"] <- "CoNS"
res2_fullname[res2_fullname %like% " \\(CoPS\\)"] <- "CoPS"
res2_fullname[res2_fullname %like% " \\(KNS\\)"] <- "KNS"
res2_fullname[res2_fullname %like% " \\(KPS\\)"] <- "KPS"
res2_fullname[res2_fullname %like% " \\(CNS\\)"] <- "CNS"
res2_fullname[res2_fullname %like% " \\(CPS\\)"] <- "CPS"
res2_fullname <- gsub("Streptococcus (group|Gruppe|gruppe|groep|grupo|gruppo|groupe) (.)",
"G\\2S",
res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(res1)]
res2_fullname[res2_fullname == mo_fullname(res1)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
". ",
suppressWarnings(mo_species(res2_fullname_vector)))
if (sum(res1 == res2, na.rm = TRUE) > 0) {
res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
". ",
suppressWarnings(mo_species(res1[res1 == res2])))
}
res1[res1 != res2] <- res2_fullname
result <- as.character(res1)
} else {
x <- AMR::as.mo(x, ...)
suppressWarnings(
result <- data.frame(mo = x) %>%
left_join(AMR::microorganisms, by = "mo") %>%
mutate(shortname = ifelse(!is.na(genus) & !is.na(species), paste0(substr(genus, 1, 1), ". ", species), NA_character_)) %>%
pull(shortname)
)
}
mo_translate(result, language = language)
}
#' @rdname mo_property
#' @export
mo_subspecies <- function(x, language = get_locale(), ...) {
mo_translate(mo_validate(x = x, property = "subspecies", ...), language = language)
}
#' @rdname mo_property
#' @export
mo_species <- function(x, language = get_locale(), ...) {
mo_translate(mo_validate(x = x, property = "species", ...), language = language)
}
#' @rdname mo_property
#' @export
mo_genus <- function(x, language = get_locale(), ...) {
mo_translate(mo_validate(x = x, property = "genus", ...), language = language)
}
#' @rdname mo_property
#' @export
mo_family <- function(x, ...) {
mo_validate(x = x, property = "family", ...)
}
#' @rdname mo_property
#' @export
mo_order <- function(x, ...) {
mo_validate(x = x, property = "order", ...)
}
#' @rdname mo_property
#' @export
mo_class <- function(x, ...) {
mo_validate(x = x, property = "class", ...)
}
#' @rdname mo_property
#' @export
mo_phylum <- function(x, ...) {
mo_validate(x = x, property = "phylum", ...)
}
#' @rdname mo_property
#' @export
mo_subkingdom <- function(x, ...) {
mo_validate(x = x, property = "subkingdom", ...)
}
#' @rdname mo_property
#' @export
mo_kingdom <- function(x, ...) {
mo_validate(x = x, property = "kingdom", ...)
}
#' @rdname mo_property
#' @export
mo_type <- function(x, language = get_locale(), ...) {
mo_translate(mo_validate(x = x, property = "kingdom", ...), language = language)
}
#' @rdname mo_property
#' @export
mo_gramstain <- function(x, language = get_locale(), ...) {
mo_translate(mo_validate(x = x, property = "gramstain", ...), language = language)
}
#' @rdname mo_property
#' @export
mo_TSN <- function(x, ...) {
mo_validate(x = x, property = "tsn", ...)
}
#' @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)])
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)])
as.integer(x)
}
#' @rdname mo_property
#' @export
mo_taxonomy <- function(x, ...) {
x <- AMR::as.mo(x, ...)
base::list(kingdom = mo_kingdom(x),
subkingdom = mo_subkingdom(x),
phylum = mo_phylum(x),
class = mo_class(x),
order = mo_order(x),
family = mo_family(x),
genus = mo_genus(x),
species = mo_species(x),
subspecies = mo_subspecies(x))
}
#' @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")
}
mo_translate(mo_validate(x = x, property = property, ...), language = language)
}
#' @importFrom dplyr %>% case_when
mo_translate <- function(x, language) {
if (is.null(language)) {
return(x)
}
if (language %in% c("en", "")) {
return(x)
}
supported <- c("en", "de", "nl", "es", "pt", "it", "fr")
if (!language %in% supported) {
stop("Unsupported language: '", language, "' - use one of: ", paste0("'", sort(supported), "'", collapse = ", "), call. = FALSE)
}
x_tobetranslated <- grepl(x = x,
pattern = "(Coagulase Negative Staphylococcus|Coagulase Positive Staphylococcus|Beta-haemolytic Streptococcus|unknown Gram negatives|unknown Gram positives|CoNS|CoPS|no MO|Gram negative|Gram positive|Bacteria|Fungi|Protozoa|biogroup|biotype|vegetative|group|Group)")
if (sum(x_tobetranslated, na.rm = TRUE) == 0) {
return(x)
}
# only translate the ones that need translation
x[x_tobetranslated] <- case_when(
# German
language == "de" ~ x[x_tobetranslated] %>%
gsub("Coagulase Negative Staphylococcus","Koagulase-negative Staphylococcus", ., fixed = TRUE) %>%
gsub("Coagulase Positive Staphylococcus","Koagulase-positive Staphylococcus", ., fixed = TRUE) %>%
gsub("Beta-haemolytic Streptococcus", "Beta-h\u00e4molytischer Streptococcus", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "unbekannte Gramnegativen", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "unbekannte Grampositiven", ., fixed = TRUE) %>%
gsub("(CoNS)", "(KNS)", ., fixed = TRUE) %>%
gsub("(CoPS)", "(KPS)", ., fixed = TRUE) %>%
gsub("(no MO)", "(kein MO)", ., fixed = TRUE) %>%
gsub("Gram negative", "Gramnegativ", ., fixed = TRUE) %>%
gsub("Gram positive", "Grampositiv", ., fixed = TRUE) %>%
gsub("Bacteria", "Bakterien", ., fixed = TRUE) %>%
gsub("Fungi", "Hefen/Pilze", ., fixed = TRUE) %>%
gsub("Protozoa", "Protozoen", ., fixed = TRUE) %>%
gsub("biogroup", "Biogruppe", ., fixed = TRUE) %>%
gsub("biotype", "Biotyp", ., fixed = TRUE) %>%
gsub("vegetative", "vegetativ", ., fixed = TRUE) %>%
gsub("([([ ]*?)group", "\\1Gruppe", .) %>%
gsub("([([ ]*?)Group", "\\1Gruppe", .) %>%
iconv(to = "UTF-8"),
# Dutch
language == "nl" ~ x[x_tobetranslated] %>%
gsub("Coagulase Negative Staphylococcus","Coagulase-negatieve Staphylococcus", ., fixed = TRUE) %>%
gsub("Coagulase Positive Staphylococcus","Coagulase-positieve Staphylococcus", ., fixed = TRUE) %>%
gsub("Beta-haemolytic Streptococcus", "Beta-hemolytische Streptococcus", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "onbekende Gram-negatieven", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "onbekende Gram-positieven", ., fixed = TRUE) %>%
gsub("(no MO)", "(geen MO)", ., fixed = TRUE) %>%
gsub("(CoNS)", "(CNS)", ., fixed = TRUE) %>%
gsub("(CoPS)", "(CPS)", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram-negatief", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram-positief", ., fixed = TRUE) %>%
gsub("Bacteria", "Bacteri\u00ebn", ., fixed = TRUE) %>%
gsub("Fungi", "Schimmels/gisten", ., fixed = TRUE) %>%
gsub("Protozoa", "protozo\u00ebn", ., fixed = TRUE) %>%
gsub("biogroup", "biogroep", ., fixed = TRUE) %>%
# gsub("biotype", "biotype", ., fixed = TRUE) %>%
gsub("vegetative", "vegetatief", ., fixed = TRUE) %>%
gsub("([([ ]*?)group", "\\1groep", .) %>%
gsub("([([ ]*?)Group", "\\1Groep", .) %>%
iconv(to = "UTF-8"),
# Spanish
language == "es" ~ x[x_tobetranslated] %>%
gsub("Coagulase Negative Staphylococcus","Staphylococcus coagulasa negativo", ., fixed = TRUE) %>%
gsub("Coagulase Positive Staphylococcus","Staphylococcus coagulasa positivo", ., fixed = TRUE) %>%
gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "Gram negativos desconocidos", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "Gram positivos desconocidos", ., fixed = TRUE) %>%
gsub("(no MO)", "(sin MO)", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
gsub("Bacteria", "Bacterias", ., fixed = TRUE) %>%
gsub("Fungi", "Hongos", ., fixed = TRUE) %>%
gsub("Protozoa", "Protozoarios", ., fixed = TRUE) %>%
gsub("biogroup", "biogrupo", ., fixed = TRUE) %>%
gsub("biotype", "biotipo", ., fixed = TRUE) %>%
gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
gsub("([([ ]*?)group", "\\1grupo", .) %>%
gsub("([([ ]*?)Group", "\\1Grupo", .) %>%
iconv(to = "UTF-8"),
# Italian
language == "it" ~ x[x_tobetranslated] %>%
gsub("Coagulase Negative Staphylococcus","Staphylococcus negativo coagulasi", ., fixed = TRUE) %>%
gsub("Coagulase Positive Staphylococcus","Staphylococcus positivo coagulasi", ., fixed = TRUE) %>%
gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-emolitico", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "Gram negativi sconosciuti", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "Gram positivi sconosciuti", ., fixed = TRUE) %>%
gsub("(no MO)", "(non MO)", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
gsub("Bacteria", "Batteri", ., fixed = TRUE) %>%
gsub("Fungi", "Fungo", ., fixed = TRUE) %>%
gsub("Protozoa", "Protozoi", ., fixed = TRUE) %>%
gsub("biogroup", "biogruppo", ., fixed = TRUE) %>%
gsub("biotype", "biotipo", ., fixed = TRUE) %>%
gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
gsub("([([ ]*?)group", "\\1gruppo", .) %>%
gsub("([([ ]*?)Group", "\\1Gruppo", .),
# French
language == "fr" ~ x[x_tobetranslated] %>%
gsub("Coagulase Negative Staphylococcus","Staphylococcus \u00e0 coagulase n\u00e9gative", ., fixed = TRUE) %>%
gsub("Coagulase Positive Staphylococcus","Staphylococcus \u00e0 coagulase positif", ., fixed = TRUE) %>%
gsub("Beta-haemolytic Streptococcus", "Streptococcus B\u00eata-h\u00e9molytique", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "Gram n\u00e9gatifs inconnus", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "Gram positifs inconnus", ., fixed = TRUE) %>%
gsub("(no MO)", "(pas MO)", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram n\u00e9gatif", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram positif", ., fixed = TRUE) %>%
gsub("Bacteria", "Bact\u00e9ries", ., fixed = TRUE) %>%
gsub("Fungi", "Champignons", ., fixed = TRUE) %>%
gsub("Protozoa", "Protozoaires", ., fixed = TRUE) %>%
gsub("biogroup", "biogroupe", ., fixed = TRUE) %>%
# gsub("biotype", "biotype", ., fixed = TRUE) %>%
gsub("vegetative", "v\u00e9g\u00e9tatif", ., fixed = TRUE) %>%
gsub("([([ ]*?)group", "\\1groupe", .) %>%
gsub("([([ ]*?)Group", "\\1Groupe", .) %>%
iconv(to = "UTF-8"),
# Portuguese
language == "pt" ~ x[x_tobetranslated] %>%
gsub("Coagulase Negative Staphylococcus","Staphylococcus coagulase negativo", ., fixed = TRUE) %>%
gsub("Coagulase Positive Staphylococcus","Staphylococcus coagulase positivo", ., fixed = TRUE) %>%
gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "Gram negativos desconhecidos", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "Gram positivos desconhecidos", ., fixed = TRUE) %>%
gsub("(no MO)", "(sem MO)", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
gsub("Bacteria", "Bact\u00e9rias", ., fixed = TRUE) %>%
gsub("Fungi", "Fungos", ., fixed = TRUE) %>%
gsub("Protozoa", "Protozo\u00e1rios", ., fixed = TRUE) %>%
gsub("biogroup", "biogrupo", ., fixed = TRUE) %>%
gsub("biotype", "bi\u00f3tipo", ., fixed = TRUE) %>%
gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
gsub("([([ ]*?)group", "\\1grupo", .) %>%
gsub("([([ ]*?)Group", "\\1Grupo", .) %>%
iconv(to = "UTF-8"))
x
}
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()) {
library("AMR")
# These data.tables are available as data sets when the AMR package is loaded:
# microorganismsDT # this one is sorted by kingdom (B<F<P), prevalence, TSN
# microorganisms.prevDT # same as microorganismsDT, but with prevalence != 9999
# microorganisms.unprevDT # same as microorganismsDT, but with prevalence == 9999
# microorganisms.oldDT # old taxonomic names, sorted by name (genus+species), TSN
}
if (!all(x %in% microorganismsDT[[property]])
| Becker %in% c(TRUE, "all")
| Lancefield %in% c(TRUE, "all")) {
exec_as.mo(x, property = property, ...)
} else {
x
}
}
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