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first inclusion of ITIS data
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174
R/mo_property.R
174
R/mo_property.R
@ -22,21 +22,17 @@
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#' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
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#' @param property one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"mo"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}
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#' @inheritParams as.mo
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#' @param language language of the returned text, defaults to the systems language. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).
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#' @source
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#' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
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#'
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#' [2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
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#'
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#' [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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#' @param language language of the returned text, defaults to the systems language but can also be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).
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#' @inheritSection as.mo ITIS
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#' @inheritSection as.mo Source
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#' @rdname mo_property
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#' @name mo_property
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#' @return A logical (in case of \code{mo_aerobic}), a list (in case of \code{mo_taxonomy}), a character otherwise
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#' @export
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#' @importFrom dplyr %>% left_join pull
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#' @seealso \code{\link{microorganisms}}
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#' @examples
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#' # All properties
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#' mo_subkingdom("E. coli") # "Negibacteria"
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#' mo_phylum("E. coli") # "Proteobacteria"
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#' mo_class("E. coli") # "Gammaproteobacteria"
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#' mo_order("E. coli") # "Enterobacteriales"
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@ -46,42 +42,30 @@
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#' mo_subspecies("E. coli") # ""
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#' mo_fullname("E. coli") # "Escherichia coli"
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#' mo_shortname("E. coli") # "E. coli"
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#' mo_gramstain("E. coli") # "Gram negative"
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#' mo_TSN("E. coli") # 285
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#' mo_type("E. coli") # "Bacteria"
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#' mo_gramstain("E. coli") # "Negative rods"
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#' mo_aerobic("E. coli") # TRUE
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#'
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#'
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#' # Abbreviations known in the field
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#' mo_genus("MRSA") # "Staphylococcus"
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#' mo_species("MRSA") # "aureus"
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#' mo_shortname("MRSA") # "S. aureus"
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#' mo_gramstain("MRSA") # "Positive cocci"
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#' mo_gramstain("MRSA") # "Gram positive"
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#'
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#' mo_genus("VISA") # "Staphylococcus"
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#' mo_species("VISA") # "aureus"
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#'
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#'
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#' # Known subspecies
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#' mo_genus("EHEC") # "Escherichia"
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#' mo_species("EHEC") # "coli"
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#' mo_subspecies("EHEC") # "EHEC"
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#' mo_fullname("EHEC") # "Escherichia coli (EHEC)"
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#' mo_shortname("EHEC") # "E. coli"
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#'
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#' mo_genus("doylei") # "Campylobacter"
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#' mo_species("doylei") # "jejuni"
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#' mo_fullname("doylei") # "Campylobacter jejuni (doylei)"
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#' mo_fullname("doylei") # "Campylobacter jejuni doylei"
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#'
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#' mo_fullname("K. pneu rh") # "Klebsiella pneumoniae (rhinoscleromatis)"
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#' mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
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#' mo_shortname("K. pneu rh") # "K. pneumoniae"
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#'
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#'
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#' # Anaerobic bacteria
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#' mo_genus("B. fragilis") # "Bacteroides"
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#' mo_species("B. fragilis") # "fragilis"
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#' mo_aerobic("B. fragilis") # FALSE
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#'
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#'
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#' # Becker classification, see ?as.mo
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#' mo_fullname("S. epi") # "Staphylococcus epidermidis"
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#' mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
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@ -99,10 +83,9 @@
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#' mo_type("E. coli", language = "de") # "Bakterium"
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#' mo_type("E. coli", language = "nl") # "Bacterie"
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#' mo_type("E. coli", language = "es") # "Bakteria"
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#' mo_gramstain("E. coli", language = "de") # "Negative Staebchen"
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#' mo_gramstain("E. coli", language = "nl") # "Negatieve staven"
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#' mo_gramstain("E. coli", language = "es") # "Bacilos negativos"
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#' mo_gramstain("Giardia", language = "pt") # "Parasitas"
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#' mo_gramstain("E. coli", language = "de") # "Gramnegativ"
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#' mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
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#' mo_gramstain("E. coli", language = "es") # "Gram negativo"
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#'
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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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@ -112,7 +95,7 @@
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#' language = "nl") # "Streptococcus groep A"
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#'
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#'
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#' # Complete taxonomy up to Phylum, returns a list
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#' # Complete taxonomy up to Subkingdom, returns a list
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#' mo_taxonomy("E. coli")
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mo_fullname <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
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mo_property(x, "fullname", Becker = Becker, Lancefield = Lancefield, language = language)
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@ -191,12 +174,24 @@ mo_phylum <- function(x) {
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mo_property(x, "phylum")
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}
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#' @rdname mo_property
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#' @export
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mo_subkingdom <- function(x) {
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mo_property(x, "subkingdom")
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}
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#' @rdname mo_property
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#' @export
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mo_type <- function(x, language = NULL) {
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mo_property(x, "type", language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_TSN <- function(x) {
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mo_property(x, "tsn")
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}
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#' @rdname mo_property
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#' @export
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mo_gramstain <- function(x, language = NULL) {
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@ -204,28 +199,32 @@ mo_gramstain <- function(x, language = NULL) {
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}
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#' @rdname mo_property
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#' @export
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mo_aerobic <- function(x) {
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mo_property(x, "aerobic")
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}
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#' @rdname mo_property
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#' @importFrom data.table data.table as.data.table setkey
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#' @export
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mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE, language = NULL) {
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property <- tolower(property[1])
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if (!property %in% colnames(AMR::microorganisms)) {
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stop("invalid property: ", property, " - use a column name of the `microorganisms` data set")
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}
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result1 <- as.mo(x = x, Becker = Becker, Lancefield = Lancefield) # this will give a warning if x cannot be coerced
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result2 <- suppressWarnings(
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data.frame(mo = result1, stringsAsFactors = FALSE) %>%
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left_join(AMR::microorganisms, by = "mo") %>%
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pull(property)
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)
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if (property != "aerobic") {
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if (Becker == TRUE | Lancefield == TRUE | !is.mo(x)) {
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# this will give a warning if x cannot be coerced
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result1 <- AMR::as.mo(x = x, Becker = Becker, Lancefield = Lancefield)
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} else {
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result1 <- x
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}
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A <- data.table(mo = result1, stringsAsFactors = FALSE)
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B <- as.data.table(AMR::microorganisms)
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setkey(B, mo)
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result2 <- B[A, on = 'mo', ..property][[1]]
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if (property == "tsn") {
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result2 <- as.integer(result2)
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} else {
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# will else not retain `logical` class
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result2[x %in% c("", NA) | result2 %in% c("", NA, "(no MO)")] <- ""
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result2 <- mo_translate(result2, language = language)
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if (property %in% c("fullname", "shortname", "genus", "species", "subspecies", "type", "gramstain")) {
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result2 <- mo_translate(result2, language = language)
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}
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}
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result2
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}
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@ -234,7 +233,8 @@ mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = F
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#' @export
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mo_taxonomy <- function(x) {
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x <- as.mo(x)
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base::list(phylum = mo_phylum(x),
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base::list(subkingdom = mo_subkingdom(x),
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phylum = mo_phylum(x),
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class = mo_class(x),
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order = mo_order(x),
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family = mo_family(x),
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@ -266,15 +266,11 @@ mo_translate <- function(x, language) {
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gsub("Coagulase Positive Staphylococcus","Koagulase-positive Staphylococcus", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Beta-h\u00e4molytischer Streptococcus", ., fixed = TRUE) %>%
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gsub("(no MO)", "(kein MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Negative St\u00e4bchen", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Negative Kokken", ., fixed = TRUE) %>%
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gsub("Positive rods", "Positive St\u00e4bchen", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Positive Kokken", ., fixed = TRUE) %>%
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gsub("Parasites", "Parasiten", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Pilze und Hefen", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bakterium", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Pilz/Hefe", ., fixed = TRUE) %>%
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gsub("Parasite", "Parasit", ., fixed = TRUE) %>%
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gsub("Gram negative", "Gramnegativ", ., fixed = TRUE) %>%
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gsub("Gram positive", "Grampositiv", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bakterien", ., fixed = TRUE) %>%
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gsub("Fungi", "Hefen/Pilze", ., fixed = TRUE) %>%
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gsub("Protozoa", "Protozoen", ., fixed = TRUE) %>%
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gsub("biogroup", "Biogruppe", ., fixed = TRUE) %>%
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gsub("biotype", "Biotyp", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativ", ., fixed = TRUE) %>%
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@ -287,15 +283,11 @@ mo_translate <- function(x, language) {
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gsub("Coagulase Positive Staphylococcus","Coagulase-positieve Staphylococcus", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Beta-hemolytische Streptococcus", ., fixed = TRUE) %>%
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gsub("(no MO)", "(geen MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Negatieve staven", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Negatieve kokken", ., fixed = TRUE) %>%
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gsub("Positive rods", "Positieve staven", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Positieve kokken", ., fixed = TRUE) %>%
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gsub("Parasites", "Parasieten", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Schimmels en gisten", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bacterie", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Schimmel/gist", ., fixed = TRUE) %>%
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gsub("Parasite", "Parasiet", ., fixed = TRUE) %>%
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gsub("Gram negative", "Gram-negatief", ., fixed = TRUE) %>%
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gsub("Gram positive", "Gram-positief", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bacteri\u00ebn", ., fixed = TRUE) %>%
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gsub("Fungi", "Schimmels/gisten", ., fixed = TRUE) %>%
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gsub("Protozoa", "protozo\u00ebn", ., fixed = TRUE) %>%
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gsub("biogroup", "biogroep", ., fixed = TRUE) %>%
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# gsub("biotype", "biotype", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetatief", ., fixed = TRUE) %>%
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@ -308,15 +300,11 @@ mo_translate <- function(x, language) {
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gsub("Coagulase Positive Staphylococcus","Staphylococcus coagulasa positivo", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
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gsub("(no MO)", "(sin MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Bacilos negativos", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Cocos negativos", ., fixed = TRUE) %>%
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gsub("Positive rods", "Bacilos positivos", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Cocos positivos", ., fixed = TRUE) %>%
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gsub("Parasites", "Par\u00e1sitos", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Hongos y levaduras", ., fixed = TRUE) %>%
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# gsub("Bacteria", "Bacteria", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Hongo/levadura", ., fixed = TRUE) %>%
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gsub("Parasite", "Par\u00e1sito", ., fixed = TRUE) %>%
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gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
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gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bacterias", ., fixed = TRUE) %>%
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gsub("Fungi", "Hongos", ., fixed = TRUE) %>%
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gsub("Protozoa", "Protozoarios", ., fixed = TRUE) %>%
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gsub("biogroup", "biogrupo", ., fixed = TRUE) %>%
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gsub("biotype", "biotipo", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
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@ -329,15 +317,11 @@ mo_translate <- function(x, language) {
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gsub("Coagulase Positive Staphylococcus","Staphylococcus coagulase positivo", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
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gsub("(no MO)", "(sem MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Bacilos negativos", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Cocos negativos", ., fixed = TRUE) %>%
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gsub("Positive rods", "Bacilos positivos", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Cocos positivos", ., fixed = TRUE) %>%
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gsub("Parasites", "Parasitas", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Cogumelos e leveduras", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bact\u00e9ria", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Cogumelo/levedura", ., fixed = TRUE) %>%
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gsub("Parasite", "Parasita", ., fixed = TRUE) %>%
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gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
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gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bact\u00e9rias", ., fixed = TRUE) %>%
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gsub("Fungi", "Fungos", ., fixed = TRUE) %>%
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gsub("Protozoa", "Protozo\u00e1rios", ., fixed = TRUE) %>%
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gsub("biogroup", "biogrupo", ., fixed = TRUE) %>%
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gsub("biotype", "bi\u00f3tipo", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
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@ -350,15 +334,11 @@ mo_translate <- function(x, language) {
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gsub("Coagulase Positive Staphylococcus","Staphylococcus positivo coagulasi", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-emolitico", ., fixed = TRUE) %>%
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gsub("(no MO)", "(non MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Bastoncini Gram-negativi", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Cocchi Gram-negativi", ., fixed = TRUE) %>%
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gsub("Positive rods", "Bastoncini Gram-positivi", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Cocchi Gram-positivi", ., fixed = TRUE) %>%
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gsub("Parasites", "Parassiti", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Funghi e lieviti", ., fixed = TRUE) %>%
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gsub("Bacteria", "Batterio", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Fungo/lievito", ., fixed = TRUE) %>%
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gsub("Parasite", "Parassita", ., fixed = TRUE) %>%
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gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
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gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
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gsub("Bacteria", "Batteri", ., fixed = TRUE) %>%
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gsub("Fungi", "Fungo", ., fixed = TRUE) %>%
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gsub("Protozoa", "Protozoi", ., fixed = TRUE) %>%
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gsub("biogroup", "biogruppo", ., fixed = TRUE) %>%
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gsub("biotype", "biotipo", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
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@ -371,15 +351,11 @@ mo_translate <- function(x, language) {
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gsub("Coagulase Positive Staphylococcus","Staphylococcus \u00e0 coagulase positif", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Streptococcus B\u00eata-h\u00e9molytique", ., fixed = TRUE) %>%
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gsub("(no MO)", "(pas MO)", ., fixed = TRUE) %>%
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gsub("Negative rods", "Bacilles n\u00e9gatif", ., fixed = TRUE) %>%
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gsub("Negative cocci", "Cocci n\u00e9gatif", ., fixed = TRUE) %>%
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gsub("Positive rods", "Bacilles positif", ., fixed = TRUE) %>%
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gsub("Positive cocci", "Cocci positif", ., fixed = TRUE) %>%
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# gsub("Parasites", "Parasites", ., fixed = TRUE) %>%
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gsub("Fungi and yeasts", "Champignons et levures", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bact\u00e9rie", ., fixed = TRUE) %>%
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gsub("Fungus/yeast", "Champignon/levure", ., fixed = TRUE) %>%
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# gsub("Parasite", "Parasite", ., fixed = TRUE) %>%
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gsub("Gram negative", "Gram n\u00e9gatif", ., fixed = TRUE) %>%
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gsub("Gram positive", "Gram positif", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bact\u00e9ries", ., fixed = TRUE) %>%
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gsub("Fungi", "Champignons", ., fixed = TRUE) %>%
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gsub("Protozoa", "Protozoaires", ., fixed = TRUE) %>%
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gsub("biogroup", "biogroupe", ., fixed = TRUE) %>%
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# gsub("biotype", "biotype", ., fixed = TRUE) %>%
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gsub("vegetative", "v\u00e9g\u00e9tatif", ., fixed = TRUE) %>%
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