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support for portuguese, language determination based on system
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208
R/mo_property.R
208
R/mo_property.R
@ -22,12 +22,13 @@
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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, either one of \code{"en"} (English), \code{"de"} (German) or \code{"nl"} (Dutch)
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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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#' @rdname mo_property
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#' @name mo_property
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#' @return Character or logical (only \code{mo_aerobic})
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#' @export
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#' @importFrom dplyr %>% left_join pull
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@ -44,14 +45,6 @@
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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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#' # language support for Spanish, German and Dutch
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#' mo_type("E. coli", "es") # "Bakteria"
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#' mo_type("E. coli", "de") # "Bakterien"
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#' mo_type("E. coli", "nl") # "Bacterie"
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#' mo_gramstain("E. coli", "es") # "Bacilos negativos"
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#' mo_gramstain("E. coli", "de") # "Negative Staebchen"
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#' mo_gramstain("E. coli", "nl") # "Negatieve staven"
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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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@ -95,26 +88,23 @@
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#' mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
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#' mo_shortname("S. pyo") # "S. pyogenes"
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#' mo_shortname("S. pyo", Lancefield = TRUE) # "GAS"
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mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE) {
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property <- tolower(property[1])
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if (!property %in% colnames(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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# 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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}
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result2
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}
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#' @rdname mo_property
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#' @export
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#'
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#'
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#' # Language support for German, Dutch, Spanish and Portuguese
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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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#'
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#' mo_fullname("S. pyo",
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#' Lancefield = TRUE,
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#' language = "de") # "Streptococcus Gruppe A"
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#' mo_fullname("S. pyo",
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#' Lancefield = TRUE,
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#' language = "nl") # "Streptococcus groep A"
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mo_family <- function(x) {
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mo_property(x, "family")
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}
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@ -127,34 +117,34 @@ mo_genus <- function(x) {
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#' @rdname mo_property
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#' @export
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mo_species <- function(x, Becker = FALSE, Lancefield = FALSE) {
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mo_property(x, "species", Becker = Becker, Lancefield = Lancefield)
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mo_species <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
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mo_property(x, "species", Becker = Becker, Lancefield = Lancefield, language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_subspecies <- function(x, Becker = FALSE, Lancefield = FALSE) {
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mo_property(x, "subspecies", Becker = Becker, Lancefield = Lancefield)
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mo_subspecies <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
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mo_property(x, "subspecies", Becker = Becker, Lancefield = Lancefield, language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_fullname <- function(x, Becker = FALSE, Lancefield = FALSE) {
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mo_property(x, "fullname", Becker = Becker, Lancefield = Lancefield)
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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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}
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#' @rdname mo_property
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#' @export
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mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE) {
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mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
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if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
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res1 <- as.mo(x)
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res2 <- suppressWarnings(as.mo(x, Becker = Becker, Lancefield = Lancefield))
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res2_fullname <- mo_fullname(res2)
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res2_fullname[res2_fullname %like% "\\(CoNS\\)"] <- "CoNS"
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res2_fullname[res2_fullname %like% "\\(CoPS\\)"] <- "CoPS"
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res2_fullname <- gsub("Streptococcus group (.*)",
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"G\\1S",
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res2_fullname) # turn "Streptococcus group A" to "GAS"
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res2_fullname <- gsub("Streptococcus (group|gruppe|Gruppe|groep|grupo) (.)",
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"G\\2S",
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res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
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res2_fullname[res2_fullname == mo_fullname(x)] <- paste0(substr(mo_genus(res2_fullname), 1, 1),
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". ",
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suppressWarnings(mo_species(res2_fullname)))
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@ -170,20 +160,20 @@ mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE) {
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result <- paste0(substr(mo_genus(x), 1, 1), ". ", suppressWarnings(mo_species(x)))
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}
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result[result %in% c(". ")] <- ""
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result
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mo_translate(result, language = language)
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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 = "en") {
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mo_property(x, paste0("type", checklang(language)))
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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_gramstain <- function(x, language = "en") {
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mo_property(x, paste0("gramstain", checklang(language)))
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mo_gramstain <- function(x, language = NULL) {
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mo_property(x, "gramstain", language = language)
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}
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#' @rdname mo_property
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@ -192,15 +182,127 @@ mo_aerobic <- function(x) {
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mo_property(x, "aerobic")
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}
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checklang <- function(language) {
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language <- tolower(language[1])
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supported <- c("en", "de", "nl", "es")
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if (!language %in% c(NULL, "", supported)) {
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stop("invalid language: ", language, " - use one of ", paste0("'", sort(supported), "'", collapse = ", "), call. = FALSE)
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#' @rdname mo_property
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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(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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if (language %in% c(NULL, "", "en")) {
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""
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} else {
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paste0("_", language)
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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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# 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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}
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result2
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}
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#' @importFrom dplyr %>% case_when
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mo_translate <- function(x, language) {
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if (is.null(language)) {
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language <- mo_getlangcode()
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} else {
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language <- tolower(language[1])
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}
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if (language %in% c("en", "")) {
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return(x)
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}
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supported <- c("en", "de", "nl", "es", "pt")
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if (!language %in% supported) {
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stop("Unsupported language: '", language, "' - use one of ", paste0("'", sort(supported), "'", collapse = ", "), call. = FALSE)
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}
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case_when(
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# German
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language == "de" ~ x %>%
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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("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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gsub("([([ ]*?)group", "\\1Gruppe", .) %>%
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gsub("([([ ]*?)Group", "\\1Gruppe", .),
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# Dutch
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language == "nl" ~ x %>%
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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("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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gsub("([([ ]*?)group", "\\1groep", .) %>%
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gsub("([([ ]*?)Group", "\\1Groep", .),
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# Spanish
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language == "es" ~ x %>%
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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("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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gsub("([([ ]*?)group", "\\1grupo", .) %>%
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gsub("([([ ]*?)Group", "\\1Grupo", .),
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# Portuguese
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language == "pt" ~ x %>%
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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("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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gsub("([([ ]*?)group", "\\1grupo", .) %>%
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gsub("([([ ]*?)Group", "\\1Grupo", .)
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)
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}
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#' @importFrom dplyr case_when
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mo_getlangcode <- function() {
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sys <- base::Sys.getlocale()
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case_when(
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sys %like% '(Deutsch|German|de_)' ~ "de",
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sys %like% '(Nederlands|Dutch|nl_)' ~ "nl",
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sys %like% '(Espa.ol|Spanish|es_)' ~ "es",
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sys %like% '(Portugu.s|Portuguese|pt_)' ~ "pt",
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TRUE ~ "en"
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)
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}
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