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246
R/mo_property.R
246
R/mo_property.R
@ -36,8 +36,9 @@
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#'
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#' The Gram stain - \code{mo_gramstain()} - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) 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 \code{NA}.
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#'
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#' All output will be \link{translate}d where possible.
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#'
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#' The function \code{mo_url()} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
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#' @inheritSection get_locale Supported languages
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#' @inheritSection catalogue_of_life Catalogue of Life
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#' @inheritSection as.mo Source
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#' @rdname mo_property
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@ -70,7 +71,7 @@
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#' mo_gramstain("E. coli") # "Gram negative"
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#' mo_type("E. coli") # "Bacteria" (equal to kingdom)
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#' mo_rank("E. coli") # "species"
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#' mo_url("E. coli") # get the direct url to the Catalogue of Life
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#' mo_url("E. coli") # get the direct url to the online database entry
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#'
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#' ## scientific reference
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#' mo_ref("E. coli") # "Castellani et al., 1919"
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@ -128,11 +129,11 @@
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#' language = "nl") # "Streptococcus groep A"
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#'
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#'
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#' # get a list with the complete taxonomy (kingdom to subspecies)
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#' # get a list with the complete taxonomy (from kingdom to subspecies)
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#' mo_taxonomy("E. coli")
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mo_fullname <- function(x, language = get_locale(), ...) {
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x <- mo_validate(x = x, property = "fullname", ...)
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mo_translate(x, language = language)
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t(x, language = language)
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}
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#' @rdname mo_property
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@ -199,49 +200,49 @@ mo_shortname <- function(x, language = get_locale(), ...) {
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}
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}
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mo_translate(result, language = language)
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t(result, 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, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "subspecies", ...), language = language)
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t(mo_validate(x = x, property = "subspecies", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_species <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "species", ...), language = language)
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t(mo_validate(x = x, property = "species", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_genus <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "genus", ...), language = language)
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t(mo_validate(x = x, property = "genus", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_family <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "family", ...), language = language)
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t(mo_validate(x = x, property = "family", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_order <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "order", ...), language = language)
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t(mo_validate(x = x, property = "order", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_class <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "class", ...), language = language)
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t(mo_validate(x = x, property = "class", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_phylum <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "phylum", ...), language = language)
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t(mo_validate(x = x, property = "phylum", ...), language = language)
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}
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#' @rdname mo_property
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@ -250,10 +251,10 @@ mo_kingdom <- function(x, language = get_locale(), ...) {
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if (all(x %in% AMR::microorganisms$kingdom)) {
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return(x)
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}
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x <- as.mo(x, language = "en", ...)
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x <- as.mo(x, ...)
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kngdm <- mo_validate(x = x, property = "kingdom", ...)
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if (language != "en") {
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kngdm[x == "UNKNOWN"] <- mo_translate(kngdm[x == "UNKNOWN"], language = language)
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kngdm[x == "UNKNOWN"] <- t(kngdm[x == "UNKNOWN"], language = language)
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}
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kngdm
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}
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@ -261,13 +262,13 @@ mo_kingdom <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @export
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mo_type <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "kingdom", ...), language = language)
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t(mo_validate(x = x, property = "kingdom", ...), 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 = get_locale(), ...) {
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x.mo <- as.mo(x, language = "en", ...)
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x.mo <- as.mo(x, ...)
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x.phylum <- mo_phylum(x.mo, language = "en")
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x[x.phylum %in% c("Actinobacteria",
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"Chloroflexi",
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@ -278,7 +279,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
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x[x.mo == "B_GRAMP"] <- "Gram positive"
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x[x.mo == "B_GRAMN"] <- "Gram negative"
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mo_translate(x, language = language)
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t(x, language = language)
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}
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#' @rdname mo_property
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@ -363,214 +364,7 @@ mo_property <- function(x, property = 'fullname', language = get_locale(), ...)
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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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mo_translate(mo_validate(x = x, property = property, ...), language = language)
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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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return(x)
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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", "it", "fr")
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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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x_tobetranslated <- grepl(x = x,
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pattern = "(Coagulase-negative Staphylococcus|Coagulase-positive Staphylococcus|Beta-haemolytic Streptococcus|unknown Gram negatives|unknown Gram positives|unknown name|unknown kingdom|unknown phylum|unknown class|unknown order|unknown family|unknown genus|unknown species|unknown subspecies|unknown rank|CoNS|CoPS|Gram negative|Gram positive|Bacteria|Fungi|Protozoa|biogroup|biotype|vegetative|group|Group)")
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if (sum(x_tobetranslated, na.rm = TRUE) == 0) {
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return(x)
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}
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# only translate the ones that need translation
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x[x_tobetranslated] <- case_when(
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# German
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language == "de" ~ x[x_tobetranslated] %>%
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gsub("Coagulase-negative Staphylococcus","Koagulase-negative Staphylococcus", ., fixed = TRUE) %>%
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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("unknown Gram negatives", "unbekannte Gramnegativen", ., fixed = TRUE) %>%
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gsub("unknown Gram positives", "unbekannte Grampositiven", ., fixed = TRUE) %>%
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gsub("unknown name", "unbekannte Name", ., fixed = TRUE) %>%
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gsub("unknown kingdom", "unbekanntes Reich", ., fixed = TRUE) %>%
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gsub("unknown phylum", "unbekannter Stamm", ., fixed = TRUE) %>%
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gsub("unknown class", "unbekannte Klasse", ., fixed = TRUE) %>%
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gsub("unknown order", "unbekannte Ordnung", ., fixed = TRUE) %>%
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gsub("unknown family", "unbekannte Familie", ., fixed = TRUE) %>%
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gsub("unknown genus", "unbekannte Gattung", ., fixed = TRUE) %>%
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gsub("unknown species", "unbekannte Art", ., fixed = TRUE) %>%
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gsub("unknown subspecies", "unbekannte Unterart", ., fixed = TRUE) %>%
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gsub("unknown rank", "unbekannter Rang", ., fixed = TRUE) %>%
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gsub("(CoNS)", "(KNS)", ., fixed = TRUE) %>%
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gsub("(CoPS)", "(KPS)", ., 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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gsub("([([ ]*?)group", "\\1Gruppe", .) %>%
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gsub("([([ ]*?)Group", "\\1Gruppe", .) %>%
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iconv(to = "UTF-8"),
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# Dutch
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language == "nl" ~ x[x_tobetranslated] %>%
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gsub("Coagulase-negative Staphylococcus","Coagulase-negatieve Staphylococcus", ., fixed = TRUE) %>%
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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("unknown Gram negatives", "onbekende Gram-negatieven", ., fixed = TRUE) %>%
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gsub("unknown Gram positives", "onbekende Gram-positieven", ., fixed = TRUE) %>%
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gsub("unknown name", "onbekende naam", ., fixed = TRUE) %>%
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gsub("unknown kingdom", "onbekend koninkrijk", ., fixed = TRUE) %>%
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gsub("unknown phylum", "onbekende fylum", ., fixed = TRUE) %>%
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gsub("unknown class", "onbekende klasse", ., fixed = TRUE) %>%
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gsub("unknown order", "onbekende orde", ., fixed = TRUE) %>%
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gsub("unknown family", "onbekende familie", ., fixed = TRUE) %>%
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gsub("unknown genus", "onbekend geslacht", ., fixed = TRUE) %>%
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gsub("unknown species", "onbekende soort", ., fixed = TRUE) %>%
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gsub("unknown subspecies", "onbekende ondersoort", ., fixed = TRUE) %>%
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gsub("unknown rank", "onbekende rang", ., fixed = TRUE) %>%
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gsub("(CoNS)", "(CNS)", ., fixed = TRUE) %>%
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gsub("(CoPS)", "(CPS)", ., 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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gsub("([([ ]*?)group", "\\1groep", .) %>%
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gsub("([([ ]*?)Group", "\\1Groep", .) %>%
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iconv(to = "UTF-8"),
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# Spanish
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language == "es" ~ x[x_tobetranslated] %>%
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# not 'negativa'
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# https://www.sciencedirect.com/science/article/pii/S0123939215000739
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gsub("Coagulase-negative Staphylococcus","Staphylococcus coagulasa negativo", ., fixed = TRUE) %>%
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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("unknown Gram negatives", "Gram negativos desconocidos", ., fixed = TRUE) %>%
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gsub("unknown Gram positives", "Gram positivos desconocidos", ., fixed = TRUE) %>%
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gsub("unknown name", "nombre desconocido", ., fixed = TRUE) %>%
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gsub("unknown kingdom", "reino desconocido", ., fixed = TRUE) %>%
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gsub("unknown phylum", "filo desconocido", ., fixed = TRUE) %>%
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gsub("unknown class", "clase desconocida", ., fixed = TRUE) %>%
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gsub("unknown order", "orden desconocido", ., fixed = TRUE) %>%
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gsub("unknown family", "familia desconocida", ., fixed = TRUE) %>%
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gsub("unknown genus", "g\u00e9nero desconocido", ., fixed = TRUE) %>%
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gsub("unknown species", "especie desconocida", ., fixed = TRUE) %>%
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gsub("unknown subspecies", "subespecie desconocida", ., fixed = TRUE) %>%
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gsub("unknown rank", "rango desconocido", ., fixed = TRUE) %>%
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gsub("(CoNS)", "(SCN)", ., fixed = TRUE) %>%
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gsub("(CoPS)", "(SCP)", ., 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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gsub("([([ ]*?)group", "\\1grupo", .) %>%
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gsub("([([ ]*?)Group", "\\1Grupo", .) %>%
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iconv(to = "UTF-8"),
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# Italian
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language == "it" ~ x[x_tobetranslated] %>%
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gsub("Coagulase-negative Staphylococcus","Staphylococcus negativo coagulasi", ., fixed = TRUE) %>%
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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("unknown Gram negatives", "Gram negativi sconosciuti", ., fixed = TRUE) %>%
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gsub("unknown Gram positives", "Gram positivi sconosciuti", ., fixed = TRUE) %>%
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gsub("unknown name", "nome sconosciuto", ., fixed = TRUE) %>%
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gsub("unknown kingdom", "regno sconosciuto", ., fixed = TRUE) %>%
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gsub("unknown phylum", "phylum sconosciuto", ., fixed = TRUE) %>%
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gsub("unknown class", "classe sconosciuta", ., fixed = TRUE) %>%
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gsub("unknown order", "ordine sconosciuto", ., fixed = TRUE) %>%
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gsub("unknown family", "famiglia sconosciuta", ., fixed = TRUE) %>%
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gsub("unknown genus", "genere sconosciuto", ., fixed = TRUE) %>%
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gsub("unknown species", "specie sconosciute", ., fixed = TRUE) %>%
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gsub("unknown subspecies", "sottospecie sconosciute", ., fixed = TRUE) %>%
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gsub("unknown rank", "grado sconosciuto", ., 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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gsub("([([ ]*?)group", "\\1gruppo", .) %>%
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gsub("([([ ]*?)Group", "\\1Gruppo", .),
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# French
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language == "fr" ~ x[x_tobetranslated] %>%
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gsub("Coagulase-negative Staphylococcus","Staphylococcus \u00e0 coagulase n\u00e9gative", ., fixed = TRUE) %>%
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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("unknown Gram negatives", "Gram n\u00e9gatifs inconnus", ., fixed = TRUE) %>%
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gsub("unknown Gram positives", "Gram positifs inconnus", ., fixed = TRUE) %>%
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gsub("unknown name", "nom inconnu", ., fixed = TRUE) %>%
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gsub("unknown kingdom", "r\u00e8gme inconnu", ., fixed = TRUE) %>%
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gsub("unknown phylum", "embranchement inconnu", ., fixed = TRUE) %>%
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gsub("unknown class", "classe inconnue", ., fixed = TRUE) %>%
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gsub("unknown order", "ordre inconnu", ., fixed = TRUE) %>%
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gsub("unknown family", "famille inconnue", ., fixed = TRUE) %>%
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gsub("unknown genus", "genre inconnu", ., fixed = TRUE) %>%
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gsub("unknown species", "esp\u00e8ce inconnue", ., fixed = TRUE) %>%
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gsub("unknown subspecies", "sous-esp\u00e8ce inconnue", ., fixed = TRUE) %>%
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gsub("unknown rank", "rang inconnu", ., 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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gsub("([([ ]*?)group", "\\1groupe", .) %>%
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gsub("([([ ]*?)Group", "\\1Groupe", .) %>%
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iconv(to = "UTF-8"),
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# Portuguese
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language == "pt" ~ x[x_tobetranslated] %>%
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gsub("Coagulase-negative Staphylococcus","Staphylococcus coagulase negativo", ., fixed = TRUE) %>%
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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("unknown Gram negatives", "Gram negativos desconhecidos", ., fixed = TRUE) %>%
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gsub("unknown Gram positives", "Gram positivos desconhecidos", ., fixed = TRUE) %>%
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gsub("unknown name", "nome desconhecido", ., fixed = TRUE) %>%
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gsub("unknown kingdom", "reino desconhecido", ., fixed = TRUE) %>%
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gsub("unknown phylum", "filo desconhecido", ., fixed = TRUE) %>%
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gsub("unknown class", "classe desconhecida", ., fixed = TRUE) %>%
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gsub("unknown order", "ordem desconhecido", ., fixed = TRUE) %>%
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gsub("unknown family", "fam\u00edlia desconhecida", ., fixed = TRUE) %>%
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gsub("unknown genus", "g\u00eanero desconhecido", ., fixed = TRUE) %>%
|
||||
gsub("unknown species", "esp\u00e9cies desconhecida", ., fixed = TRUE) %>%
|
||||
gsub("unknown subspecies", "subesp\u00e9cies desconhecida", ., fixed = TRUE) %>%
|
||||
gsub("unknown rank", "classifica\u00e7\u00e3o desconhecido", ., 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
|
||||
t(mo_validate(x = x, property = property, ...), language = language)
|
||||
}
|
||||
|
||||
mo_validate <- function(x, property, ...) {
|
||||
@ -591,7 +385,7 @@ mo_validate <- function(x, property, ...) {
|
||||
}
|
||||
|
||||
# try to catch an error when inputting an invalid parameter
|
||||
# so the call can be set to FALSE
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% AMR::microorganisms[1, property],
|
||||
error = function(e) stop(e$message, call. = FALSE))
|
||||
|
||||
|
||||
Reference in New Issue
Block a user