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DSMZ data
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@ -26,7 +26,7 @@
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#' @param property one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}
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#' @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.
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#' @param ... other parameters passed on to \code{\link{as.mo}}
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#' @param open browse the URL using \code{\link[utils]{browseURL}}
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#' @param open browse the URL using \code{\link[utils]{browseURL}()}
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#' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
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#' \itemize{
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#' \item{\code{mo_fullname("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)}
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@ -34,9 +34,9 @@
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#' \item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
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#' }
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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 (ref: \url{https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097}). 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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#' 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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#' The function \code{mo_url()} will return the direct URL to the species in the Catalogue of Life.
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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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@ -99,7 +99,7 @@
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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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#' mo_fullname("S. epi", Becker = TRUE) # "Coagulase-negative Staphylococcus (CoNS)"
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#' mo_shortname("S. epi") # "S. epidermidis"
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#' mo_shortname("S. epi", Becker = TRUE) # "CoNS"
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#'
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@ -320,14 +320,24 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
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#' @rdname mo_property
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#' @importFrom utils browseURL
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#' @importFrom dplyr %>% left_join select mutate case_when
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#' @export
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mo_url <- function(x, open = FALSE, ...) {
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u <- mo_validate(x = x, property = "species_id", ...)
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u[u != ""] <- paste0(catalogue_of_life$url, "/details/species/id/", u)
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names(u) <- mo_fullname(x = x, ... = ...)
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mo <- AMR::as.mo(x = x, ... = ...)
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df <- data.frame(mo, stringsAsFactors = FALSE) %>%
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left_join(select(AMR::microorganisms, mo, source, species_id), by = "mo") %>%
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mutate(url = case_when(source == "CoL" ~
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paste0(gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE), "details/species/id/", species_id),
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source == "DSMZ" ~
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paste0(catalogue_of_life$url_DSMZ, "?bnu_no=", species_id, "#", species_id),
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TRUE ~
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NA_character_))
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u <- df$url
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names(u) <- mo_fullname(mo)
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if (open == TRUE) {
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if (length(u) > 1) {
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warning("only the first URL will be opened, as `browseURL` only suports one string.")
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warning("only the first URL will be opened, as `browseURL()` only suports one string.")
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}
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browseURL(u[1L])
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}
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@ -364,7 +374,7 @@ mo_translate <- function(x, language) {
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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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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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@ -374,8 +384,8 @@ mo_translate <- function(x, language) {
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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("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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@ -405,8 +415,8 @@ mo_translate <- function(x, language) {
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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("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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@ -436,8 +446,8 @@ mo_translate <- function(x, language) {
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# Spanish
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language == "es" ~ x[x_tobetranslated] %>%
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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("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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@ -465,8 +475,8 @@ mo_translate <- function(x, language) {
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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("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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@ -493,8 +503,8 @@ mo_translate <- function(x, language) {
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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("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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@ -522,8 +532,8 @@ mo_translate <- function(x, language) {
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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("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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@ -550,7 +560,6 @@ mo_translate <- function(x, language) {
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iconv(to = "UTF-8"))
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x
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}
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mo_validate <- function(x, property, ...) {
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