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mo_rank mo_url, added Tremellales

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dr. M.S. (Matthijs) Berends
2019-02-22 22:12:10 +01:00
parent c2aea67e84
commit 41ad7a22c8
42 changed files with 518 additions and 472 deletions
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37
R/mo_property.R
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@ -26,6 +26,7 @@
#' @param property one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}
#' @param language language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.
#' @param ... other parameters passed on to \code{\link{as.mo}}
#' @param open browse the URL using \code{\link[utils]{browseURL}}
#' @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:
#' \itemize{
#' \item{\code{mo_fullname("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)}
@ -44,14 +45,14 @@
#' @return \itemize{
#' \item{An \code{integer} in case of \code{mo_year}}
#' \item{A \code{list} in case of \code{mo_taxonomy}}
#' \item{A named \code{character} in case of \code{mo_url}}
#' \item{A \code{character} in all other cases}
#' }
#' @export
#' @seealso \code{\link{microorganisms}}
#' @inheritSection AMR Read more on our website!
#' @examples
#' # All properties of Escherichia coli
#' ## taxonomic properties
#' ## taxonomic tree
#' mo_kingdom("E. coli") # "Bacteria"
#' mo_phylum("E. coli") # "Proteobacteria"
#' mo_class("E. coli") # "Gammaproteobacteria"
@ -68,10 +69,12 @@
#' ## other properties
#' mo_gramstain("E. coli") # "Gram negative"
#' mo_type("E. coli") # "Bacteria" (equal to kingdom)
#' mo_rank("E. coli") # "species"
#' mo_url("E. coli") # get the direct url to the Catalogue of Life
#'
#' ## scientific reference
#' mo_ref("E. coli") # "Castellani and Chalmers, 1919"
#' mo_authors("E. coli") # "Castellani and Chalmers"
#' mo_ref("E. coli") # "Castellani et al., 1919"
#' mo_authors("E. coli") # "Castellani et al."
#' mo_year("E. coli") # 1919
#'
#'
@ -107,7 +110,7 @@
#' mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" ('Group A streptococci')
#'
#'
#' # Language support for German, Dutch, Spanish, Portuguese, Italian and French
#' # language support for German, Dutch, Spanish, Portuguese, Italian and French
#' mo_gramstain("E. coli", language = "de") # "Gramnegativ"
#' mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
#' mo_gramstain("E. coli", language = "es") # "Gram negativo"
@ -125,7 +128,7 @@
#' language = "nl") # "Streptococcus groep A"
#'
#'
#' # Get a list with the complete taxonomy (kingdom to subspecies)
#' # get a list with the complete taxonomy (kingdom to subspecies)
#' mo_taxonomy("E. coli")
mo_fullname <- function(x, language = get_locale(), ...) {
x <- mo_validate(x = x, property = "fullname", ...)
@ -259,9 +262,9 @@ mo_ref <- function(x, ...) {
#' @export
mo_authors <- function(x, ...) {
x <- mo_validate(x = x, property = "ref", ...)
# remove last 4 digits and presumably the comma and space that preceed them
# remove last 4 digits and presumably the comma and space that preceeds them
x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
x
suppressWarnings(x)
}
#' @rdname mo_property
@ -270,7 +273,13 @@ mo_year <- function(x, ...) {
x <- mo_validate(x = x, property = "ref", ...)
# get last 4 digits
x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)])
as.integer(x)
suppressWarnings(as.integer(x))
}
#' @rdname mo_property
#' @export
mo_rank <- function(x, ...) {
mo_validate(x = x, property = "rank", ...)
}
#' @rdname mo_property
@ -288,10 +297,18 @@ mo_taxonomy <- function(x, ...) {
}
#' @rdname mo_property
#' @importFrom utils browseURL
#' @export
mo_url <- function(x, ...) {
mo_url <- function(x, open = FALSE, ...) {
u <- mo_validate(x = x, property = "species_id", ...)
u[u != ""] <- paste0(catalogue_of_life$url, "/details/species/id/", u)
names(u) <- mo_fullname(x = x, ... = ...)
if (open == TRUE) {
if (length(u) > 1) {
warning("only the first URL will be opened, as `browseURL` only suports one string.")
}
browseURL(u[1L])
}
u
}