P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 11:51:59 +02:00
Code Releases Activity

Catalogue of life

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-02-20 00:04:48 +01:00
parent 54f8258f8c
commit fb1fc3686c
55 changed files with 2070 additions and 816 deletions
Download Patch File Download Diff File Expand all files Collapse all files

26
R/mo_property.R
View File

@ -26,14 +26,18 @@
#' @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}}
#' @details All functions will return the most recently known taxonomic property according to ITIS, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
#' @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)}
#' \item{\code{mo_ref("Chlamydia psittaci")} will return \code{"Page, 1968"} (with a warning about the renaming)}
#' \item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
#' }
#'
#' 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}.
#'
#' The function \code{mo_url()} will return the direct URL to the species in the Catalogue of Life.
#' @inheritSection get_locale Supported languages
#' @inheritSection ITIS ITIS
#' @inheritSection catalogue_of_life Catalogue of Life
#' @inheritSection as.mo Source
#' @rdname mo_property
#' @name mo_property
@ -49,14 +53,13 @@
#' # All properties of Escherichia coli
#' ## taxonomic properties
#' mo_kingdom("E. coli") # "Bacteria"
#' mo_subkingdom("E. coli") # "Negibacteria"
#' mo_phylum("E. coli") # "Proteobacteria"
#' mo_class("E. coli") # "Gammaproteobacteria"
#' mo_order("E. coli") # "Enterobacteriales"
#' mo_family("E. coli") # "Enterobacteriaceae"
#' mo_genus("E. coli") # "Escherichia"
#' mo_species("E. coli") # "coli"
#' mo_subspecies("E. coli") # NA
#' mo_subspecies("E. coli") # ""
#'
#' ## colloquial properties
#' mo_fullname("E. coli") # "Escherichia coli"
@ -220,12 +223,6 @@ mo_phylum <- function(x, ...) {
mo_validate(x = x, property = "phylum", ...)
}
#' @rdname mo_property
#' @export
mo_subkingdom <- function(x, ...) {
mo_validate(x = x, property = "subkingdom", ...)
}
#' @rdname mo_property
#' @export
mo_kingdom <- function(x, ...) {
@ -290,6 +287,15 @@ mo_taxonomy <- function(x, ...) {
subspecies = mo_subspecies(x))
}
#' @rdname mo_property
#' @export
mo_url <- function(x, ...) {
u <- mo_validate(x = x, property = "species_id", ...)
u[u != ""] <- paste0(catalogue_of_life$url, "/details/species/id/", u)
u
}
#' @rdname mo_property
#' @importFrom data.table data.table as.data.table setkey
#' @export