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(v0.8.0.9036) complete documentation rewrite

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dr. M.S. (Matthijs) Berends
2019-11-28 22:32:17 +01:00
parent 7c28b392b1
commit c5f00f4a9f
138 changed files with 2797 additions and 2484 deletions
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44
R/mo_property.R
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@ -21,36 +21,33 @@
#' Property of a microorganism
#'
#' Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with \code{\link{as.mo}}, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.
#' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
#' @param property one of the column names 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_name("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)}
#' }
#' Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with [as.mo()], which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.
#' @param x any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param property one of the column names of the [microorganisms] data set or `"shortname"`
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
#' @param ... other parameters passed on to [as.mo()]
#' @param open browse the URL using [utils::browseURL()]
#' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for [mo_ref()], [mo_authors()] and [mo_year()]. This leads to the following results:
#' - `mo_name("Chlamydia psittaci")` will return `"Chlamydophila psittaci"` (with a warning about the renaming)
#' - `mo_ref("Chlamydia psittaci")` will return `"Page, 1968"` (with a warning about the renaming)
#' - `mo_ref("Chlamydophila psittaci")` will return `"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. 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 Gram stain - [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 `NA`.
#'
#' All output will be \link{translate}d where possible.
#' All output will be [translate]d where possible.
#'
#' 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.
#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
#' @inheritSection catalogue_of_life Catalogue of Life
#' @inheritSection as.mo Source
#' @rdname mo_property
#' @name mo_property
#' @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}
#' }
#' @return
#' - An [`integer`] in case of [mo_year()]
#' - A [`list`] in case of [mo_taxonomy()]
#' - A named [`character`] in case of [mo_url()]
#' - A [`character`] in all other cases
#' @export
#' @seealso \code{\link{microorganisms}}
#' @seealso [microorganisms]
#' @inheritSection AMR Read more on our website!
#' @examples
#' # taxonomic tree -----------------------------------------------------------
@ -132,7 +129,7 @@
#'
#' # get a list with the complete taxonomy (from kingdom to subspecies)
#' mo_taxonomy("E. coli")
#' # get a list with the taxonomy, the authors and the URL to the online database
#' # get a list with the taxonomy, the authors, Gram-stain and URL to the online database
#' mo_info("E. coli")
#' }
mo_name <- function(x, language = get_locale(), ...) {
@ -336,6 +333,7 @@ mo_info <- function(x, language = get_locale(), ...) {
info <- lapply(x, function(y)
c(mo_taxonomy(y, language = language),
list(synonyms = mo_synonyms(y),
gramstain = mo_gramstain(y, language = language),
url = unname(mo_url(y, open = FALSE)),
ref = mo_ref(y))))
if (length(info) > 1) {