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(v1.4.0.9033) documentation update

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dr. M.S. (Matthijs) Berends
2020-12-08 12:37:25 +01:00
parent 1bdb136b3a
commit 2145f1d1ba
110 changed files with 839 additions and 576 deletions
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8
man/mo_property.Rd
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@@ -85,7 +85,7 @@ mo_url(x, open = FALSE, language = get_locale(), ...)
mo_property(x, property = "fullname", language = get_locale(), ...)
}
\arguments{
\item{x}{any character (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
\item{x}{any character (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be omitted for auto-guessing in \verb{mo_is_*()} functions when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}, please see \emph{Examples}.}
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Also used to translate text like "no growth". Use \code{language = NULL} or \code{language = ""} to prevent translation.}
@@ -95,7 +95,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
\item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}}
\item{property}{one of the column names of the \link{microorganisms} data set or \code{"shortname"}}
\item{property}{one of the column names of the \link{microorganisms} data set: "\code{mo}", "\code{fullname}", "\code{kingdom}", "\code{phylum}", "\code{class}", "\code{order}", "\code{family}", "\code{genus}", "\code{species}", "\code{subspecies}", "\code{rank}", "\code{ref}", "\code{species_id}", "\code{source}", "\code{prevalence}", "\code{snomed}", or must be \code{"shortname"}}
}
\value{
\itemize{
@@ -161,9 +161,9 @@ All matches are sorted descending on their matching score and for all user input
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, \url{http://www.catalogueoflife.org}). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, \href{https://lpsn.dsmz.de}{lpsn.dsmz.de}). This supplementation is needed until the \href{https://github.com/Sp2000/colplus}{CoL+ project} is finished, which we await.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}.
}
\section{Source}{