P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-08-28 11:52:13 +02:00
Code Releases Activity

(v0.8.0.9036) complete documentation rewrite

Browse Source
This commit is contained in:
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
Download Patch File Download Diff File Expand all files Collapse all files

51
man/mo_property.Rd
View File

@@ -70,58 +70,57 @@ mo_url(x, open = FALSE, ...)
mo_property(x, property = "fullname", language = get_locale(), ...)
}
\arguments{
\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}}
\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
\item{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.}
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{...}{other parameters passed on to \code{\link{as.mo}}}
\item{...}{other parameters passed on to \code{\link[=as.mo]{as.mo()}}}
\item{open}{browse the URL using \code{\link[utils]{browseURL}()}}
\item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}}
\item{property}{one of the column names of the \code{\link{microorganisms}} data set or \code{"shortname"}}
\item{property}{one of the column names of the \link{microorganisms} data set or \code{"shortname"}}
}
\value{
\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}
\item An \code{\link{integer}} in case of \code{\link[=mo_year]{mo_year()}}
\item A \code{\link{list}} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}}
\item A named \code{\link{character}} in case of \code{\link[=mo_url]{mo_url()}}
\item A \code{\link{character}} in all other cases
}
}
\description{
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.
Use these functions to return a specific property of a microorganism. All input values will be evaluated internally with \code{\link[=as.mo]{as.mo()}}, which makes it possible for input of these functions to use microbial abbreviations, codes and names. See Examples.
}
\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:
All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{\link[=mo_ref]{mo_ref()}}, \code{\link[=mo_authors]{mo_authors()}} and \code{\link[=mo_year]{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)}
\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)
}
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 - \code{\link[=mo_gramstain]{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}.
All output will be \link{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 \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
}
\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.
\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}()}.
\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()}}.
}
\section{Source}{
[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
[2] Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect. \url{https://doi.org/10.1016/j.cmi.2019.02.028}
[3] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
[4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
\enumerate{
\item Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
\item Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect. \url{https://doi.org/10.1016/j.cmi.2019.02.028}
\item Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
\item Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
}
}
\section{Read more on our website!}{
@@ -209,10 +208,10 @@ mo_fullname("S. pyogenes",
# 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")
}
}
\seealso{
\code{\link{microorganisms}}
\link{microorganisms}
}