LaTeX Utilities for Vignettes — latex

latex_preamble outputs/returns command definition LaTeX commands to be put in the preamble of vignettes.

latex_preamble(
  PACKAGE,
  R = TRUE,
  CRAN = TRUE,
  Bioconductor = TRUE,
  GEO = TRUE,
  ArrayExpress = TRUE,
  biblatex = FALSE,
  only = FALSE,
  file = ""
)

latex_bibliography(PACKAGE, file = "")

Arguments

PACKAGE	package name
R	logical that indicate if general R commands should be added (e.g. package names, inline R code format commands)
CRAN	logical that indicate if general CRAN commands should be added (e.g. CRAN package citations)
Bioconductor	logical that indicate if general Bioconductor commands should be added (e.g. Bioc package citations)
GEO	logical that indicate if general GEOmnibus commands should be added (e.g. urls to GEO datasets)
ArrayExpress	logical that indicate if general ArrayExpress commands should be added (e.g. urls to ArrayExpress datasets)
biblatex	logical that indicates if a `\bibliography` command should be added to include references from the package's REFERENCES.bib file.
only	a logical that indicates if the only the commands whose dedicated argument is not missing should be considered.
file	connection where to print. If `NULL` the result is returned silently.

Details

Argument PACKAGE is not required for latex_preamble, but must be correctly specified to ensure biblatex=TRUE generates the correct bibliography command.

Functions

latex_bibliography: latex_bibliography prints or return a LaTeX command that includes a package bibliography file if it exists.

Examples


latex_preamble()
#> %%%% PKGMAKER COMMANDS %%%%%%
#> \usepackage{xspace}
#> 
#> % R
#> \let\proglang=\textit
#> \let\code=\texttt 
#> \providecommand{\Rcode}{\code}
#> \providecommand{\pkgname}[1]{\textit{#1}\xspace}
#> \providecommand{\Rpkg}[1]{\pkgname{#1} package\xspace}
#> \providecommand{\citepkg}[1]{\cite{#1}}
#> 
#> % CRAN
#> \providecommand{\CRANurl}[1]{\url{https://cran.r-project.org/package=#1}}
#> %% CRANpkg
#> \makeatletter
#> \def\CRANpkg{\@ifstar\@CRANpkg\@@CRANpkg}
#> \def\@CRANpkg#1{\href{https://cran.r-project.org/package=#1}{\pkgname{#1}}\footnote{\CRANurl{#1}}}
#> \def\@@CRANpkg#1{\href{https://cran.r-project.org/package=#1}{\pkgname{#1}} package\footnote{\CRANurl{#1}}}
#> \makeatother
#> %% citeCRANpkg
#> \makeatletter
#> \def\citeCRANpkg{\@ifstar\@citeCRANpkg\@@citeCRANpkg}
#> \def\@citeCRANpkg#1{\CRANpkg{#1}\cite*{Rpackage:#1}}
#> \def\@@citeCRANpkg#1{\CRANpkg{#1}~\cite{Rpackage:#1}}
#> \makeatother
#> \providecommand{\CRANnmf}{\href{https://cran.r-project.org/package=NMF}{CRAN}}
#> \providecommand{\CRANnmfURL}{\url{https://cran.r-project.org/package=NMF}}
#> 
#> % Bioconductor
#> \providecommand{\BioCurl}[1]{\url{http://www.bioconductor.org/packages/release/bioc/html/#1.html}}
#> \providecommand{\BioCpkg}[1]{\href{http://www.bioconductor.org/packages/release/bioc/html/#1.html}{\pkgname{#1}} package\footnote{\BioCurl{#1}}}
#> \providecommand{\citeBioCpkg}[1]{\BioCpkg{#1}~\cite{Rpackage:#1}}
#> % Bioconductor annotation
#> \providecommand{\BioCAnnurl}[1]{\url{http://www.bioconductor.org/packages/release/data/annotation/html/#1.html}}
#> \providecommand{\BioCAnnpkg}[1]{\href{http://www.bioconductor.org/packages/release/data/annotation/html/#1.html}{\Rcode{#1}} annotation package\footnote{\BioCAnnurl{#1}}}
#> \providecommand{\citeBioCAnnpkg}[1]{\BioCAnnpkg{#1}~\cite{Rpackage:#1}}
#> 
#> % GEO
#> \providecommand{\GEOurl}[1]{\href{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=#1}{#1}\xspace}
#> \providecommand{\GEOhref}[1]{\GEOurl{#1}\footnote{\url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=#1}}}
#> 
#> % ArrayExpress
#> \providecommand{\ArrayExpressurl}[1]{\href{http://www.ebi.ac.uk/arrayexpress/experiments/#1}{#1}\xspace}
#> \providecommand{\ArrayExpresshref}[1]{\ArrayExpressurl{#1}\footnote{\url{http://www.ebi.ac.uk/arrayexpress/experiments/#1}}}
#> 
#> %%%% END: PKGMAKER COMMANDS %%%%%%
latex_preamble(R=TRUE, only=TRUE)
#> %%%% PKGMAKER COMMANDS %%%%%%
#> \usepackage{xspace}
#> 
#> % R
#> \let\proglang=\textit
#> \let\code=\texttt 
#> \providecommand{\Rcode}{\code}
#> \providecommand{\pkgname}[1]{\textit{#1}\xspace}
#> \providecommand{\Rpkg}[1]{\pkgname{#1} package\xspace}
#> \providecommand{\citepkg}[1]{\cite{#1}}
#> 
#> %%%% END: PKGMAKER COMMANDS %%%%%%
latex_preamble(R=FALSE, CRAN=FALSE, GEO=FALSE)
#> %%%% PKGMAKER COMMANDS %%%%%%
#> \usepackage{xspace}
#> 
#> % Bioconductor
#> \providecommand{\BioCurl}[1]{\url{http://www.bioconductor.org/packages/release/bioc/html/#1.html}}
#> \providecommand{\BioCpkg}[1]{\href{http://www.bioconductor.org/packages/release/bioc/html/#1.html}{\pkgname{#1}} package\footnote{\BioCurl{#1}}}
#> \providecommand{\citeBioCpkg}[1]{\BioCpkg{#1}~\cite{Rpackage:#1}}
#> % Bioconductor annotation
#> \providecommand{\BioCAnnurl}[1]{\url{http://www.bioconductor.org/packages/release/data/annotation/html/#1.html}}
#> \providecommand{\BioCAnnpkg}[1]{\href{http://www.bioconductor.org/packages/release/data/annotation/html/#1.html}{\Rcode{#1}} annotation package\footnote{\BioCAnnurl{#1}}}
#> \providecommand{\citeBioCAnnpkg}[1]{\BioCAnnpkg{#1}~\cite{Rpackage:#1}}
#> 
#> % ArrayExpress
#> \providecommand{\ArrayExpressurl}[1]{\href{http://www.ebi.ac.uk/arrayexpress/experiments/#1}{#1}\xspace}
#> \providecommand{\ArrayExpresshref}[1]{\ArrayExpressurl{#1}\footnote{\url{http://www.ebi.ac.uk/arrayexpress/experiments/#1}}}
#> 
#> %%%% END: PKGMAKER COMMANDS %%%%%%
latex_preamble(GEO=TRUE, only=TRUE)
#> %%%% PKGMAKER COMMANDS %%%%%%
#> \usepackage{xspace}
#> 
#> % GEO
#> \providecommand{\GEOurl}[1]{\href{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=#1}{#1}\xspace}
#> \providecommand{\GEOhref}[1]{\GEOurl{#1}\footnote{\url{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=#1}}}
#> 
#> %%%% END: PKGMAKER COMMANDS %%%%%%