#\DeclareLyXModule[graphicx.sty,fancyvrb.sty,tikz.sty,pgfsweave->latex]{pgfSweave}
#DescriptionBegin
#Allows to use the R language as a literate programming tool via the pgfSweave package. Major differences with Sweave: pgfSweave supports cache for both R objects (the cacheSweave package) and graphics (tikz externalization); it uses tikz graphics by default which has consistent styles with the LaTeX document; R code highlighted by default (the highlight package); chunk option 'tidy' to reformat R code (the formatR package). 
#See pgfsweave.lyx in examples.
#DescriptionEnd
#Category: literate
#Excludes: lilypond | sweave

Format 35
OutputType             literate
OutputFormat           pgfsweave

ClassOptions
        Other          "noae"
End

Preamble
        %\usepackage{Sweave}
        \ifdefined\Sinput
        \else
        \IfFileExists{Sweave.sty}{
          \usepackage{Sweave}
        }{
          \usepackage{graphicx,fancyvrb}
          \DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
          \DefineVerbatimEnvironment{Soutput}{Verbatim}{}
          \DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
          \newenvironment{Schunk}{}{}
          \newcommand{\Sconcordance}[1]{%
            \ifx\pdfoutput\undefined%
              \csname newcount\endcsname\pdfoutput\fi%
              \ifcase\pdfoutput\special{##1}%
            \else%
              \begingroup%
              \pdfcompresslevel=0%
              \immediate\pdfobj stream{##1}%
              \pdfcatalog{/SweaveConcordance \the\pdflastobj\space 0 R}%
              \endgroup%
            \fi}
        }
        \fi
        \usepackage{tikz}
EndPreamble

Style Chunk
        Category              Sweave
        LatexType             Paragraph
        LatexName             dummy
        AlignPossible         Block, Left, Right, Center
        TopSep                0.7
        BottomSep             0.7
        NewLine               0
        FreeSpacing           1
        PassThru              1
        ParbreakIsNewline     1
        Spellcheck            0
        TextFont
          Color               latex
          Family              Typewriter
        EndFont
End

Style Scrap
        ObsoletedBy           Chunk
End

InsetLayout "Flex:Sweave Options"
        LabelString           "Sweave opts"
        LatexType             Command
        LaTexName             SweaveOpts
        LyXType               Custom
        Decoration            Classic
        Font
          Color               latex
          Family              typewriter
        EndFont
        LabelFont
          Color               latex
          Size                Small
        EndFont
        MultiPar              false
        PassThru              1
        ParbreakIsNewline     1
        Spellcheck            0
        FreeSpacing           true
        ForceLTR              true
End

InsetLayout "Flex:S/R expression"
        LabelString           "S/R expr"
        LatexType             Command
        LaTexName             Sexpr
        LyXType               Custom
        Decoration            Conglomerate
        Font
          Color               latex
          Family              typewriter
        EndFont
        LabelFont
          Color               latex
          Size                Small
        EndFont
        MultiPar              false
        PassThru              1
        ParbreakIsNewline     1
        Spellcheck            0
        FreeSpacing           true
        ForceLTR              true
End

InsetLayout "Flex:Sweave Input File"
        LabelString           "Sweave Input File"
        LatexType             Command
        LaTexName             SweaveInput
        LyXType               Custom
        Decoration            Classic
        Font
          Color               latex
          Family              typewriter
        EndFont
        LabelFont
          Color               latex
          Size                Small
        EndFont
        MultiPar              false
        PassThru              1
        ParbreakIsNewline     1
        Spellcheck            0
        FreeSpacing           true
        ForceLTR              true
End