Beamer Rmarkdown, changing slide count for backup slides

Question

I am trying to implement this question but in an Rmarkdown beamer presentation:

https://tex.stackexchange.com/questions/70448/dont-count-backup-slides

Can anyone help me out? When I try to put the TeX into the markdown, I get all kinds of errors, often:

    ! Missing \endgroup inserted.
<inserted text> 
                \endgroup 
l.437 \end{frame}

pandoc: Error producing PDF
Error: pandoc document conversion failed with error 43
Execution halted

To give example code, I run this in the latex preamble:

\usepackage{appendixnumberbeamer}

Then in the Rmarkdown:

###Slide 1

Text here

###Slide 2

Text here

\appendix

###First extension slide

Text here

####Second Extension Slide

Text here

Answer 1

The package appendixnumberbeamer is breaking the default pandoc template, specifically the section in the following conditional block when section titles exist:

$if(section-titles)$
\AtBeginPart{
  \let\insertpartnumber\relax
  \let\partname\relax
  \frame{\partpage}
}
\AtBeginSection{
  \ifbibliography
  \else
    \let\insertsectionnumber\relax
    \let\sectionname\relax
    \frame{\sectionpage}
  \fi
}
\AtBeginSubsection{
  \let\insertsubsectionnumber\relax
  \let\subsectionname\relax
  \frame{\subsectionpage}
}
$endif$

You could choose to modify the template to suit your needs, you can find a copy with the command pandoc -D beamer. Then include the template (.tex) in the YAML of your rmarkdown document.

I offer a more simple solution, if you do not want to muck around too much with the template to suit your specific needs. That is to make minor changes to the template and manually set the frame counter for the last 'normal' slide and first of your appendix.

my_header.tex

I've included lipsum to make the example more complete, though not required.

\usepackage{appendixnumberbeamer}
\usepackage{lipsum}

my_template.tex

\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(handout)$handout,$endif$$if(colorlinks)$dvipsnames,$endif$$if(beamer)$ignorenonframetext,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}
\setbeamertemplate{caption}[numbered]
\setbeamertemplate{caption label separator}{: }
\setbeamercolor{caption name}{fg=normal text.fg}
\beamertemplatenavigationsymbols$if(navigation)$$navigation$$else$empty$endif$
$if(fontfamily)$
\usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
$else$
\usepackage{lmodern}
$endif$
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
  \usepackage[utf8]{inputenc}
$if(euro)$
  \usepackage{eurosym}
$endif$
\else % if luatex or xelatex
  \ifxetex
    \usepackage{mathspec}
  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
$for(fontfamilies)$
  \newfontfamily{$fontfamilies.name$}[$fontfamilies.options$]{$fontfamilies.font$}
$endfor$
$if(euro)$
  \newcommand{\euro}{€}
$endif$
$if(mainfont)$
    \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
$endif$
$if(sansfont)$
    \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
$endif$
$if(monofont)$
    \setmonofont[Mapping=tex-ansi$if(monofontoptions)$,$for(monofontoptions)$$monofontoptions$$sep$,$endfor$$endif$]{$monofont$}
$endif$
$if(mathfont)$
    \setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
$endif$
$if(CJKmainfont)$
    \usepackage{xeCJK}
    \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
$endif$
\fi
$if(theme)$
\usetheme[$for(themeoptions)$$themeoptions$$sep$,$endfor$]{$theme$}
$endif$
$if(colortheme)$
\usecolortheme{$colortheme$}
$endif$
$if(fonttheme)$
\usefonttheme{$fonttheme$}
$endif$
$if(mainfont)$
\usefonttheme{serif} % use mainfont rather than sansfont for slide text
$endif$
$if(innertheme)$
\useinnertheme{$innertheme$}
$endif$
$if(outertheme)$
\useoutertheme{$outertheme$}
$endif$
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
$if(lang)$
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
$if(babel-newcommands)$
  $babel-newcommands$
$endif$
\else
  \usepackage{polyglossia}
  \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
$for(polyglossia-otherlangs)$
  \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
$endfor$
\fi
$endif$
\newif\ifbibliography
$if(natbib)$
\usepackage{natbib}
\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
$endif$
$if(biblatex)$
\usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex}
$for(bibliography)$
\addbibresource{$bibliography$}
$endfor$
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
$endif$
\hypersetup{
$if(title-meta)$
            pdftitle={$title-meta$},
$endif$
$if(author-meta)$
            pdfauthor={$author-meta$},
$endif$
$if(keywords)$
            pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
$endif$
$if(colorlinks)$
            colorlinks=true,
            linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
            citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
            urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
$else$
            pdfborder={0 0 0},
$endif$
            breaklinks=true}
\urlstyle{same}  % don't use monospace font for urls
$if(verbatim-in-note)$
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$if(listings)$
\usepackage{listings}
$endif$
$if(lhs)$
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(tables)$
\usepackage{longtable,booktabs}
\usepackage{caption}
% These lines are needed to make table captions work with longtable:
\makeatletter
\def\fnum@table{\tablename~\thetable}
\makeatother
$endif$
$if(graphics)$
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight0.8\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
$endif$

% Prevent slide breaks in the middle of a paragraph:
\widowpenalties 1 10000
\raggedbottom

% comment out the breaking section of the standard template
%$if(section-titles)$
%\AtBeginPart{
%  \let\insertpartnumber\relax
%  \let\partname\relax
%  \frame{\partpage}
%}
%\AtBeginSection{
%  \ifbibliography
%  \else
%    \let\insertsectionnumber\relax
%    \let\sectionname\relax
%    \frame{\sectionpage}
%  \fi
%}
%\AtBeginSubsection{
%  \let\insertsubsectionnumber\relax
%  \let\subsectionname\relax
%  \frame{\subsectionpage}
%}
%$endif$

$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
$endif$
$if(strikeout)$
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
$endif$
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
$if(numbersections)$
\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
$else$
\setcounter{secnumdepth}{0}
$endif$
$if(dir)$
\ifxetex
  % load bidi as late as possible as it modifies e.g. graphicx
  $if(latex-dir-rtl)$
  \usepackage[RTLdocument]{bidi}
  $else$
  \usepackage{bidi}
  $endif$
\fi
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \TeXXeTstate=1
  \newcommand{\RL}[1]{\beginR #1\endR}
  \newcommand{\LR}[1]{\beginL #1\endL}
  \newenvironment{RTL}{\beginR}{\endR}
  \newenvironment{LTR}{\beginL}{\endL}
\fi
$endif$
$for(header-includes)$
$header-includes$
$endfor$

$if(title)$
\title{$title$}
$endif$
$if(subtitle)$
\subtitle{$subtitle$}
$endif$
$if(author)$
\author{$for(author)$$author$$sep$ \and $endfor$}
$endif$
$if(institute)$
\institute{$for(institute)$$institute$$sep$ \and $endfor$}
$endif$
\date{$date$}
$if(titlegraphic)$
\titlegraphic{\includegraphics{$titlegraphic$}}
$endif$
$if(logo)$
\logo{\includegraphics{$logo$}}
$endif$

\begin{document}
$if(title)$
\frame{\titlepage}
$endif$

$for(include-before)$
$include-before$

$endfor$
$if(toc)$
\begin{frame}
\tableofcontents[hideallsubsections]
\end{frame}

$endif$
$body$

$if(natbib)$
$if(bibliography)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\begin{frame}[allowframebreaks]{$biblio-title$}
\bibliographytrue
\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
\end{frame}

$endif$
$endif$
$if(biblatex)$
\begin{frame}[allowframebreaks]{$biblio-title$}
\bibliographytrue
\printbibliography[heading=none]
\end{frame}

$endif$
$for(include-after)$
$include-after$

$endfor$
\end{document}

my_rmarkdown.Rmd

---
output:
  beamer_presentation:
    theme: Madrid
    includes:
      in_header: my_header.tex
    template: my_template.tex
---

### Slide 1

\lipsum[1]

### Slide 2

\lipsum[2]
\appendix
\setcounter{framenumber}{2}

### First extension slide

\setcounter{framenumber}{1}
\lipsum[3]

### Second Extension Slide

\lipsum[4]

This will give you page numbering 1/2, 2/2, 1/2, 2/2.