## How to get Beamer Rmarkdown appendixnumberbeamer package to work to not count appendix pages?

I am trying to compile a Beamer presentation in Rmarkdown that counts slides, but doesn't count slides in the appendix. The same question has been asked here before: https://stackoverflow.com/questions/45228938/beamer-rmarkdown-changing-slide-count-for-backup-slides

But the answer given is not satisfying (to me) and I cannot comment on it due to lack of reputation. The reason why is that it gives weird numberings the moment I dont have the same number of main slides as appendix slides.

In standard Latex, one can include \usepackage{appendixnumberbeamer} in the preamble and simple specify \appendix before the backup slides. In Rmarkdown, 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}
}
$endif$


The proposed solution for the previous answer was to basically comment out this code chunk, providing in the YAML both a header that includes the appendixnumberbeamer package and a template.tex file that comments out the code part that throws the error.

\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$$sep,endfor]{documentclass} \setbeamertemplate{caption}[numbered] \setbeamertemplate{caption label separator}{: } \setbeamercolor{caption name}{fg=normal text.fg} \beamertemplatenavigationsymbolsif(navigation)$$navigation$$elseemptyendif if(fontfamily) \usepackage[for(fontfamilyoptions)$$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$$elseT1endif]{fontenc} \usepackage[utf8]{inputenc} if(euro) \usepackage{eurosym} endif \else % if luatex or xelatex \ifxetex \usepackage{mathspec} \else \usepackage{fontspec} \fi \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase} for(fontfamilies) \newfontfamily{fontfamilies.name}[fontfamilies.options]{fontfamilies.font} endfor if(euro) \newcommand{\euro}{€} endif if(mainfont) \setmainfont[for(mainfontoptions)$$mainfontoptions$$sep,endfor]{mainfont} endif if(sansfont) \setsansfont[for(sansfontoptions)$$sansfontoptions$$sep,endfor]{sansfont} endif if(monofont) \setmonofont[Mapping=tex-ansiif(monofontoptions),for(monofontoptions)$$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
$for(bibliography)$
\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$, $endfor$},
$endif$
$if(colorlinks)$
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},
$endif$
\urlstyle{same}  % don't use monospace font for urls
$if(verbatim-in-note)$
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$if(listings)$
\usepackage{listings}
$endif$
$if(lhs)$
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(tables)$
\usepackage{longtable,booktabs}
\usepackage{caption}
% These lines are needed to make table captions work with longtable:
\makeatletter
\def\[email protected]{\tablename~\thetable}
\makeatother
$endif$
$if(graphics)$
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\[email protected]@width>\linewidth\linewidth\else\[email protected]@width\fi}
\def\maxheight{\ifdim\[email protected]@height>\textheight0.8\textheight\else\[email protected]@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}
%}
%$endif$

$if(links-as-notes)$
\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
\end{frame}

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

$endfor$
\end{document}


The main Rmd file is then simply:

## my_rmarkdown.Rmd

---
output:
beamer_presentation:
includes:
template: my_template.tex
---

### Slide 1

\lipsum[1]

### Slide 2

\lipsum[2]
\appendix

### First extension slide

\lipsum[3]

### Second Extension Slide

\lipsum[4]


However, if I change the main Rmd file slightly, I get weird page counts and I don't understand how to use \setcounter{framenumber}{..} to solve it.

Specifically, if I add another Slide 3 in the main part as follows:

---
output:
beamer_presentation:
includes:
template: my_template.tex
---

### Slide 1

\lipsum[1]

### Slide 2

\lipsum[2]

### Slide 3

\lipsum[3]
\appendix

### First extension slide

\lipsum[3]

### Second Extension Slide

\lipsum[4]


I get the slide count 1/2, 2/2, 3/2, 1/2, 2/2. If alternatively, I set the second counter to \setcounter{framenumber}{2}, I get: 1/3, 2/3, 3/3, 2/3, 3/3. This is slightly better since the main slides are at least correct. But I am still wondering whether there exists a way to get both main and appendix slide numbering to work correctly? In general, whenever the number of appendix slides and number of main slides are unequal, I only managed to get one of the two counted correctly.

• if your beamer version is new enough, you don't need the appendixnumberbeamer package, instead you can use the build in option \setbeamertemplate{page number in head/foot}[appendixframenumber]

• remove ignorenonframetext from your template

• and place the appendix between frames:

---
output:
beamer_presentation:
includes:
template: my_template.tex
keep_tex: true
---

### Slide 1

\lipsum[1]

### Slide 2

\lipsum[2]

### Slide 3

\lipsum[3]

 {=latex}
\end{frame}
\appendix
\begin{frame}{First extension slide}


\lipsum[3]

### Second Extension Slide

\lipsum[4]