added iqss rmarkdown beamer template, added metropolis vignette

.gitignore

@@ -2,3 +2,8 @@
 .Rhistory
 .RData
 .Ruserdata
+vignettes/*_cache
+vignettes/*_files
+vignettes/auto
+*auto/
+*.tar.gz

ChangeLog

@@ -1,10 +1,26 @@
+2018-09-16  Dirk Eddelbuettel  <edd@debian.org>
+
+	* R/binb.R (iqss): Process IQSS theme (translated to Markdown)
+
+	* inst/rmarkdown/templates/iqss/skeleton/: Style files adapted
+	from IQSS LaTeX example, along with png and pdf inputs used
+	* inst/rmarkdown/templates/iqss/resources/template.tex: Idem
+
+	* inst/rmarkdown/templates/metropolis/resources/template.tex: Switch
+	to rounded parenthesis in natbib
+
+	* vignettes/metropolisDemo.Rmd: Added extended RMarkdown demo
+	* vignettes/metropolis/demo.bib: Demo bibliography
+	* vignettes/metropolis/header.tex: Some extra definitions
+
 2018-09-15  Dirk Eddelbuettel  <edd@debian.org>
 
 	* DESCRIPTION (Version, Date): Initial pre-release version
-	* binb.R (metropolis): Process Metropolis theme
+	* binb.R (metropolis): Process Metropolis (translated to Markdown)
+	* man/metropolis.Rd: Documentation
 	* inst/rmarkdown/templates/metropolis/skeleton/skeleton.Rmd:
 	Example skeleton taken from my samples=rmarkdown-metropolis repo
-	* inst/rmarkdown/templates/metropolis/resources/template.tex):
+	* inst/rmarkdown/templates/metropolis/resources/template.tex:
 	Generic template for beamer presentations
 
 

DESCRIPTION

@@ -16,4 +16,4 @@ Imports: rmarkdown, knitr
 VignetteBuilder: knitr
 License: GPL (>= 2)
 Encoding: UTF-8
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0

NAMESPACE

@@ -1,3 +1,3 @@
-export("metropolis")
+export("metropolis", "iqss")
 import("knitr")
 import("rmarkdown")

R/binb.R

@@ -18,7 +18,7 @@
 ##' @param keep_tex A logical variable defaulting to \code{FALSE}.
 ##' @param latex_engine A character variable defaulting to \dQuote{xelatex}.
 ##' @param citation_package An optional character variable with possible value
-##' \dQuote{none} (the default), \dQuote{natbib} or \dQuote{biblatex}.
+##' \dQuote{none}, \dQuote{natbib} (the default), or \dQuote{biblatex}.
 ##' @param includes An optional character variable defaulting to \code{NULL}.
 ##' @param md_extensions An optional character variable defaulting to \code{NULL}.
 ##' @param pandoc_args An optional character variable defaulting to \code{NULL}.
@@ -42,7 +42,6 @@ metropolis <- function(toc = FALSE,
                        md_extensions = NULL,
                        pandoc_args = NULL) {
 
-
     template <- system.file("rmarkdown", "templates", "metropolis",
                             "resources", "template.tex",
                             package="binb")
@@ -69,6 +68,58 @@ metropolis <- function(toc = FALSE,
 
 }
 
+##' @rdname metropolis
+iqss <- function(toc = FALSE,
+                 slide_level = 3,
+                 incremental = FALSE,
+                 fig_width = 10,
+                 fig_height = 7,
+                 fig_crop = TRUE,
+                 fig_caption = TRUE,
+                 dev = 'pdf',
+                 df_print = "default",
+                 fonttheme = "default",
+                 highlight = "haddock",
+                 keep_tex = FALSE,
+                 latex_engine = "xelatex",
+                 citation_package = c("none", "natbib", "biblatex"),
+                 includes = NULL,
+                 md_extensions = NULL,
+                 pandoc_args = NULL) {
+
+    for (f in c("beamercolorthemeiqss.sty", "beamerfontthemeiqss.sty",
+                "beamerthemeiqss.sty", "header.png", "figs/"))
+        if (!file.exists(f))
+            file.copy(system.file("rmarkdown", "templates", "iqss", "skeleton", f, package="binb"),
+                      ".", recursive=TRUE)
+
+    template <- system.file("rmarkdown", "templates", "iqss",
+                            "resources", "template.tex",
+                            package="binb")
+
+    rmarkdown::beamer_presentation(template = template,
+                                   toc = toc,
+                                   slide_level = slide_level,
+                                   incremental = incremental,
+                                   fig_width = fig_width,
+                                   fig_height = fig_height,
+                                   fig_crop = fig_crop,
+                                   fig_caption = fig_caption,
+                                   dev = dev,
+                                   df_print = df_print,
+                                   theme = "iqss",
+                                   fonttheme = fonttheme,
+                                   highlight = highlight,
+                                   keep_tex = keep_tex,
+                                   latex_engine = latex_engine,
+                                   citation_package = citation_package,
+                                   includes = includes,
+                                   md_extensions = md_extensions,
+                                   pandoc_args = pandoc_args)
+
+}
+
+
 # Call rmarkdown::pdf_documet and mark the return value as inheriting pdf_document
 inherit_pdf_document <- function(...) {
     fmt <- rmarkdown::pdf_document(...)

inst/rmarkdown/templates/iqss/resources/template.tex

@@ -0,0 +1,378 @@
+\PassOptionsToPackage{unicode=true}{hyperref} % options for packages loaded elsewhere
+\PassOptionsToPackage{hyphens}{url}
+\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$$sep$,$endfor$]{$fontfamily$}
+$else$
+\usepackage{lmodern}
+$endif$
+\usepackage{amssymb}
+\usepackage{amsmath}
+\usepackage{ifxetex,ifluatex}
+\usepackage{fixltx2e} % provides \textsubscript
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \usepackage[$if(fontenc)$$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)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
+  $if(babel-newcommands)$
+    $babel-newcommands$
+  $endif$
+\else
+  \usepackage{polyglossia}
+  \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
+  $for(polyglossia-otherlangs)$
+    \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
+  $endfor$
+\fi
+$endif$
+
+\newif\ifbibliography
+$if(natbib)$
+  \usepackage[round]{natbib}
+  \bibliographystyle{$if(biblio-style)$$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}  % 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
+
+$if(section-titles)$
+  \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
+$endif$
+
+$for(header-includes)$
+  $header-includes$
+$endfor$
+
+%% IQSS overrides
+\iqsssectiontitle{Outline}
+
+\AtBeginSection[]{
+  \title{\insertsectionhead}
+  {
+    \definecolor{white}{rgb}{0.776,0.357,0.157}
+    \definecolor{iqss@orange}{rgb}{1,1,1}
+    \ifnum \insertmainframenumber > \insertframenumber
+    \frame{
+      \frametitle{\iqsssectiontitleheader}
+      \tableofcontents[currentsection]
+    }
+    \else
+    \frame{
+      \frametitle{Backup Slides}
+      \tableofcontents[sectionstyle=shaded/shaded,subsectionstyle=shaded/shaded/shaded]
+    }
+    \fi
+  }
+}
+
+\AtBeginSubsection[]{}
+
+%% 
+
+
+$if(title)$
+  \title[$shorttitle$]{$title$}
+$endif$
+
+$if(subtitle)$
+  \subtitle{$subtitle$}
+$endif$
+
+$if(author)$
+  \author[
+    $if(short-author)$
+    $for(short-author)$$short-author$$sep$ \and $endfor$
+  $else$
+    $for(author)$$author$$sep$ \and $endfor$
+  $endif$
+  ]{$for(author)$$author$$sep$ \and $endfor$}
+$endif$
+
+$if(institute)$
+  \institute[
+  $if(short-institute)$
+    $for(short-institute)$$short-institute$$sep$ \and $endfor$
+  $endif$
+  ]{
+  $if(department)$
+    $for(department)$$department$$sep$ \and $endfor$ \\
+  $endif$
+  $for(institute)$$institute$$sep$ \and $endfor$
+  $if(email)$
+    \\ $for(email)$ \href{mailto:$email$}{\nolinkurl{$email$}}$sep$ \and $endfor$
+  $endif$
+  }
+$endif$
+
+\date[
+  $if(short-date)$
+    $short-date$
+  $else$
+    $date$
+  $endif$]{
+  $if(date)$
+    $date$
+    $if(license)$
+      \\ \vspace{5mm}
+    $endif$
+  $endif$
+  $if(license)$
+    {\scriptsize $license$}
+  $endif$
+}
+
+\begin{document}
+
+% Hide progress bar and footline on titlepage
+$if(title)$
+  \begin{frame}[plain]
+  \titlepage
+  \end{frame}
+$endif$
+
+$for(include-before)$
+  $include-before$
+$endfor$
+
+$if(toc)$
+  \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}

inst/rmarkdown/templates/iqss/skeleton/beamercolorthemeiqss.sty

@@ -0,0 +1,236 @@
+% Modified from beamerclorthemedefault.sty.
+% Original work Copyright 2007 by Till Tantau
+% Copyright 2012,2015 by Vedran Mileti\'c, Joseph Wright
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Public License.
+%
+
+\RequirePackage{listings}
+
+\mode<presentation>
+
+% - Main color BLUE (Title, bullets, arrows)
+% - First accent ORANGE (math, or RED)
+% - Second accent PURPLE
+% - Third accent GREEN
+% - Fourth accent RED
+% - Fifth accent YELLOW
+
+%        red green  blue
+%Orange  0.776 0.357 0.157
+%Blue    0.208 0.380 1.000
+%Purple  0.471 0.000 0.471
+%Yellow  0.808 0.616 0.133
+%Green   0.341 0.553 0.090
+
+\definecolor{iqss@orange}{rgb}{0.776,0.357,0.157}
+\definecolor{iqss@blue}{rgb}{0.19,0.55,0.91}
+\definecolor{iqss@purple}{rgb}{0.471, 0.000 0.471}
+\definecolor{iqss@yellow}{rgb}{0.808, 0.616 0.133}
+\definecolor{iqss@green}{rgb}{0.341, 0.553 0.090}
+\definecolor{iqss@red}{rgb}{0.65, 0.11 0.19}
+\definecolor{iqss@gray}{rgb}{0.95,0.95,0.95}
+
+\lstset{ %
+  basicstyle=\ttfamily\footnotesize,
+  backgroundcolor=\color{iqss@gray},
+  commentstyle=\color{iqss@green},
+  keywordstyle=\color{iqss@blue},
+  stringstyle=\color{iqss@purple},
+  keepspaces=true,
+  showspaces=false,
+  showstringspaces=false,
+  showtabs=false
+}
+
+\newcommand<>{\alertb}[1]{\setbeamercolor{alerted text}{fg=iqss@red}%
+  \begin{alertenv}#2\relax#1\end{alertenv}%
+  \setbeamercolor{alerted text}{fg=iqss@blue}%
+}
+\newcommand<>{\alertc}[1]{\setbeamercolor{alerted text}{fg=iqss@green}%
+  \begin{alertenv}#2\relax#1\end{alertenv}%
+  \setbeamercolor{alerted text}{fg=iqss@blue}%
+}
+\newcommand<>{\alertd}[1]{\setbeamercolor{alerted text}{fg=iqss@yellow}%
+  \begin{alertenv}#2\relax#1\end{alertenv}%
+  \setbeamercolor{alerted text}{fg=iqss@blue}%
+}
+\newcommand<>{\alerte}[1]{\setbeamercolor{alerted text}{fg=iqss@purple}%
+  \begin{alertenv}#2\relax#1\end{alertenv}%
+  \setbeamercolor{alerted text}{fg=iqss@blue}%
+}
+
+
+\setbeamercolor{normal text}{fg=black,bg=white}
+\setbeamercolor{alerted text}{fg=iqss@blue}
+\setbeamercolor{example text}{fg=iqss@green}
+
+\setbeamercolor{structure}{fg=iqss@orange}
+
+\setbeamercolor{background canvas}{parent=normal text}
+\setbeamercolor{background}{parent=background canvas}
+
+\setbeamercolor{palette primary}{use=structure,fg=structure.fg}
+\setbeamercolor{palette secondary}{use=structure,fg=structure.fg!75!black}
+\setbeamercolor{palette tertiary}{use=structure,fg=structure.fg!50!black}
+\setbeamercolor{palette quaternary}{fg=black}
+
+\setbeamercolor{palette sidebar primary}{use=normal text,fg=normal text.fg}
+\setbeamercolor{palette sidebar secondary}{use=structure,fg=structure.fg}
+\setbeamercolor{palette sidebar tertiary}{use=normal text,fg=normal text.fg}
+\setbeamercolor{palette sidebar quaternary}{use=structure,fg=structure.fg}
+
+\setbeamercolor{math text}{}
+\setbeamercolor{math text inlined}{parent=math text}
+\setbeamercolor{math text displayed}{parent=math text}
+
+\setbeamercolor{normal text in math text}{}
+
+\setbeamercolor{local structure}{parent=structure}
+
+\setbeamercolor{titlelike}{parent=structure}
+
+%Edd \setbeamercolor{title}{parent=titlelike,fg=white,bg=iqss@orange}
+\setbeamercolor{title}{parent=titlelike,fg=iqss@orange}
+\setbeamercolor{title in head/foot}{parent=palette quaternary}
+\setbeamercolor{title in sidebar}{parent=palette sidebar quaternary}
+
+\setbeamercolor{subtitle}{parent=title}
+
+\setbeamercolor{author}{}
+\setbeamercolor{author in head/foot}{parent=palette primary}
+\setbeamercolor{author in sidebar}{use=palette sidebar tertiary,fg=palette sidebar tertiary.fg}
+
+\setbeamercolor{institute}{}
+\setbeamercolor{institute in head/foot}{parent=palette tertiary}
+\setbeamercolor{institute in sidebar}{use=palette sidebar tertiary,fg=palette sidebar tertiary.fg}
+
+\setbeamercolor{date}{}
+\setbeamercolor{date in head/foot}{parent=palette secondary}
+\setbeamercolor{date in sidebar}{use=palette sidebar tertiary,fg=palette sidebar tertiary.fg}
+
+\setbeamercolor{titlegraphic}{}
+
+\setbeamercolor{part name}{}
+\setbeamercolor{part title}{parent=title}
+
+\setbeamercolor{section name}{}
+\setbeamercolor{section title}{parent=title}
+
+\setbeamercolor{section in toc}{parent=structure}
+\setbeamercolor{section in toc shaded}{parent=section in toc}
+\setbeamercolor{section in head/foot}{parent=palette tertiary}
+\setbeamercolor{section in sidebar}{parent=palette sidebar secondary}
+\setbeamercolor{section in sidebar shaded}{use=section in sidebar,fg=section in sidebar.fg!40!bg}
+\setbeamercolor{section number projected}{parent=item projected}
+
+\setbeamercolor{subsection name}{}
+\setbeamercolor{subsection title}{parent=titlelike}
+
+\setbeamercolor{subsection in toc}{}
+\setbeamercolor{subsection in toc shaded}{parent=subsection in toc}
+\setbeamercolor{subsection in head/foot}{parent=palette secondary}
+\setbeamercolor{subsection in sidebar}{parent=palette sidebar primary}
+\setbeamercolor{subsection in sidebar shaded}{use=subsection in sidebar,fg=subsection in sidebar.fg!40!bg}
+\setbeamercolor{subsection number projected}{parent={subitem projected}}
+
+\setbeamercolor{subsubsection in toc}{parent=subsection in toc}
+\setbeamercolor{subsubsection in toc shaded}{parent=subsubsection in toc}
+\setbeamercolor{subsubsection in head/foot}{parent=subsection in head/foot}
+\setbeamercolor{subsubsection in sidebar}{parent=subsection in sidebar}
+\setbeamercolor{subsubsection in sidebar shaded}{parent=subsection in sidebar shaded}
+\setbeamercolor{subsubsection number projected}{parent=subsubitem projected}
+
+\setbeamercolor{headline}{}
+\setbeamercolor{footline}{}
+
+\setbeamercolor{sidebar}{}
+\setbeamercolor{sidebar left}{parent=sidebar}
+\setbeamercolor{sidebar right}{parent=sidebar}
+
+\setbeamercolor{logo}{parent=palette secondary}
+
+\setbeamercolor{frametitle}{parent=titlelike}
+\setbeamercolor{framesubtitle}{parent=frametitle}
+
+\setbeamercolor{frametitle right}{parent=frametitle}
+
+\setbeamercolor{caption}{}
+\setbeamercolor{caption name}{parent=structure}
+
+\setbeamercolor{button}{use=local structure,bg=local structure.fg!50!bg,fg=white}
+\setbeamercolor{button border}{use=button,fg=button.bg}
+\setbeamercolor{navigation symbols}{use=structure,fg=structure.fg!40!bg}
+\setbeamercolor{navigation symbols dimmed}{use=structure,fg=structure.fg!20!bg}
+\setbeamercolor{mini frame}{parent=section in head/foot}
+
+\setbeamercolor{block body}{}
+\setbeamercolor{block body alerted}{}
+\setbeamercolor{block body example}{}
+\setbeamercolor{block title}{parent=structure,bg=iqss@gray}
+\setbeamercolor{block title alerted}{parent=alerted text,bg=iqss@gray}
+\setbeamercolor{block title example}{parent=example text,bg=iqss@gray}
+
+\setbeamercolor{item}{parent=local structure}
+\setbeamercolor{subitem}{parent=item}
+\setbeamercolor{subsubitem}{parent=subitem}
+
+\setbeamercolor{item projected}{parent=item,use=item,fg=white,bg=item.fg}
+\setbeamercolor{subitem projected}{parent=item projected}
+\setbeamercolor{subsubitem projected}{parent=subitem projected}
+
+\setbeamercolor{enumerate item}{parent=item}
+\setbeamercolor{enumerate subitem}{parent=subitem}
+\setbeamercolor{enumerate subsubitem}{parent=subsubitem}
+
+\setbeamercolor{itemize item}{parent=item}
+\setbeamercolor{itemize subitem}{parent=subitem}
+\setbeamercolor{itemize subsubitem}{parent=subsubitem}
+
+\setbeamercolor{itemize/enumerate body}{}
+\setbeamercolor{itemize/enumerate subbody}{}
+\setbeamercolor{itemize/enumerate subsubbody}{}
+
+\setbeamercolor{description item}{parent=item}
+
+\setbeamercolor{description body}{}
+
+\setbeamercolor{bibliography item}{parent=item}
+
+\setbeamercolor{bibliography entry author}{use=structure,fg=structure.fg}
+\setbeamercolor{bibliography entry title}{use=normal text,fg=normal text.fg}
+\setbeamercolor{bibliography entry location}{use=structure,fg=structure.fg!65!bg}
+\setbeamercolor{bibliography entry note}{use=structure,fg=structure.fg!65!bg}
+
+\setbeamercolor{separation line}{}
+
+\setbeamercolor{upper separation line head}{parent=separation line}
+\setbeamercolor{middle separation line head}{parent=separation line}
+\setbeamercolor{lower separation line head}{parent=separation line}
+
+\setbeamercolor{upper separation line foot}{parent=separation line}
+\setbeamercolor{middle separation line foot}{parent=separation line}
+\setbeamercolor{lower separation line foot}{parent=separation line}
+
+\setbeamercolor{abstract}{}
+\setbeamercolor{abstract title}{parent=structure}
+
+\setbeamercolor{verse}{}
+
+\setbeamercolor{quotation}{}
+\setbeamercolor{quote}{parent=quotation}
+
+%\setbeamercolor{page number in head/foot}{fg=fg!50!bg}
+\setbeamercolor{page number in head/foot}{fg=iqss@orange}
+
+\setbeamercolor{qed symbol}{parent=structure}
+
+\setbeamercolor{note page}{bg=white!90!black, fg=black}
+\setbeamercolor{note title}{bg=white!80!black, fg=black}
+\setbeamercolor{note date}{parent=note title}
+
+\mode
+<all>

inst/rmarkdown/templates/iqss/skeleton/beamerfontthemeiqss.sty

@@ -0,0 +1,7 @@
+\usefonttheme{professionalfonts}
+\RequirePackage{fontspec}
+
+\setmainfont{Libertinus Serif}
+\setsansfont{Libertinus Sans}
+\setmathfont{Libertinus Math}
+\setmonofont{Libertinus Mono}

inst/rmarkdown/templates/iqss/skeleton/beamerthemeiqss.sty

@@ -0,0 +1,123 @@
+% Modified from beamerthemedefault.sty.
+% Original work Copyright 2007 by Till Tantau
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Public License.
+%
+
+% Requirement
+\RequirePackage{tikz}
+%\RequirePackage{amsmath}       % DEdd: side-effects, and loaded later
+%\RequirePackage{unicode-math}  % DEdd: side-effects
+
+\mode<presentation>
+
+\hypersetup{colorlinks=true,allcolors=iqss@orange}
+
+\def \iqsssectiontitleheader {}
+
+\newcommand{\iqsssectiontitle}[1]{
+  \def \iqsssectiontitleheader{#1}
+}
+
+\@ifundefined{insertmainframenumber}
+{%
+  % \insertmainframenumber not defined
+  \newcommand{\insertmainframenumber}{\inserttotalframenumber}
+}
+{%
+  % \insertmainframenumber already defined
+}%
+
+
+%\setbeamertemplate{footline}[frame number]
+\setbeamertemplate{footline}
+{ \usebeamercolor[fg]{page number in head/foot}%
+  \usebeamerfont{page number in head/foot}%
+  \hspace{1em}\insertsectionhead%
+  \hfill%
+  \insertframenumber\,/\,\hyperlinkappendixstart{\insertmainframenumber}
+  \ifnum \thepage = \insertframeendpage{\small .}\else{\phantom{\small .}}\fi
+  \hspace{1em}
+  \vskip2pt%
+}
+
+% Edd
+\titlegraphic{\includegraphics[width=\paperwidth]{header.png}}
+%This works:  \titlegraphic{\includegraphics[width=0.4in]{illinois_logo_tm.eps}}
+
+\setbeamertemplate{title page}
+{
+
+  %  \node[anchor=north west,xshift=-1.2mm,yshift=1.2mm] at (current page.north west){%
+  \begin{tikzpicture}[remember picture,overlay]
+    %\node[anchor=north east] at (current page.north east){%
+    \node[anchor=north west,xshift=-1.2mm,yshift=1.2mm] at (current page.north west){%
+      \noindent\inserttitlegraphic\par
+    };
+  \end{tikzpicture}
+  \vskip1em
+  \vbox{}
+  \begingroup
+  \centering
+  \usebeamercolor[fg]{titlegraphic}
+    \begin{beamercolorbox}[sep=8pt,center]{title}
+      \usebeamerfont{title}\inserttitle\par%
+      \ifx\insertsubtitle\@empty%
+      \else%
+        \vskip0.25em%
+        {\usebeamerfont{subtitle}\usebeamercolor[fg]{subtitle}\insertsubtitle\par}%
+      \fi%
+    \end{beamercolorbox}%
+    \vskip1em\par
+    \begin{beamercolorbox}[sep=8pt,center]{author}
+      \usebeamerfont{author}\insertauthor
+    \end{beamercolorbox}
+    \begin{beamercolorbox}[sep=8pt,center]{institute}
+      \usebeamerfont{institute}\insertinstitute
+    \end{beamercolorbox}
+    \begin{beamercolorbox}[sep=8pt,center]{date}
+      \usebeamerfont{date}\insertdate
+    \end{beamercolorbox}
+  \endgroup
+  \vfill
+}
+
+\setbeamertemplate{navigation symbols}{}
+\setbeamertemplate{blocks}[rounded][shadow=true]
+
+\usefonttheme{iqss}
+\usecolortheme{iqss}
+\useinnertheme{default}
+\useoutertheme{default}
+
+\setbeamertemplate{itemize items}[circle]
+
+\AtBeginSection[]{
+  \title{\insertsectionhead}
+  {
+    \definecolor{white}{rgb}{0.776,0.357,0.157}
+    \definecolor{iqss@orange}{rgb}{1,1,1}
+    \ifnum \insertmainframenumber > \insertframenumber
+    \frame{
+      \frametitle{\iqsssectiontitleheader}
+      \tableofcontents[currentsection]
+    }
+    \else
+    \frame{
+      \frametitle{Backup Slides}
+      \tableofcontents[sectionstyle=shaded/shaded,subsectionstyle=shaded/shaded/shaded]
+    }
+    \fi
+  }
+}
+
+
+\mode
+<all>
+
+% Local Variables:
+% TeX-engine: xetex
+% End:

inst/rmarkdown/templates/iqss/skeleton/skeleton.Rmd

@@ -0,0 +1,243 @@
+---
+author: Gary King and Ista Zahn
+classoption: compress
+fontsize: 12pt
+title: Beamer Class Demonstration
+date: \today
+institute: IQSS 
+output: binb::iqss
+---
+
+
+# Beamer Features
+
+## Some of Gary's Examples
+
+### What's this course about? 
+
+
+::: incremental 
+
+- \alert{Specific statistical methods for many research problems}
+      - How to learn (or create) new methods
+      - Inference: \underline{Using facts you know to learn about
+        facts you don't know}
+- \alert{How to write a publishable scholarly paper}
+- \alert{All the practical tools of research} --- theory,
+    applications, simulation, programming, word processing, plumbing,
+    whatever is useful
+- $\leadsto$ \alert{Outline and class materials:}
+    - \mbox{{\huge\parbox[b][.5in][t]{1in}{\alert{j.mp/G2001}}}
+        $\qquad\qquad$\includegraphics[width=.95in]{figs/phbAr.png}}
+    - The syllabus gives topics, not a weekly plan.
+    - We will go as fast as possible subject to everyone following along
+    - We cover different amounts of material each week
+
+:::
+
+### How much math will you scare us with?
+
+- All math requires two parts: \alertb{proof} and \alertb{concepts \& intuition}
+- Different classes emphasize:
+    - \alert{Baby Stats}: dumbed down proofs, vague intuition
+    - \alert{Math Stats}: rigorous mathematical proofs
+    - \alert{\underline{Practical Stats}}: deep concepts and intuition, proofs when needed
+        - Goal: how to do empirical research, in depth
+        - Use rigorous statistical theory --- when needed
+        - Insure we understand the intuition --- always
+        - Always traverse from theoretical foundations to practical applications
+        - Includes ``how to'' computation
+        - $\leadsto$ Fewer proofs, more concepts, better practical knowledge
+- Do you have the background for this class? 
+
+. . .
+
+\alert{A Test: What's this?
+    \begin{align*}
+      b=(X'X)^{-1}X'y
+    \end{align*} }
+
+
+### Systematic Components: Examples
+
+\includegraphics[width=8cm]{figs/functionalForms}
+
+- \alertb{$E(Y_i) \equiv \mu_i = X_i\beta = \beta_0 +
+      \beta_1X_{1i} +\dots+\beta_kX_{ki}$}
+- \alertc{$\Pr(Y_i=1) \equiv \pi_i =
+      \frac{1}{1+e^{-x_i\beta}}$}
+- \alertd{$V(Y_i)\equiv \sigma_i^2 = e^{x_i\beta}$}
+- Interpretation:
+    - Each is a \alert{class of functional forms}
+    - Set $\beta$ and it picks out one \alert{member of the class}
+    - \alert{$\beta$} in each is an ``effect parameter'' vector,
+      with different meaning
+
+
+### Negative Binomial Derivation
+
+\uncover<+->{Recall:}
+
+\begin{equation*}
+    \uncover<+->{\Pr(A|B)=\frac{\Pr(AB)}{\Pr(B)} \implies 
+        \alertb{\Pr(AB)}=\alerte{\Pr(A|B)}\alertd{\Pr(B)}}
+\end{equation*}
+
+\alertb<1-1>{one}
+\alertc<2-2>{two}
+\alertd<3-3>{three}
+
+\begin{align*}
+  \uncover<+->{\text{NegBin}(y|\phi,\sigma^2) &= \int_0^\infty
+    \alerte{\text{Poisson}(y|\lambda)}
+    \times\alertd{\text{gamma}(\lambda|\phi,\sigma^2)}d\lambda\\}
+  \uncover<+->{&= \int_0^\infty
+    \alertb{\P(y,\lambda|\phi,\sigma^2) }d\lambda\\}
+  \uncover<+->{&=
+    \frac{\Gamma\left(\frac{\phi}{\sigma^2-1}+y_i\right)}
+    {y_i!\Gamma\left(\frac{\phi}{\sigma^2-1}\right)}
+    \left(\frac{\sigma^2-1}{\sigma^2}\right)^{y_i}
+    \left(\sigma^2\right)^{\frac{-\phi}{\sigma^2-1}}}
+\end{align*}
+
+
+# Other Features
+
+## Structural Features
+
+### Structural Features
+
+#### Levels of Structure
+
+- usual \LaTeX\ \textbackslash\ section, \textbackslash\ subsection commands
+- `frame` environments provide slides
+- `block` environments divide slides into logical sections
+- `columns` environments divide slides vertically (example later)
+- overlays (\`a la prosper) change content of slides dynamically
+  
+#### \alertc{Overlay Alerts}
+
+On the first overlay, \alert<1>{this text} is highlighted (or \emph{alerted}).  
+On the second, \alert<2>{this text} is. 
+
+
+### Code blocks
+
+\footnotesize
+
+```r
+# Say hello in R
+hello <- function(name) paste("hello", name)
+```
+ 
+. . .
+
+```python
+# Say hello in Python
+def hello(name):
+return("Hello" + " " + name)
+```
+
+. . .
+
+```haskell
+-- Say hello in Haskell
+hello name = "Hello" ++ " " ++ name
+```
+
+. . .
+
+```c
+/* Say hello in C */
+#include <stdio.h>
+int main()
+{
+  char name[256];
+  fgets(name, sizeof(name), stdin);
+  printf("Hello %s", name);
+  return(0);
+}
+```
+
+\normalsize
+
+
+### Alerts
+
+- First level \alert{alert}
+- Second level \alertb{alert}
+- Third level \alertc{alert}
+- Fourth level \alertd{alert}
+- Fifth level \alerte{alert}
+
+# More Features 
+
+## Blocks
+
+### Other Features
+
+#### Levels of Structure
+
+- Clean, extensively customizable visual style
+- Hyperlinks ([http://github.com/izahn/iqss-beamer-theme](click here_) 
+- No weird scaling prosper
+    - slides are 96~mm~$\times$~128~mm
+    - text is 10-12pt on slide
+    - slide itself magnified with Adobe Reader/xpdf/gv to fill screen
+- pgf graphics framework easy to use
+- include external JPEG/PNG/PDF figures
+- output directly to pdf: no PostScript hurdles
+- detailed User's Manual (with good presentation advice, too)
+
+
+### Theorems and Proofs
+\framesubtitle{The proof uses \textit{reductio ad absurdum}.}
+
+#### Theorem
+There is no largest prime number.
+
+#### Proof
+> - Suppose $p$ were the largest prime number.
+> - Let $q$ be the product of the first $p$ numbers.
+> - Then $q+1$ is not divisible by any of them.
+> - But $q + 1$ is greater than $1$, thus divisible by some prime
+    number not in the first $p$ numbers. \qedhere
+
+### Blocks
+
+#### Normal block
+A \alert{set} consists of elements.
+
+
+#### \alert{Alert block}
+$2=2$.
+
+#### \alertc{Example block}
+The set $\{1,2,3,5\}$ has four elements.
+
+
+# Appendix
+
+---
+
+Backup Slides
+
+<!-- \subsection{More stuff} -->
+
+---
+
+Details
+
+---
+
+Text omitted in main talk.
+
+<!-- \subsection{Even more additional material} -->
+
+---
+
+More details
+
+---
+
+Even more details

inst/rmarkdown/templates/iqss/template.yaml

@@ -0,0 +1,3 @@
+name: Binb is not Beamer - IQSS (pdf)
+description: A custom R Markdown Beamer presentation theme.
+create_dir: true

inst/rmarkdown/templates/metropolis/resources/template.tex

@@ -106,7 +106,7 @@ $endif$
 
 \newif\ifbibliography
 $if(natbib)$
-  \usepackage{natbib}
+  \usepackage[round]{natbib}
   \bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
 $endif$
 $if(biblatex)$

man/metropolis.Rd

@@ -2,14 +2,24 @@
 % Please edit documentation in R/binb.R
 \name{metropolis}
 \alias{metropolis}
+\alias{iqss}
 \title{Binb is not Beamer - Metropolis-themed PDF Presentation}
 \usage{
 metropolis(toc = FALSE, slide_level = 2, incremental = FALSE,
-  fig_width = 10, fig_height = 7, fig_crop = TRUE, fig_caption = TRUE,
-  dev = "pdf", df_print = "default", fonttheme = "default",
-  highlight = "tango", keep_tex = FALSE, latex_engine = "xelatex",
-  citation_package = c("none", "natbib", "biblatex"), includes = NULL,
-  md_extensions = NULL, pandoc_args = NULL)
+  fig_width = 10, fig_height = 7, fig_crop = TRUE,
+  fig_caption = TRUE, dev = "pdf", df_print = "default",
+  fonttheme = "default", highlight = "tango", keep_tex = FALSE,
+  latex_engine = "xelatex", citation_package = c("none", "natbib",
+  "biblatex"), includes = NULL, md_extensions = NULL,
+  pandoc_args = NULL)
+
+iqss(toc = FALSE, slide_level = 3, incremental = FALSE,
+  fig_width = 10, fig_height = 7, fig_crop = TRUE,
+  fig_caption = TRUE, dev = "pdf", df_print = "default",
+  fonttheme = "default", highlight = "haddock", keep_tex = FALSE,
+  latex_engine = "xelatex", citation_package = c("none", "natbib",
+  "biblatex"), includes = NULL, md_extensions = NULL,
+  pandoc_args = NULL)
 }
 \arguments{
 \item{toc}{A logical variable defaulting to \code{FALSE}.}
@@ -39,7 +49,7 @@ metropolis(toc = FALSE, slide_level = 2, incremental = FALSE,
 \item{latex_engine}{A character variable defaulting to \dQuote{xelatex}.}
 
 \item{citation_package}{An optional character variable with possible value
-\dQuote{none} (the default), \dQuote{natbib} or \dQuote{biblatex}.}
+\dQuote{none}, \dQuote{natbib} (the default), or \dQuote{biblatex}.}
 
 \item{includes}{An optional character variable defaulting to \code{NULL}.}
 

vignettes/metropolis/demo.bib

@@ -0,0 +1,43 @@
+@article{Knuth92,
+        author = "D.E. Knuth",
+        title = "Two notes on notation",
+        journal = "Amer. Math. Monthly",
+        volume = "99",
+        year = "1992",
+        pages = "403--422",
+}
+
+@book{ConcreteMath,
+        author = "R.L. Graham and D.E. Knuth and O. Patashnik",
+        title = "Concrete mathematics",
+        publisher = "Addison-Wesley",
+        address = "Reading, MA",
+        year = "1989"
+}
+
+@unpublished{Simpson,
+        author = "H. Simpson",
+        title = "Proof of the {R}iemann {H}ypothesis",
+        note = "preprint (2003), available at
+        \texttt{http://www.math.drofnats.edu/riemann.ps}",
+        year = "2003"
+}
+
+@incollection{Er01,
+        author = "P. Erd{\H o}s",
+        title = "A selection of problems and results in combinatorics",
+        booktitle = "Recent trends in combinatorics (Matrahaza, 1995)",
+        publisher = "Cambridge Univ. Press",
+        address = "Cambridge",
+        pages = "1--6",
+        year = "1995"
+}
+@article{greenwade93,
+    author  = "George D. Greenwade",
+    title   = "The {C}omprehensive {T}ex {A}rchive {N}etwork ({CTAN})",
+    year    = "1993",
+    journal = "TUGBoat",
+    volume  = "14",
+    number  = "3",
+    pages   = "342--351"
+}

vignettes/metropolis/header.tex

@@ -0,0 +1,18 @@
+\usepackage{appendixnumberbeamer}
+
+\usepackage{booktabs}
+\usepackage[scale=2]{ccicons}
+
+\usepackage{pgfplots}
+\usepgfplotslibrary{dateplot}
+
+\usepackage{xspace}
+\newcommand{\themename}{\textbf{\textsc{metropolis}}\xspace}
+
+\metroset{titleformat frame=smallcaps}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:
+

vignettes/metropolisDemo.Rmd

@@ -0,0 +1,398 @@
+---
+author: Matthias Vogelgesang
+title: Metropolis
+subtitle: A modern beamer theme
+institute: Center for modern beamer themes
+date: \today
+output: 
+  binb::metropolis:
+    citation_package: natbib
+    includes:
+      in_header: metropolis/header.tex
+bibliography: metropolis/demo.bib
+biblio-style: abbrvnat
+toc: true
+vignette: >
+  %\VignetteIndexEntry{binb Metropolis Demo}
+  %\VignetteKeywords{binb,vignette}
+  %\VignettePackage{binb}
+  %\VignetteEngine{knitr::rmarkdown}
+---
+
+```{r,setup, include=FALSE}
+knitr::opts_chunk$set(cache=TRUE)
+```
+
+# Introduction
+
+## Metropolis
+
+The \themename theme is a Beamer theme with minimal visual noise inspired
+by the [hsrm](https://github.com/hsrmbeamertheme/hsrmbeamertheme) Beamer
+Theme by Benjamin Weiss.
+
+Enable the theme (in \LaTeX) by loading
+
+```tex
+\documentclass{beamer}
+\usetheme{metropolis}
+```
+
+Note, that you have to have Mozilla's \emph{Fira Sans} font and XeTeX
+installed to enjoy this wonderful typography.
+
+\scriptsize In R you can of course use this package directly, see its documentation.
+
+## Sections
+
+Sections group slides of the same topic
+
+```
+## Elements
+```
+
+for which \themename provides a nice progress indicator \ldots
+
+
+# Title formats
+
+## Metropolis title formats
+
+\themename supports 4 different title formats:
+
+- Regular
+- \textsc{Small caps}
+- \textsc{all small caps}
+- ALL CAPS
+
+They can either be set at once for every title type or individually.
+
+
+<!-- \metroset{titleformat frame=smallcaps} -->
+<!-- ## Small caps -->
+
+<!-- This frame uses the \texttt{smallcaps} title format. -->
+
+<!-- \begin{alertblock}{Potential Problems} -->
+<!-- Be aware that not every font supports small caps. If for example you -->
+<!-- typeset your presentation with pdfTeX and the Computer Modern Sans Serif -->
+<!-- font, every text in small caps will be typeset with the Computer Modern -->
+<!-- Serif font instead.  -->
+<!-- \end{alertblock} -->
+
+
+
+
+<!-- \metroset{titleformat frame=allsmallcaps} -->
+<!-- ## All small caps -->
+
+<!-- This frame uses the \texttt{allsmallcaps} title format. -->
+
+<!-- \begin{alertblock}{Potential problems} -->
+<!-- As this title format also uses small caps you face the same problems as -->
+<!-- with the \texttt{smallcaps} title format. Additionally this format can -->
+<!-- cause some other problems. Please refer to the documentation if you -->
+<!-- consider using it. -->
+
+<!-- As a rule of thumb: just use it for plaintext-only titles. -->
+<!-- \end{alertblock} -->
+
+
+# Elements
+
+## Typography
+
+```
+The theme provides sensible defaults to
+\emph{emphasize} text, \alert{accent} parts
+or show \textbf{bold} results.
+```
+
+\begin{center}becomes\end{center}
+
+The theme provides sensible defaults to \emph{emphasize} text,
+\alert{accent} parts or show \textbf{bold} results.
+
+
+## Font feature test
+
+- Regular
+- \textit{Italic} (also _Italic_)
+- \textsc{Small Caps}
+- \textbf{Bold} (also **Bold**)
+- \textbf{\textit{Bold Italic}} (also **_Italic_**)
+- \textbf{\textsc{Bold Small Caps}}
+- \texttt{Monospace}
+- \texttt{\textit{Monospace Italic}}
+- \texttt{\textbf{Monospace Bold}}
+- \texttt{\textbf{\textit{Monospace Bold Italic}}}
+
+
+## Lists
+\begin{columns}[T,onlytextwidth]
+  \column{0.33\textwidth}
+    Items
+    \begin{itemize}
+      \item Milk \item Eggs \item Potatoes
+    \end{itemize}
+
+  \column{0.33\textwidth}
+    Enumerations
+    \begin{enumerate}
+      \item First, \item Second and \item Last.
+    \end{enumerate}
+
+  \column{0.33\textwidth}
+    Descriptions
+    \begin{description}
+      \item[PowerPoint] Meeh. \item[Beamer] Yeeeha.
+    \end{description}
+\end{columns}
+
+
+## Animation (using \LaTeX\ )
+
+\begin{itemize}[<+- | alert@+>]
+  \item \alert<4>{This is\only<4>{ really} important}
+  \item Now this
+  \item And now this
+\end{itemize}
+
+\bigskip
+\scriptsize This uses \LaTeX\ for aninmation. The next slides uses RMarkdown
+
+## Animation (using RMarkdown, plus one \LaTeX\ trick)
+
+::: incremental 
+
+- \alert<4>{This is\only<4>{ really} important}
+- Now this
+- And now this
+
+:::
+
+
+
+## Figures (using \LaTeX)
+
+\begin{figure}
+  \newcounter{density}
+  \setcounter{density}{20}
+  \begin{tikzpicture}
+    \def\couleur{alerted text.fg}
+    \path[coordinate] (0,0)  coordinate(A)
+                ++( 90:5cm) coordinate(B)
+                ++(0:5cm) coordinate(C)
+                ++(-90:5cm) coordinate(D);
+    \draw[fill=\couleur!\thedensity] (A) -- (B) -- (C) --(D) -- cycle;
+    \foreach \x in {1,...,40}{%
+        \pgfmathsetcounter{density}{\thedensity+20}
+        \setcounter{density}{\thedensity}
+        \path[coordinate] coordinate(X) at (A){};
+        \path[coordinate] (A) -- (B) coordinate[pos=.10](A)
+                            -- (C) coordinate[pos=.10](B)
+                            -- (D) coordinate[pos=.10](C)
+                            -- (X) coordinate[pos=.10](D);
+        \draw[fill=\couleur!\thedensity] (A)--(B)--(C)-- (D) -- cycle;
+    }
+  \end{tikzpicture}
+  \caption{Rotated square from
+  \href{http://www.texample.net/tikz/examples/rotated-polygons/}{texample.net}.}
+\end{figure}
+
+\scriptsize This used a \LaTeX\ feature. All RMarkdown features are also at our disposal.
+
+
+## Tables (using \LaTeX})
+
+\begin{table}
+  \caption{Largest cities in the world (source: Wikipedia)}
+  \begin{tabular}{@{} lr @{}}
+    \toprule
+    City & Population\\
+    \midrule
+    Mexico City & 20,116,842\\
+    Shanghai & 19,210,000\\
+    Peking & 15,796,450\\
+    Istanbul & 14,160,467\\
+    \bottomrule
+  \end{tabular}
+\end{table}
+
+\scriptsize This used a \LaTeX\ feature. All RMarkdown features are also at our disposal.
+
+
+## Blocks
+
+Three different block environments are pre-defined and may be styled with an
+optional background color.
+
+\begin{columns}[T,onlytextwidth]
+  \column{0.5\textwidth}
+    \begin{block}{Default}
+      Block content.
+    \end{block}
+
+    \begin{alertblock}{Alert}
+      Block content.
+    \end{alertblock}
+
+    \begin{exampleblock}{Example}
+      Block content.
+    \end{exampleblock}
+
+  \column{0.5\textwidth}
+
+     \metroset{block=fill}
+
+    \begin{block}{Default}
+      Block content.
+    \end{block}
+
+    \begin{alertblock}{Alert}
+      Block content.
+    \end{alertblock}
+
+    \begin{exampleblock}{Example}
+      Block content.
+    \end{exampleblock}
+
+\end{columns}
+
+\bigskip
+
+\scriptsize The right side uses the `\metroset{block=fill}` option. Blocks
+can also used in Markdown using `###` (if slide-level=2).
+
+
+## Math
+
+\begin{equation*}
+    e = \lim_{n\to \infty} \left(1 + \frac{1}{n}\right)^n
+\end{equation*}
+
+## Line plots
+
+\begin{figure}
+  \begin{tikzpicture}
+    \begin{axis}[
+      mlineplot,
+      width=0.9\textwidth,
+      height=6cm,
+    ]
+
+      \addplot {sin(deg(x))};
+      \addplot+[samples=100] {sin(deg(2*x))};
+
+    \end{axis}
+  \end{tikzpicture}
+\end{figure}
+
+
+## Bar charts
+
+\begin{figure}
+  \begin{tikzpicture}
+    \begin{axis}[
+      mbarplot,
+      xlabel={Foo},
+      ylabel={Bar},
+      width=0.9\textwidth,
+      height=6cm,
+    ]
+
+    \addplot plot coordinates {(1, 20) (2, 25) (3, 22.4) (4, 12.4)};
+    \addplot plot coordinates {(1, 18) (2, 24) (3, 23.5) (4, 13.2)};
+    \addplot plot coordinates {(1, 10) (2, 19) (3, 25) (4, 15.2)};
+
+    \legend{lorem, ipsum, dolor}
+
+    \end{axis}
+  \end{tikzpicture}
+\end{figure}
+
+
+## Quotes
+
+> Veni, Vidi, Vici
+
+## References
+
+Some references \citep{knuth92,ConcreteMath,Simpson,Er01,greenwade93}
+
+\bigskip
+
+\scriptsize `allowframebreaks` is not used or needed, also changed `\cite` to
+`\citep`, and defaulted `natbib` to option `[round]`.
+
+# Conclusion
+
+## Summary
+
+Get the source of this theme and the demo presentation from
+
+\begin{center}\url{https://github.com/matze/mtheme}\end{center}
+
+The theme \emph{itself} is licensed under a [Creative Commons
+Attribution-ShareAlike 4.0 International
+License](http://creativecommons.org/licenses/by-sa/4.0/)
+
+\begin{center}\ccbysa\end{center}
+
+\scriptsize Source and documentation for the RMarkdown variant are at \url{https://github.com/eddelbuettel/binb}.
+
+_ _ _
+
+Questions?
+
+
+
+
+## Backup slides
+
+Sometimes, it is useful to add slides at the end of your presentation to
+refer to during audience questions.
+
+The best way to do this is to include the `appendixnumberbeamer`
+package in your preamble and call `\appendix` before your backup slides.
+
+\themename will automatically turn off slide numbering and progress bars for
+slides in the appendix.
+
+\scriptsize Calling `\appendix` currently leads to an error in when using `binb`.
+
+## R Appendix: R Figure Example
+
+The following code generates the plot on the next slide (taken from
+`help(bxp)` and modified slightly):
+
+```{r pressureCode, eval=FALSE}
+library(stats)
+set.seed(753)
+bx.p <- boxplot(split(rt(100, 4),
+                      gl(5, 20)), plot=FALSE)
+bxp(bx.p, notch = FALSE, boxfill = "lightblue",
+    frame = FALSE, outl = TRUE,
+    main = "Example from help(bxp)")
+```  
+
+## R Appendix: R Figure Example
+  
+```{r pressureFig, echo=FALSE}
+library(stats)
+set.seed(753)
+bx.p <- boxplot(split(rt(100, 4),
+                      gl(5, 20)), plot=FALSE)
+bxp(bx.p, notch = FALSE, boxfill = "lightblue",
+    frame = FALSE, outl = TRUE,
+    main = "Example from help(bxp)")
+```  
+
+## R Appendix: R Table Example
+  
+A simple `knitr::kable` example:  
+
+```{r kableEx}
+knitr::kable(mtcars[1:5, 1:8],
+             caption="(Parts of) the mtcars dataset")
+```