updated vignettes, skeleton and manual page

ChangeLog

@@ -1,3 +1,15 @@
+2018-09-18  Dirk Eddelbuettel  <edd@debian.org>
+
+	* vignettes/iqssDemo.Rmd: Added vignette for IQSS, based on skeleton
+
+	* vignettes/*: Addedd required IQSS support files, figures in iqss/
+
+	* inst/rmarkdown/templates/iqss/skeleton/skeleton.Rmd: Updated
+ 	* inst/rmarkdown/templates/metropolis/skeleton/skeleton.Rmd: Idem
+
+	* R/binb.R: Manual page update
+	* man/metropolis.Rd: Idem
+
 2018-09-17  Dirk Eddelbuettel  <edd@debian.org>
 
 	* README.md: Added initial README

R/binb.R

@@ -1,11 +1,13 @@
-##' A template for RMarkdown-based Beamer presentations in the \sQuote{Metropolis}
+##' Templates for RMarkdown-based Beamer PDF presentations supporting
-##' style by Matthias Vogelgesang and others.
+##' the \sQuote{Metropolis} style by Matthias Vogelgesang and others,
+##' and the \sQuote{IQSS} style by Ista Zahn and Gary King.
 ##'
-##' Not all options and customizations available at the LaTeX level are implemented
+##' Note that not all options and customizations available at the LaTeX
-##' yet.
+##' level are implemented or supported yet.
-##' @title Binb is not Beamer - Metropolis-themed PDF Presentation
+##' @title Binb is not Beamer - PDF Presentation Themes
 ##' @param toc A logical variable defaulting to \code{FALSE}.
-##' @param slide_level A numeric variable defaulting to two.
+##' @param slide_level A numeric variable defaulting to two for
+##' \sQuote{Metrpolis} and three for \sQuote{IQSS}.
 ##' @param incremental A logical variable defaulting to \code{FALSE}.
 ##' @param fig_width A numeric variable defaulting to ten.
 ##' @param fig_height A numeric variable defaulting to seven.
@@ -24,6 +26,13 @@
 ##' @param pandoc_args An optional character variable defaulting to \code{NULL}.
 ##' @return RMarkdown content processed for rendering.
 ##' @author Dirk Eddelbuettel
+##' @examples
+##' \dontrun{
+##' library(rmarkdown)
+##' draft("myslides.Rmd", template="metropolis", package="binb", edit=FALSE)
+##' setwd("myslides")       ## template creates a new subdir
+##' render("myslides.Rmd")
+##' }
 metropolis <- function(toc = FALSE,
                        slide_level = 2,
                        incremental = FALSE,

binb.Rproj

@@ -17,3 +17,4 @@ StripTrailingWhitespace: Yes
 
 BuildType: Package
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd

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

@@ -1,8 +1,8 @@
 ---
-author: Gary King and Ista Zahn
+author: Ista Zahn and Gary King
 classoption: compress
 fontsize: 12pt
-title: Beamer Class Demonstration
+title: IQSS Beamer Class Demonstration
 date: \today
 institute: IQSS 
 output: binb::iqss
@@ -15,9 +15,6 @@ output: binb::iqss
 
 ### 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
@@ -33,8 +30,6 @@ output: binb::iqss
     - 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}
@@ -49,9 +44,6 @@ output: binb::iqss
         - 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
@@ -74,53 +66,6 @@ output: binb::iqss
       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
@@ -130,23 +75,17 @@ On the second, \alert<2>{this text} is.
 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>
@@ -157,7 +96,6 @@ int main()
   printf("Hello %s", name);
   return(0);
 }
-```
 
 \normalsize
 
@@ -187,7 +125,7 @@ int main()
 - 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)
+- detailed User Manual (with good presentation advice, too)
 
 
 ### Theorems and Proofs
@@ -215,29 +153,51 @@ $2=2$.
 #### \alertc{Example block}
 The set $\{1,2,3,5\}$ has four elements.
 
+# RMarkdown Examples
 
-# Appendix
+### R Figure 
 
----
+The following code generates the plot on the next slide (taken from
+`help(bxp)` and modified slightly):
 
-Backup Slides
+```{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)")
+```  
 
-<!-- \subsection{More stuff} -->
 
----
+### R Figure 
+  
+```{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)")
+```  
 
-Details
+### R Table 
+  
+A simple `knitr::kable` example:  
 
----
+\small
 
-Text omitted in main talk.
+```{r kableEx}
+knitr::kable(mtcars[1:5, 1:8],
+             caption="(Parts of) the mtcars dataset")
+```
 
-<!-- \subsection{Even more additional material} -->
+### Resources
 
----
+#### For more information:
-
+- See the [IQSS repository](https://github.com/IQSS/iqss-beamer-theme) for more on the IQSS them
-More details
+- See the [RMarkdown repository](https://github.com/rstudio/rmarkdown) for more on RMarkdown
-
+- See the [binb repository](https://github.com/eddelbuettel/binb) for more on binb 
----
+- See the [binb vignettes](https://github.com/eddelbuettel/binb/vignettes) for more examples.
-
-Even more details

inst/rmarkdown/templates/metropolis/skeleton/skeleton.Rmd

@@ -1,99 +1,102 @@
 ---
-author: Your Name Here and Some Other Person
+title: A minimal example
-title: "Something really clever here: \\newline And maybe a second line"
+subtitle: With a subtitle
-subtitle: You can also have a subtitle
+author: Matthias Vogelgesang
-date: 2018-09-15
+date: \today
+institute: Centre for Modern Beamer Themes
 output: binb::metropolis
+fontsize: 12pt
 ---
 
 ```{r,setup, include=FALSE}
 knitr::opts_chunk$set(cache=TRUE)
 ```
 
-# A Section Header
+# First Section
 
-## A Slide Header
+## First Frame
 
-### A Subtitle
+Hello, world!
 
-- Point A
+# Second Section
-- Point B
-- Point C
 
-# Principal Resources
+## Second Frame
 
-## Metropolis
+### Bulleted Lists
+- Element A
+- Element B
+    - B.1
+    - B.2
+- Element C    
 
-### Main Repos
+# Elements
 
-- [Official GitHub Repo of Metropolis](https://github.com/matze/mtheme)
+## Typography
-  (formerly mtheme); older version in TeXLive 
-- [My GitHub Repo for a local Ubuntu package of Metropolis](https://github.com/eddelbuettel/pkg-latex-metropolis) -- formerly mtheme
-- [My GitHub Repo for a local Ubuntu package for the Fira font](https://github.com/eddelbuettel/pkg-fonts-fira) 
 
-## Ubuntu and Launchpad
+```
+The theme provides sensible defaults to
+\emph{emphasize} text, \alert{accent} parts
+or show \textbf{bold} results.
 
-### Briefly
+In Markdown, you can also use _emphasize_ and **bold**.
+```
 
-- The packages which can be built (ie not Fira as it needs external fonts
+\begin{center}becomes\end{center}
-  which we cannot download during build) are
-  [in this repo](https://launchpad.net/~edd/+archive/ubuntu/misc/+packages)
-- If you're not on Ubuntu, it is probably more work to get
-    - Metropolis into your \LaTeX environment
-    - the Fira font into your \LaTeX environment
-- I *did* try without (on plain Ubuntu 16.04) and it _builds_ but looks less
-crisp
-- So for the time being you probably want these fresh from source, or via my
-helpers. YMMV.
 
-## Local Adaption
+The theme provides sensible defaults to \emph{emphasize} text,
+\alert{accent} parts or show \textbf{bold} results.
 
-- mtheme and metropolis changed a bit since I first used them
+In Markdown, you can also use _emphasize_ and **bold**.
-- I started with a local modification I called m2; the package is still in
-the launchpad repo
-- I generally include a file `header.tex` from the YAML for color, font,
-  ... tweaking at the \LaTeX level, but as these are presentation-specific I
-  didn't include any changes here.
-
-_ _ _
-
-\LARGE Breakout page 
-
-## Using LaTeX Parts: Equations
-
-### Linear Model
-
-$$ \hat{\beta} = \text{argmin}_{b \in \mathbb{R}} S(b) = \left( \frac{1}{n} \sum_{i=1}^n x_i x_i^T \right)^{-1} \cdot \frac{1}{n} \sum_{i=1}^n x_i y_i  $$
-or in matrix form
-
-$$ \hat{\beta} = (X^TX)^{-1} X^T y $$
 
 
-## Using LaTeX Parts: Blocks
+## Math
 
-As one example of falling back into \LaTeX, consider the example of
+\begin{equation*}
-three different block environments are pre-defined and may be styled
+    e = \lim_{n\to \infty} \left(1 + \frac{1}{n}\right)^n
-with an optional background color.
+\end{equation*}
 
-<!-- this sets the background -->
-\metroset{block=fill} 
 
-\begin{block}{Default}
+## R Figure Example
-  Block content.
-\end{block}
 
-\begin{alertblock}{Alert}
+The following code generates the plot on the next slide (taken from
-  Block content.
+`help(bxp)` and modified slightly):
-\end{alertblock}
 
-\begin{exampleblock}{Example}
+```{r pressureCode, eval=FALSE}
-  Block content.
+library(stats)
-\end{exampleblock}
+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)")
+```  
 
-## Finally
 
-### Going Forward
+## 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)")
+```  
 
-- Questions etc: Open issue tickets [at the GitHub repo](https://github.com/eddelbuettel/samples-rmarkdown-metropolis/issues)
+## R Table Example
-- Pull requests welcome for bug fixes, extensions, examples, ...
+  
+A simple `knitr::kable` example:  
 
+```{r kableEx}
+knitr::kable(mtcars[1:5, 1:8],
+             caption="(Parts of) the mtcars dataset")
+```
+
+## Resources
+
+### For more information:
+- See the [Metropolis repository](https://github.com/matze/mtheme) for more on Metropolis
+- See the [RMarkdown repository](https://github.com/rstudio/rmarkdown) for more on RMarkdown
+- See the [binb repository](https://github.com/eddelbuettel/binb) for more on binb 
+- See the [binb vignettes](https://github.com/eddelbuettel/binb/vignettes) for more examples.

man/metropolis.Rd

@@ -3,7 +3,7 @@
 \name{metropolis}
 \alias{metropolis}
 \alias{iqss}
-\title{Binb is not Beamer - Metropolis-themed PDF Presentation}
+\title{Binb is not Beamer - PDF Presentation Themes}
 \usage{
 metropolis(toc = FALSE, slide_level = 2, incremental = FALSE,
   fig_width = 10, fig_height = 7, fig_crop = TRUE,
@@ -24,7 +24,8 @@ iqss(toc = FALSE, slide_level = 3, incremental = FALSE,
 \arguments{
 \item{toc}{A logical variable defaulting to \code{FALSE}.}
 
-\item{slide_level}{A numeric variable defaulting to two.}
+\item{slide_level}{A numeric variable defaulting to two for
+\sQuote{Metrpolis} and three for \sQuote{IQSS}.}
 
 \item{incremental}{A logical variable defaulting to \code{FALSE}.}
 
@@ -61,12 +62,21 @@ iqss(toc = FALSE, slide_level = 3, incremental = FALSE,
 RMarkdown content processed for rendering.
 }
 \description{
-A template for RMarkdown-based Beamer presentations in the \sQuote{Metropolis}
+Templates for RMarkdown-based Beamer PDF presentations supporting
-style by Matthias Vogelgesang and others.
+the \sQuote{Metropolis} style by Matthias Vogelgesang and others,
+and the \sQuote{IQSS} style by Ista Zahn and Gary King.
 }
 \details{
-Not all options and customizations available at the LaTeX level are implemented
+Note that not all options and customizations available at the LaTeX
-yet.
+level are implemented or supported yet.
+}
+\examples{
+\dontrun{
+library(rmarkdown)
+draft("myslides.Rmd", template="metropolis", package="binb", edit=FALSE)
+setwd("myslides")       ## template creates a new subdir
+render("myslides.Rmd")
+}
 }
 \author{
 Dirk Eddelbuettel

vignettes/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>

vignettes/beamerfontthemeiqss.sty

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

vignettes/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:

vignettes/iqssDemo.Rmd

@@ -0,0 +1,248 @@
+---
+author: Ista Zahn and Gary King
+classoption: compress
+fontsize: 12pt
+title: IQSS Beamer Class Demonstration
+date: \today
+institute: IQSS 
+output: binb::iqss
+vignette: >
+  %\VignetteIndexEntry{binb IQSS Demo}
+  %\VignetteKeywords{binb,vignette}
+  %\VignettePackage{binb}
+  %\VignetteEngine{knitr::rmarkdown}
+---
+
+
+# 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]{iqss/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]{iqss/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

vignettes/metropolisDemo.Rmd

@@ -396,3 +396,4 @@ A simple `knitr::kable` example:
 knitr::kable(mtcars[1:5, 1:8],
              caption="(Parts of) the mtcars dataset")
 ```
+