IQSS vignette now in inst/iqssDemo as Libertinus not universal

inst/iqssDemo/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/iqssDemo/beamerfontthemeiqss.sty

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+\usefonttheme{professionalfonts}
+\RequirePackage{fontspec}
+
+\setmainfont{Libertinus Serif}
+\setsansfont{Libertinus Sans}
+\setmathfont{Libertinus Math}
+\setmonofont{Libertinus Mono}

inst/iqssDemo/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/iqssDemo/iqssDemo.Rmd

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+---
+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]{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