Browse Source

updated vignettes, skeleton and manual page

pull/4/head
Dirk Eddelbuettel 3 years ago
parent
commit
0134a90819
17 changed files with 770 additions and 160 deletions
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      ChangeLog
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      inst/rmarkdown/templates/metropolis/skeleton/skeleton.Rmd
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      man/metropolis.Rd
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      vignettes/figs/functionalForms.pdf
  11. BIN
      vignettes/figs/phbAr.png
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      vignettes/header.png
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      vignettes/iqss/functionalForms.pdf
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ChangeLog View File

@ -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


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R/binb.R View File

@ -1,11 +1,13 @@
##' A template for RMarkdown-based Beamer presentations in the \sQuote{Metropolis}
##' style by Matthias Vogelgesang and others.
##' Templates for RMarkdown-based Beamer PDF presentations supporting
##' 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
##' yet.
##' @title Binb is not Beamer - Metropolis-themed PDF Presentation
##' Note that not all options and customizations available at the LaTeX
##' level are implemented or supported yet.
##' @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,


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binb.Rproj View File

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

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

@ -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
---
Backup Slides
<!-- \subsection{More stuff} -->
### R Figure
---
The following code generates the plot on the next slide (taken from
`help(bxp)` and modified slightly):
Details
```{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)")
```
---
Text omitted in main talk.
<!-- \subsection{Even more additional material} -->
### 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)")
```
### R Table
A simple `knitr::kable` example:
---
\small
More details
```{r kableEx}
knitr::kable(mtcars[1:5, 1:8],
caption="(Parts of) the mtcars dataset")
```
---
### Resources
Even more details
#### For more information:
- See the [IQSS repository](https://github.com/IQSS/iqss-beamer-theme) for more on the IQSS them
- 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.

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

@ -1,99 +1,102 @@
---
author: Your Name Here and Some Other Person
title: "Something really clever here: \\newline And maybe a second line"
subtitle: You can also have a subtitle
date: 2018-09-15
title: A minimal example
subtitle: With a subtitle
author: Matthias Vogelgesang
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
- Point B
- Point C
# Second Section
# 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)
(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)
## Typography
## Ubuntu and Launchpad
### Briefly
- The packages which can be built (ie not Fira as it needs external fonts
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
- mtheme and metropolis changed a bit since I first used them
- 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.
```
The theme provides sensible defaults to
\emph{emphasize} text, \alert{accent} parts
or show \textbf{bold} results.
_ _ _
In Markdown, you can also use _emphasize_ and **bold**.
```
\LARGE Breakout page
\begin{center}becomes\end{center}
## Using LaTeX Parts: Equations
The theme provides sensible defaults to \emph{emphasize} text,
\alert{accent} parts or show \textbf{bold} results.
### Linear Model
In Markdown, you can also use _emphasize_ and **bold**.
$$ \hat{\beta} = \text{argmin}_{b \in \mathbb{R}} S(b) = \left( \frac{1}{n} \sum_{i=1}^n x_i x_i^T \right)^{-1} \cdot \frac{1}{n} \sum_{i=1}^n x_i y_i $$
or in matrix form
$$ \hat{\beta} = (X^TX)^{-1} X^T y $$
## Math
\begin{equation*}
e = \lim_{n\to \infty} \left(1 + \frac{1}{n}\right)^n
\end{equation*}
## Using LaTeX Parts: Blocks
As one example of falling back into \LaTeX, consider the example of
three different block environments are pre-defined and may be styled
with an optional background color.
## R Figure Example
<!-- this sets the background -->
\metroset{block=fill}
The following code generates the plot on the next slide (taken from
`help(bxp)` and modified slightly):
\begin{block}{Default}
Block content.
\end{block}
```{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)")
```
\begin{alertblock}{Alert}
Block content.
\end{alertblock}
\begin{exampleblock}{Example}
Block content.
\end{exampleblock}
## 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)")
```
## Finally
## R Table Example
A simple `knitr::kable` example:
### Going Forward
```{r kableEx}
knitr::kable(mtcars[1:5, 1:8],
caption="(Parts of) the mtcars dataset")
```
- Questions etc: Open issue tickets [at the GitHub repo](https://github.com/eddelbuettel/samples-rmarkdown-metropolis/issues)
- Pull requests welcome for bug fixes, extensions, examples, ...
## 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.

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man/metropolis.Rd View File

@ -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}
style by Matthias Vogelgesang and others.
Templates for RMarkdown-based Beamer PDF presentations supporting
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
yet.
Note that not all options and customizations available at the LaTeX
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


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vignettes/beamercolorthemeiqss.sty View File

@ -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>

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

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% 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:

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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]{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

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

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