LaTeX/binb
LaTeX
/
binb
mirror of https://github.com/eddelbuettel/binb
1
0
Fork 0
Code Issues Releases Wiki Activity

updated vignettes, skeleton and manual page

This commit is contained in:
Dirk Eddelbuettel 2018-09-18 20:22:22 -05:00
parent 2cff356a9f
commit 0134a90819
17 changed files with 771 additions and 161 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
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

21
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,

1
binb.Rproj
View File

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

122
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
### 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
---
More details
---
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.

139
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
```
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
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.
\begin{center}becomes\end{center}
## 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
- 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
$$ \hat{\beta} = (X^TX)^{-1} X^T y $$
In Markdown, you can also use _emphasize_ and **bold**.
## Using LaTeX Parts: Blocks
## Math
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.
\begin{equation*}
e = \lim_{n\to \infty} \left(1 + \frac{1}{n}\right)^n
\end{equation*}
<!-- this sets the background -->
\metroset{block=fill}
\begin{block}{Default}
Block content.
\end{block}
## R Figure Example
\begin{alertblock}{Alert}
Block content.
\end{alertblock}
The following code generates the plot on the next slide (taken from
`help(bxp)` and modified slightly):
\begin{exampleblock}{Example}
Block content.
\end{exampleblock}
```{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)")
```
## 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)
- Pull requests welcome for bug fixes, extensions, examples, ...
## R Table Example
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.

22
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

236
vignettes/beamercolorthemeiqss.sty Normal file
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>

7
vignettes/beamerfontthemeiqss.sty Normal file
View File

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

123
vignettes/beamerthemeiqss.sty Normal file
View File

@ -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:

BIN
vignettes/figs/functionalForms.pdf Normal file
View File

Binary file not shown.

BIN
vignettes/figs/phbAr.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 4.8 KiB

BIN
vignettes/header.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 16 KiB

BIN
vignettes/iqss/functionalForms.pdf Normal file
View File

Binary file not shown.

BIN
vignettes/iqss/phbAr.png Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 4.8 KiB

248
vignettes/iqssDemo.Rmd Normal file
View File

@ -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

BIN
vignettes/iqssDemo.pdf Normal file
View File

Binary file not shown.

1
vignettes/metropolisDemo.Rmd
View File

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