#LyX 2.1 created this file. For more info see http://www.lyx.org/
\lyxformat 474
\begin_document
\begin_header
\textclass beamer
\begin_preamble
\usetheme{PaloAlto}
\end_preamble
\use_default_options true
\begin_modules
knitr
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\end_header

\begin_body

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

<<setup, include=FALSE>>=
\end_layout

\begin_layout Plain Layout

library(knitr)
\end_layout

\begin_layout Plain Layout

opts_chunk$set(fig.path='figure/beamer-',fig.align='center',fig.show='hold',size='f
ootnotesize')
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

\begin_layout Title
\begin_inset Argument 1
status collapsed

\begin_layout Plain Layout
knitr, Beamer, and FragileFrame
\end_layout

\end_inset

A Minimal Demo of knitr with Beamer and Fragile Frames
\end_layout

\begin_layout Author
Yihui Xie
\begin_inset Foot
status open

\begin_layout Plain Layout
I thank Richard E.
 Goldberg for providing this demo.
\end_layout

\end_inset


\end_layout

\begin_layout Frame
\begin_inset Argument 4
status open

\begin_layout Plain Layout
Background
\end_layout

\end_inset


\end_layout

\begin_deeper
\begin_layout Itemize
The 
\series bold
knitr
\emph on
 
\series default
\emph default
package allows you to embed R code and figures in LaTeX documents
\end_layout

\begin_deeper
\begin_layout Itemize
It has functionality similar to Sweave but looks nicer and gives you more
 control
\end_layout

\end_deeper
\begin_layout Itemize
If you already have Sweave working in LyX, getting 
\series bold
knitr
\series default
 to work is trivial
\end_layout

\begin_deeper
\begin_layout Enumerate
Install the 
\series bold
knitr
\series default
 package in 
\emph on
R
\end_layout

\begin_layout Enumerate
Read 
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status collapsed

\begin_layout Plain Layout

https://yihui.name/knitr/demo/lyx/
\end_layout

\end_inset


\end_layout

\end_deeper
\begin_layout Itemize
If you use Sweave or 
\series bold
knitr
\series default
 with Beamer in LyX, you must use the
\emph on
 FragileFrame
\emph default
 environment for the frames that contain R code chunks.
 Let's see if 
\series bold
knitr
\series default
 works with Beamer in this small demo.
 
\end_layout

\end_deeper
\begin_layout Section
First Test
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status open

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First Test
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\begin_deeper
\begin_layout Standard
OK, let's get started with just some text:
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\begin_layout Standard
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status open

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<<echo=FALSE,results='hide'>>=
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\begin_layout Plain Layout

# some setup
\end_layout

\begin_layout Plain Layout

options(width=60)  # make the printing fit on the page
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\begin_layout Plain Layout

set.seed(1121)   # make the results repeatable
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\begin_layout Plain Layout

@
\end_layout

\begin_layout Plain Layout

\end_layout

\begin_layout Plain Layout

<<>>= 
\end_layout

\begin_layout Plain Layout

# create some random numbers
\end_layout

\begin_layout Plain Layout

(x=rnorm(20))  
\end_layout

\begin_layout Plain Layout

mean(x);var(x)  
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\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

\begin_layout Standard
BTW, the first element of 
\family typewriter
x
\family default
 is 
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status open

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\backslash
Sexpr{x[1]}
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\end_inset

.
 (Did you notice the use of
\family typewriter
 
\backslash
Sexpr{}
\family default
?)
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\end_deeper
\begin_layout Section
Second Test
\end_layout

\begin_layout FragileFrame
\begin_inset Argument 4
status open

\begin_layout Plain Layout
Second Test
\end_layout

\end_inset


\end_layout

\begin_deeper
\begin_layout Standard
Text is nice but let's see what happens if we make a couple of plots in
 our chunk:
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

<<boring-plots,fig.width=4,fig.height=4,out.width='.45
\backslash

\backslash
linewidth'>>=
\end_layout

\begin_layout Plain Layout

par(las=1,mar=c(4,4,.1,.1))  # tick labels direction
\end_layout

\begin_layout Plain Layout

boxplot(x) 
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\begin_layout Plain Layout

hist(x,main='',col="blue",probability=TRUE) 
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\begin_layout Plain Layout

lines(density(x),col="red")
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

\end_deeper
\begin_layout Section
The Big Question
\end_layout

\begin_layout Frame
\begin_inset Argument 4
status open

\begin_layout Plain Layout
The Big Question
\end_layout

\end_inset


\end_layout

\begin_deeper
\begin_layout Standard
Do the above chunks work? You should be able to compile the LyX document
 and get a nice-looking PDF slide presentation.
 If not, time to double-check everything...
\end_layout

\end_deeper
\end_body
\end_document
