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#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
\end_modules
\maintain_unincluded_children false
\language english
\language_package none
\inputencoding default
\fontencoding global
\font_roman default
\font_sans default
\font_typewriter default
\font_math auto
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
\graphics default
\default_output_format default
\output_sync 0
\bibtex_command default
\index_command default
\paperfontsize 10
\spacing single
\use_hyperref true
\pdf_bookmarks true
\pdf_bookmarksnumbered false
\pdf_bookmarksopen false
\pdf_bookmarksopenlevel 1
\pdf_breaklinks false
\pdf_pdfborder true
\pdf_colorlinks false
\pdf_backref false
\pdf_pdfusetitle true
\papersize default
\use_geometry true
\use_package amsmath 1
\use_package amssymb 1
\use_package cancel 1
\use_package esint 1
\use_package mathdots 1
\use_package mathtools 1
\use_package mhchem 1
\use_package stackrel 1
\use_package stmaryrd 1
\use_package undertilde 1
\cite_engine basic
\cite_engine_type default
\biblio_style plain
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
\justification true
\use_refstyle 1
\index Index
\shortcut idx
\color #008000
\end_index
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\paragraph_indentation default
\quotes_language english
\papercolumns 1
\papersides 1
\paperpagestyle default
\tracking_changes false
\output_changes false
\html_math_output 0
\html_css_as_file 0
\html_be_strict false
\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
\begin_inset Flex URL
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
\end_layout
\begin_layout FragileFrame
\begin_inset Argument 4
status open
\begin_layout Plain Layout
First Test
\end_layout
\end_inset
\end_layout
\begin_deeper
\begin_layout Standard
OK, let's get started with just some text:
\end_layout
\begin_layout Standard
\begin_inset ERT
status open
\begin_layout Plain Layout
<<echo=FALSE,results='hide'>>=
\end_layout
\begin_layout Plain Layout
# some setup
\end_layout
\begin_layout Plain Layout
options(width=60) # make the printing fit on the page
\end_layout
\begin_layout Plain Layout
set.seed(1121) # make the results repeatable
\end_layout
\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)
\end_layout
\begin_layout Plain Layout
@
\end_layout
\end_inset
\end_layout
\begin_layout Standard
BTW, the first element of
\family typewriter
x
\family default
is
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
Sexpr{x[1]}
\end_layout
\end_inset
.
(Did you notice the use of
\family typewriter
\backslash
Sexpr{}
\family default
?)
\end_layout
\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)
\end_layout
\begin_layout Plain Layout
hist(x,main='',col="blue",probability=TRUE)
\end_layout
\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