#LyX 2.0 created this file. For more info see http://www.lyx.org/
\lyxformat 413
\begin_document
\begin_header
\textclass article
\use_default_options true
\begin_modules
knitr
\end_modules
\maintain_unincluded_children false
\language english
\language_package none
\inputencoding default
\fontencoding global
\font_roman palatino
\font_sans default
\font_typewriter default
\font_default_family default
\use_non_tex_fonts false
\font_sc true
\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 default
\spacing single
\use_hyperref true
\pdf_bookmarks true
\pdf_bookmarksnumbered true
\pdf_bookmarksopen true
\pdf_bookmarksopenlevel 2
\pdf_breaklinks false
\pdf_pdfborder false
\pdf_colorlinks false
\pdf_backref false
\pdf_pdfusetitle true
\pdf_quoted_options "pdfstartview={XYZ null null 1}"
\papersize default
\use_geometry true
\use_amsmath 1
\use_esint 1
\use_mhchem 1
\use_mathdots 1
\cite_engine basic
\use_bibtopic false
\use_indices false
\paperorientation portrait
\suppress_date false
\use_refstyle 1
\index Index
\shortcut idx
\color #008000
\end_index
\leftmargin 2.5cm
\topmargin 2.5cm
\rightmargin 2.5cm
\bottommargin 2.5cm
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\paragraph_indentation default
\quotes_language english
\papercolumns 1
\papersides 1
\paperpagestyle default
\listings_params "language=R"
\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, cache=FALSE>>=
\end_layout

\begin_layout Plain Layout

library(knitr)
\end_layout

\begin_layout Plain Layout

opts_chunk$set(fig.path = 'figure/listings-')
\end_layout

\begin_layout Plain Layout

options(formatR.arrow = TRUE)
\end_layout

\begin_layout Plain Layout

render_listings()
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

\begin_layout Title
Using listings with knitr
\end_layout

\begin_layout Author
Yihui Xie
\end_layout

\begin_layout Standard
To use the 
\series bold
listings
\series default
 package with 
\series bold
knitr
\series default
, all you need to do is to call a function in your first setup chunk (that
 chunk should be hidden from the output with 
\family typewriter
include=FALSE
\family default
 and should not be cached):
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

% I just want to echo the 2nd line
\end_layout

\begin_layout Plain Layout

<<setup, echo=2>>=
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

\begin_layout Standard
This function modifies the output hooks and header information so that the
 output is written in 
\series bold
listings
\series default
 environments, which are kindly provided by Frank Harrell and can be found
 in 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

https://github.com/yihui/knitr/blob/master/inst/misc/Sweavel.sty
\end_layout

\end_inset

.
 Of course you have to install the 
\series bold
listings
\series default
 package if your LaTeX toolset does not include this package.
\end_layout

\begin_layout Standard
Now we can see how the results look like with our new settings:
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

<<boring-random>>=
\end_layout

\begin_layout Plain Layout

set.seed(1121)  # for reproducibility
\end_layout

\begin_layout Plain Layout

options(width=85)
\end_layout

\begin_layout Plain Layout

x=rnorm(20)
\end_layout

\begin_layout Plain Layout

x
\end_layout

\begin_layout Plain Layout

mean(x)
\end_layout

\begin_layout Plain Layout

sqrt(-1)  # this will give you a warning message
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

\begin_layout Standard
Another chunk:
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

<<rgl-hook-demo,eval=FALSE>>=
\end_layout

\begin_layout Plain Layout

hook_rgl = function(before, options, envir) {
\end_layout

\begin_layout Plain Layout

    ## after a chunk has been evaluated
\end_layout

\begin_layout Plain Layout

    if (before || !require('rgl') || rgl.cur() == 0) return()  # no active
 device
\end_layout

\begin_layout Plain Layout

    name = paste(valid_prefix(options$fig.path), options$label, sep = '')
\end_layout

\begin_layout Plain Layout

    par3d(windowRect = 100 + options$dpi * c(0, 0, options$width, options$height
))
\end_layout

\begin_layout Plain Layout

    Sys.sleep(.05) # need time to respond to window size change
\end_layout

\begin_layout Plain Layout

\end_layout

\begin_layout Plain Layout

    fmt = opts_knit$get('out.format')
\end_layout

\begin_layout Plain Layout

    if (fmt %in% c('html', 'markdown', 'gfm', 'jekyll')) options$dev = 'png'
\end_layout

\begin_layout Plain Layout

\end_layout

\begin_layout Plain Layout

    ## support 3 formats: eps, pdf and png (default)
\end_layout

\begin_layout Plain Layout

    switch(options$dev,
\end_layout

\begin_layout Plain Layout

           postscript = rgl.postscript(paste(name, '.eps', sep = ''), fmt
 = 'eps'),
\end_layout

\begin_layout Plain Layout

           pdf = rgl.postscript(paste(name, '.pdf', sep = ''), fmt = 'pdf'),
\end_layout

\begin_layout Plain Layout

           rgl.snapshot(paste(name, '.png', sep = ''), fmt = 'png'))
\end_layout

\begin_layout Plain Layout

\end_layout

\begin_layout Plain Layout

    if (fmt == 'html') return(.plot.hook.html(c(name, 'png'), options))
\end_layout

\begin_layout Plain Layout

    if (fmt %in% c('markdown', 'gfm', 'jekyll'))
\end_layout

\begin_layout Plain Layout

        return(.plot.hook.markdown(c(name, 'png'), options))
\end_layout

\begin_layout Plain Layout

\end_layout

\begin_layout Plain Layout

    paste(ifelse(options$align == 'center', '
\backslash

\backslash
centering{}', ''), '
\backslash

\backslash
includegraphics[',
\end_layout

\begin_layout Plain Layout

          sprintf('width=%s', options$out.width), ']{', name, '}
\backslash
n', sep = '')
\end_layout

\begin_layout Plain Layout

}
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

\begin_layout Standard
Well, we can do crazier things with 
\series bold
knitr
\series default
.
 Here we use the 
\family typewriter
fig.cap
\family default
 option to write plots into the 
\family typewriter
figure
\family default
 environment automatically, and the caption is generated from data dynamically
 (see Figure 
\begin_inset ERT
status collapsed

\begin_layout Plain Layout


\backslash
ref{fig:boxplot-ex}
\end_layout

\end_inset

):
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

% set an option first
\end_layout

\begin_layout Plain Layout

<<eval-opts, echo=FALSE>>=
\end_layout

\begin_layout Plain Layout

opts_knit$set(eval.after = 'fig.cap') # evaluate fig.cap after the chunk
\end_layout

\begin_layout Plain Layout

\end_layout

\begin_layout Plain Layout

<<boxplot-ex, fig.height=2, out.width='.8
\backslash

\backslash
linewidth', fig.cap=sprintf('This is a boxplot; the median is %.2f.', median(x))>>=
\end_layout

\begin_layout Plain Layout

par(mar=c(4,4,.1,.1))
\end_layout

\begin_layout Plain Layout

boxplot(x, horizontal=TRUE)
\end_layout

\begin_layout Plain Layout

@
\end_layout

\end_inset


\end_layout

\begin_layout Standard
As we know, 
\family typewriter
figure
\family default
 is a float environment, so it has floated away from the R code to the top
 of this page.
 This should not be surprising to LaTeX users.
\end_layout

\begin_layout Standard
You should be able to compile the TeX document and get a PDF file like this
 one: 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

https://github.com/yihui/knitr/releases/download/doc/knitr-listings.pdf
\end_layout

\end_inset

.
 For more information about out hooks, see 
\begin_inset Flex URL
status collapsed

\begin_layout Plain Layout

https://yihui.org/knitr/hooks/
\end_layout

\end_inset

.
\end_layout

\end_body
\end_document
