demo_alt.lyx

#LyX 2.0 created this file. For more info see http://www.lyx.org/
\lyxformat 413
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knitr
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\begin_body

\begin_layout Title
An example LyX file
\begin_inset Newline newline
\end_inset

Illustrating use of R, bash, and Python code chunks
\end_layout

\begin_layout Author
Christopher Paciorek
\end_layout

\begin_layout Date
August 2015
\end_layout

\begin_layout Chunk

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

\begin_layout Chunk

# include any code here you don't want to show up in the document,
\end_layout

\begin_layout Chunk

# e.g., package and dataset loading
\end_layout

\begin_layout Chunk

require(ggplot2)
\end_layout

\begin_layout Chunk

set.seed(0)
\end_layout

\begin_layout Chunk

# also a good place to set global chunk options
\end_layout

\begin_layout Chunk

library(knitr) # need this for opts_chunk command
\end_layout

\begin_layout Chunk

opts_chunk$set(fig.width = 5, fig.height = 5)
\end_layout

\begin_layout Chunk

# if we wanted chunks by default not to be evaluated
\end_layout

\begin_layout Chunk

# opts_chunk$set(eval = FALSE) 
\end_layout

\begin_layout Chunk

@ 
\end_layout

\begin_layout Section
How to generate a document from this file
\end_layout

\begin_layout Standard
If you open this file in LyX, you can run this document through the 
\emph on
knitr
\emph default
 package for R to generate a PDF using
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{verbatim}
\end_layout

\begin_layout Plain Layout

File -> Export -> PDF (pdflatex)
\end_layout

\begin_layout Plain Layout


\backslash
end{verbatim}
\end_layout

\end_inset

There are other options using that same menu to export in a variety of formats,
 including HTML.
 
\end_layout

\begin_layout Standard
Note that to use code chunks in LyX, you need to enable the knitr module
 in the file.
 After opening a new or existing LyX document, you'll need to go to
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
begin{verbatim}
\end_layout

\begin_layout Plain Layout

Document -> Settings -> Modules
\end_layout

\begin_layout Plain Layout


\backslash
end{verbatim}
\end_layout

\end_inset

 and select 
\family typewriter
Rnw (knitr)
\family default
 from the 
\family typewriter
Available
\family default
 list and click on 
\family typewriter
Add
\family default
 to add it to the 
\family typewriter
Selected
\family default
 list.
 Once you do this, you'll see that 
\family typewriter
Chun
\family default
k will show up in the pull-down menu listing the available formats.
 You can then tags lines of code with the 
\family typewriter
Chunk
\family default
 tag, so it gets evaluated as code.
\end_layout

\begin_layout Section
LaTeX
\end_layout

\begin_layout Standard
This document will focus on embedding code and not on standard LaTeX or
 LyX.
 For a quick introduction to LaTeX, including some details on LyX, see 
\begin_inset CommandInset href
LatexCommand href
name "our tutorial"
target "https://github.com/berkeley-scf/tutorial-latex-intro"

\end_inset

.
\end_layout

\begin_layout Standard
The process for producing an output document described in the previous section
 processes the LyX + Sweave format, evaluating the R code chunks, and creating
 a standard LaTeX file with the code snippets and output created by the
 code properly formatted as standard LaTeX, before compiling the LaTeX file
 to PDF.
 
\end_layout

\begin_layout Section
Embedding equations using LaTeX
\end_layout

\begin_layout Standard
LyX is a front end for LaTeX, so you can just use LaTeX math syntax after
 entering math mode.
\end_layout

\begin_layout Standard
Here is an inline equation 
\begin_inset Formula $f(x)=\int f(y,x)dy$
\end_inset

, where I access math mode by entering 
\family typewriter
Ctrl-m
\family default
 (note the lowercase 
\begin_inset Quotes eld
\end_inset

m
\begin_inset Quotes erd
\end_inset

).
\end_layout

\begin_layout Standard
Here's a displayed equation, where I enter math mode by entering 
\family typewriter
Ctrl-M
\family default
 (note the upper-case 
\begin_inset Quotes eld
\end_inset

M
\begin_inset Quotes erd
\end_inset

): 
\begin_inset Formula 
\[
f_{\theta}(x)=\int f_{\theta}(y,x)dy.
\]

\end_inset


\end_layout

\begin_layout Section
Embedding R code
\end_layout

\begin_layout Standard
Here's an R code chunk using standard Sweave formatting but making sure
 to tag the lines using the Chunk tag from the pulldown menu at the left
 of the toolbar near the top of the LyX window.
\end_layout

\begin_layout Chunk

<<r-chunk1>>= 
\end_layout

\begin_layout Chunk

a <- c(7, 3)
\end_layout

\begin_layout Chunk

mean(a)
\end_layout

\begin_layout Chunk

b <- a + 3
\end_layout

\begin_layout Chunk

mean(b)
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
noindent
\end_layout

\end_inset

 Unfortunately, we need to use the 
\emph on
noindent
\emph default
 command (in LaTeX mode) to prevent the text after a chunk from being considered
 as a new paragraph.
 Here's another chunk:
\end_layout

\begin_layout Chunk
\noindent

<<r-chunk2>>= 
\end_layout

\begin_layout Chunk
\noindent

mean(b)
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Standard
When running R code, output is printed interspersed with the code, as one
 would generally want.
 Also, later chunks have access to result from earlier chunks (i.e., state
 is preserved between chunks).
\end_layout

\begin_layout Standard
Let's make a plot
\end_layout

\begin_layout Chunk

<<r-plot, fig.height = 3>>=
\end_layout

\begin_layout Chunk

hist(rnorm(20)) 
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Standard
And here's some inline R code: What is 3 plus 5? 
\begin_inset ERT
status open

\begin_layout Plain Layout


\backslash
Sexpr{3+5}
\end_layout

\end_inset

.
 Note that we need to use the 
\family typewriter

\backslash
Sexpr
\family default
 command within a LaTeX environment, so we need to select the command and
 use the TeX button in the toolbar.
\end_layout

\begin_layout Standard
You have control over whether code in chunks is echoed into the document
 and evaluated using the 
\emph on
include
\emph default
, 
\emph on
echo
\emph default
, and 
\emph on
eval
\emph default
 flags.
\end_layout

\begin_layout Chunk

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

\begin_layout Chunk

cat("this code is evaluated but nothing is printed in the document")
\end_layout

\begin_layout Chunk

library(fields)
\end_layout

\begin_layout Chunk

# fields package should now be loaded for use by later chunks 
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Chunk

<<echo, echo=FALSE>>=
\end_layout

\begin_layout Chunk

cat("this code is not printed in the document but results of evaluating
 the code are printed")
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Chunk

<<eval, eval=FALSE>>=
\end_layout

\begin_layout Chunk

cat("this code is not evaluated but the code itself is printed in the document")
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Standard
Intensive calculations can be saved using the 
\family typewriter
cache=TRUE
\family default
 tag so they don't need to be rerun every time you compile the document.
\end_layout

\begin_layout Chunk

<<slow-step, cache=TRUE>>=
\end_layout

\begin_layout Chunk

mean(rnorm(5e7))
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Section
Embedding bash and Python code
\end_layout

\begin_layout Subsection
bash
\end_layout

\begin_layout Standard
A bash chunk:
\end_layout

\begin_layout Chunk

<<bash-chunk1, engine='bash'>>=
\end_layout

\begin_layout Chunk

df -h 
\end_layout

\begin_layout Chunk

cd /tmp 
\end_layout

\begin_layout Chunk

pwd
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Standard
Unfortunately, output from bash chunks occurs after all the code is printed.
 Also, state is not preserved between chunks.
 
\end_layout

\begin_layout Chunk

<<bash-chunk2, engine='bash'>>=
\end_layout

\begin_layout Chunk

pwd
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Standard
Inline bash code won't work.
\end_layout

\begin_layout Subsection
Embedding Python code
\end_layout

\begin_layout Chunk

<<py-chunk1, engine='python'>>=
\end_layout

\begin_layout Chunk

import numpy as np 
\end_layout

\begin_layout Chunk

x = np.array((3, 5, 7)) 
\end_layout

\begin_layout Chunk

print(x.sum()) 
\end_layout

\begin_layout Chunk

x.min() # note not printed 
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Chunk

<<py-chunk2, engine='python'>>= 
\end_layout

\begin_layout Chunk

try: 
\end_layout

\begin_layout Chunk

	print(x[0]) 
\end_layout

\begin_layout Chunk

except NameError: 
\end_layout

\begin_layout Chunk

	print('x does not exist') 
\end_layout

\begin_layout Chunk

@ 
\end_layout

\begin_layout Standard
As with bash chunks, all output occurs after the code is printed.
 Also, state is not preserved between chunks.
 Finally, you need explicit print statements; you won't see what would normally
 be printed to the screen.
 
\end_layout

\begin_layout Standard
There is no facility for inline Python code evaluation.
\end_layout

\begin_layout Section
Reading code from an external file
\end_layout

\begin_layout Standard
It's sometimes nice to draw code in from a separate file.
 Note that a good place for reading the source file via 
\backslash
texttt{read
\backslash
_chunk()} is in an initial setup chunk at the beginning of the document.
\end_layout

\begin_layout Chunk

<<read-chunk, echo=FALSE>>=
\end_layout

\begin_layout Chunk

library(knitr)
\end_layout

\begin_layout Chunk

read_chunk('demo.R')
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Chunk

<<external_chunk_1>>=
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Chunk

<<external_chunk_2>>=
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Section
Formatting of long lines of code and of output
\end_layout

\begin_layout Subsection
R code
\end_layout

\begin_layout Standard
Having long lines be nicely formatted and other aspects of formatting can
 be a challenge.
 Also, results can differ depending on your output format (e.g., PDF vs.
 HTML).
 In general the code in this section will often overflow the page width
 in PDF but not in HTML, but even in the HTML the line breaks may be awkwardly
 positioned.
 
\end_layout

\begin_layout Chunk

<<r-long>>=
\end_layout

\begin_layout Chunk

b <- "Statistics at UC Berkeley: We are a community engaged in research
 and education in probability and statistics.
 In addition to developing fundamental theory and methodology, we are actively"
\end_layout

\begin_layout Chunk

# Statistics at UC Berkeley: We are a community engaged in research and
 education in probability and statistics.
 In addition to developing fundamental theory and methodology, we are actively
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# this should work but often doesn't
\end_layout

\begin_layout Chunk

cat(b, fill = TRUE)
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

vecLongName = rnorm(100)
\end_layout

\begin_layout Chunk

a = length(mean(5 * vecLongName + vecLongName - exp(vecLongName) + vecLongName
 * vecLongName, na.rm = TRUE))
\end_layout

\begin_layout Chunk

a = length(mean(5 * vecLongName + vecLongName)) # this is a comment that
 goes over the line by a good long ways
\end_layout

\begin_layout Chunk

a = length(mean(5 * vecLongName + vecLongName - exp(vecLongName) + vecLongName,
 na.rm = TRUE)) # this is a comment that goes over the line by a good long
 long long long long long long long ways
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# long output usually is fine
\end_layout

\begin_layout Chunk

rnorm(100)
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Standard
Sometimes you can format things manually for better results.
 You may need to tag the chunk with 
\family typewriter
tidy=FALSE
\family default
, but I have not done that here.
\end_layout

\begin_layout Chunk

<<r-long-tidy>>=
\end_layout

\begin_layout Chunk

# breaking up a string
\end_layout

\begin_layout Chunk

b <- "Statistics at UC Berkeley: We are a community engaged in research
 
\end_layout

\begin_layout Chunk

and education in probability and statistics.
 In addition to developing 
\end_layout

\begin_layout Chunk

fundamental theory and methodology, we are actively"
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# breaking up a comment
\end_layout

\begin_layout Chunk

# Statistics at UC Berkeley: We are a community engaged in research and
\end_layout

\begin_layout Chunk

# education in probability and statistics.
 In addition to developing
\end_layout

\begin_layout Chunk

# fundamental theory and methodology, we are actively
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# breaking up code lines
\end_layout

\begin_layout Chunk

vecLongName = rnorm(100)
\end_layout

\begin_layout Chunk

a <- length(mean(5 * vecLongName + vecLongName - exp(vecLongName) + 
\end_layout

\begin_layout Chunk

vecLongName * vecLongName, na.rm = TRUE))
\end_layout

\begin_layout Chunk

a <- length(mean(5 * vecLongName + vecLongName)) # this is a comment that
 
\end_layout

\begin_layout Chunk

# goes over the line by a good long ways
\end_layout

\begin_layout Chunk

a <- length(mean(5 * vecLongName + vecLongName - exp(vecLongName) + 
\end_layout

\begin_layout Chunk

vecLongName, na.rm = TRUE)) # this is a comment that goes over the line
\end_layout

\begin_layout Chunk

# by a good long long long long long long long long ways 
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Subsection
bash code
\end_layout

\begin_layout Standard
In bash, we have similar problems with lines overflowing in PDF output,
 but bash allows us to use a backslash to break lines of code.
 However that strategy doesn't help with long lines of output.
 
\end_layout

\begin_layout Chunk

<<bash1, engine='bash'>>=
\end_layout

\begin_layout Chunk

echo "Statistics at UC Berkeley: We are a community engaged in research
 and education in probability and statistics.
 In addition to developing fundamental theory and methodology, we are actively"
 > tmp.txt
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

echo "Second try: Statistics at UC Berkeley: We are a community engaged
 
\backslash

\end_layout

\begin_layout Chunk

in research and education in probability and statistics.
 In addition to 
\backslash

\end_layout

\begin_layout Chunk

developing fundamental theory and methodology, we are actively" 
\backslash

\end_layout

\begin_layout Chunk

>> tmp.txt
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

cat tmp.txt
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Standard
We also have problems with long comments, so would need to manually format
 them.
\end_layout

\begin_layout Chunk

<<bash2, engine='bash'>>=
\end_layout

\begin_layout Chunk

# the following long comment line is not broken in my test:
\end_layout

\begin_layout Chunk

# asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla lakjsdf aljdkfad
 kljafda kaljdf afdlkja lkajdfsa lajdfa adlfjaf jkladf afdl
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# instead manually break it:
\end_layout

\begin_layout Chunk

# asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla 
\end_layout

\begin_layout Chunk

# lakjsdf aljdkfad kljafda kaljdf afdlkja lkajdfsa lajdfa 
\end_layout

\begin_layout Chunk

# adlfjaf jkladf afdl
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Subsection
Python code
\end_layout

\begin_layout Standard
In Python, there is similar trouble with lines overflowing in PDF output
 too.
 
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

<<test-python, engine='python'>>=
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# this overflows the page in some contexts
\end_layout

\begin_layout Chunk

b = "asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla lakjsdf aljdkfad
 kljafda kaljdf afdlkja lkajdfsa lajdfa adlfjaf jkladf afdl"
\end_layout

\begin_layout Chunk

print(b)
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# this code overflows the page in some contexts
\end_layout

\begin_layout Chunk

zoo = {"lion": "Simba", "panda": None, "whale": "Moby", "numAnimals": 3,
 "bear": "Yogi", "killer whale": "shamu", "bunny:": "bugs"}
\end_layout

\begin_layout Chunk

print(zoo)
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# instead manually break the code
\end_layout

\begin_layout Chunk

zoo = {"lion": "Simba", "panda": None, "whale": "Moby", 
\end_layout

\begin_layout Chunk

	"numAnimals": 3, "bear": "Yogi", "killer whale": "shamu", 
\end_layout

\begin_layout Chunk

	"bunny:": "bugs"}
\end_layout

\begin_layout Chunk

print(zoo)
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# long comments overflow too
\end_layout

\begin_layout Chunk

# asdl lkjsdf jklsdf kladfj jksfd alkfd klasdf klad kla lakjsdf aljdkfad
 kljafda kaljdf afdlkja lkajdfsa lajdfa adlfjaf jkladf afdl
\end_layout

\begin_layout Chunk

\end_layout

\begin_layout Chunk

# and the long output that will appear next in the resulting document (from
 evaluation of the code above) also overflows:
\end_layout

\begin_layout Chunk

@
\end_layout

\begin_layout Section
References
\end_layout

\begin_layout Standard
Here's how to use BibTeX style references.
 
\begin_inset CommandInset citation
LatexCommand citet
key "Bane:etal:2008"

\end_inset

 proposed a useful method.
 This was confirmed 
\begin_inset CommandInset citation
LatexCommand citep
key "Cres:Joha:2008"

\end_inset

.
\end_layout

\begin_layout Standard
The list of references is placed at the end of the document.
 
\end_layout

\begin_layout Standard
\begin_inset CommandInset bibtex
LatexCommand bibtex
bibfiles "refs"
options "plainnat"

\end_inset


\end_layout

\end_body
\end_document