Embed Size (px)
Citation preview
Mix source code and documentation togetherWrite R code in LATEX using knitr, xtable and RStudio
Julyan Arbel
CREST-INSEE, Universite Paris-Dauphine
February 28, 2013
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 1 / 10
Goal
To have a single document which includes source code for easy update.
Use a single software: R interfaces LATEX, as it does with C++, JAGS,(Word, Excel?), etc.
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 2 / 10
First things
We will use the knitr package which allows you to embed R code and figuresin LATEX documents (it is an evolution of Sweave). See the packagehomepage http://yihui.name/knitr/
You need a valid LATEX distribution
We will use knitr in RStudio, because it’s well integrated in it
install.packages("knitr")
library("knitr")
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 3 / 10
Write a first document
Open a new ”R Sweave” document in RStudio
You can check that the toolbar now includes Format and Compile PDFbuttons
\documentclass{article}
\begin{document}
\end{document}
Write your text, and insert
code chunks [Ctrl+Alt+I] for graphs or tables. A code chunk consists in Rcode inside the following lines (mind to write both on single lines, with nocomment)
<<>>=@
code values in the text with
Compile [Ctrl+Shift+I]
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 4 / 10
What to put in code chunks
Any code that you want to evaluate / not to evaluate, or show / hide: you caneither show the code, or its result, or both.
Functions
Graphs
Tables
Global options
Set working directory, etc.
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 5 / 10
Number of R packages (lien)
2001
−06
−21
2001
−12
−17
2002
−06
−12
2003
−05
−27
2003
−11
−16
2004
−06
−05
2004
−10
−12
2005
−06
−18
2005
−12
−16
2006
−05
−31
2006
−12
−12
2007
−04
−12
2007
−11
−16
2008
−03
−18
2008
−10
−18
2009
−09
−17
100100
200
300
400
500
600
800
1200
1500
2000
Num
ber
of C
RA
N P
acka
ges
1.3
1.4
1.5
1.7
1.8
1.9
2 2.1
2.2
2.3
2.4
2.5
2.6
2.7
2.8
2.9
R Version
110129
162
219
273
357406
548
647739
9111000
130014271614
1952
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 6 / 10
Number of R packages: now the code
rv <- seq(1.3, 2.9, .1)
pckg.num <- c(110,129,162,219,273,357,406,548,647,739,911,1000,1300,1427,1614,1952)
rv.dates <- c("2001-6-21", "2001-12-17","2002-06-12","2003-05-27",
"2003-11-16","2004-06-05","2004-10-12","2005-06-18","2005-12-16", "2006-05-31",
"2006-12-12","2007-04-12","2007-11-16","2008-03-18","2008-10-18","2009-09-17")
pckg.fit <- lm(pckg.num~rv)
par(mar=c(7, 5, 5, 3), las=2)
plot(as.POSIXct(rv.dates), pckg.num, xlab="",ylab="",col="red", log="y", pch=19, axes=F)
axis.POSIXct(1, 1:16, rv.dates, format="%Y-%m-%d")
axis(2, at=c(100,200,300,400,500,600,800,100,1200,1500,2000))
mtext("Number of CRAN Packages", side=2, line=3, las=3)
axis.POSIXct(3, rv.dates, rv.dates, labels=as.character(rv))
mtext("R Version", side=3, line=3, las=1)
axis(4, pckg.num)
abline(v=as.POSIXct(rv.dates), col="lightgray", lty="dashed")
abline(h=pckg.num, col="lightgray", lty="dashed")
abline(lm(log10(pckg.num)~as.POSIXct(rv.dates)), col="red")
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 7 / 10
To show graphs
Use that kind of code chunk
<<echo=FALSE,out.width=’.7\\textwidth’,fig=TRUE,include=TRUE>>=
library(ggplot2)
qplot(speed, dist, data=cars)+geom_smooth()
@
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 8 / 10
To show graphs: result
0
50
100
5 10 15 20 25speed
dist
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 9 / 10
To show data tables
Use that kind of code chunk
<<echo=FALSE,results=asis>>=
load(file="data.Rdata")
row.names(data) = c(...)
library(xtable)
tab=xtable(data)
digits(tab)=1
print(tab,floating=FALSE,include.rownames=TRUE,type="latex")
@
Julyan Arbel (CREST-INSEE) R code in LATEX February 28, 2013 10 / 10
