Hi,
With the following Sweave minimal file:
---<--------------------cut
here---------------start------------------->---
\documentclass{article}
\usepackage{Sweave}
\begin{document}
<<binom-sim>>thetas <- seq(0, 1, by=0.001)
prior <- rep(1, length(thetas)) / length(thetas)
lik <- dbinom(1, 1, thetas)
lik.p <- prior * lik
post <- lik.p / sum(lik.p)
<<binom-sim-fig, fig=TRUE, include=FALSE, height=3,
echo=FALSE>>layout(matrix(1:2, ncol=2)); par(mar=c(5, 4, 2, 1), cex=0.75)
matplot(thetas, cbind(prior, lik, post), type="l", lty=c(2, 1, 1),
xlab="theta", ylab="probability density")
lik <- dbinom(60, 100, thetas)
lik.p <- prior * lik
post <- lik.p / sum(lik.p)
matplot(thetas, cbind(prior, lik, post), type="l", lty=c(2, 1, 1),
xlab="theta", ylab="probability density")
@
\includegraphics[width=\linewidth]{test-binom-sim-fig}
\end{document}
---<--------------------cut
here---------------end--------------------->---
If the embedded chunks are evaluated directly in an R session, two
different panel data are produced by layout(), as expected. However,
when weaving and latexing the file produces, then the two panels show
the same data, corresponding to the last data set. This doesn't happen
if the data are much simpler, say using matplot() with simple sequences
of numbers. Any ideas what is causing this and how to get around it?
Cheers,
--
Seb
On 1/5/2009 2:52 PM, Sebastian P. Luque wrote:> Hi, > > With the following Sweave minimal file: > > > ---<--------------------cut here---------------start------------------->--- > \documentclass{article} > > \usepackage{Sweave} > > \begin{document} > > <<binom-sim>>> thetas <- seq(0, 1, by=0.001) > prior <- rep(1, length(thetas)) / length(thetas) > lik <- dbinom(1, 1, thetas) > lik.p <- prior * lik > post <- lik.p / sum(lik.p)You missed an @ after this chunk. If this is true in the original, I'm surprised Sweave didn't report an error, but it probably ate up the second chunk as part of the first.> > <<binom-sim-fig, fig=TRUE, include=FALSE, height=3, echo=FALSE>>> layout(matrix(1:2, ncol=2)); par(mar=c(5, 4, 2, 1), cex=0.75) > matplot(thetas, cbind(prior, lik, post), type="l", lty=c(2, 1, 1), > xlab="theta", ylab="probability density") > lik <- dbinom(60, 100, thetas)It's a bad idea to generate random values in a fig=TRUE chunk, because the code gets evaluated multiple times, but I don't think this would cause your error. Duncan Murdoch> lik.p <- prior * lik > post <- lik.p / sum(lik.p) > > matplot(thetas, cbind(prior, lik, post), type="l", lty=c(2, 1, 1), > xlab="theta", ylab="probability density") > @ > > \includegraphics[width=\linewidth]{test-binom-sim-fig} > > > \end{document} > ---<--------------------cut here---------------end--------------------->--- > > If the embedded chunks are evaluated directly in an R session, two > different panel data are produced by layout(), as expected. However, > when weaving and latexing the file produces, then the two panels show > the same data, corresponding to the last data set. This doesn't happen > if the data are much simpler, say using matplot() with simple sequences > of numbers. Any ideas what is causing this and how to get around it? > > > > Cheers, >
On Mon, Jan 05, 2009 at 01:52:00PM -0600, Sebastian P. Luque wrote:> <<binom-sim-fig, fig=TRUE, include=FALSE, height=3, echo=FALSE>>> layout(matrix(1:2, ncol=2)); par(mar=c(5, 4, 2, 1), cex=0.75) > matplot(thetas, cbind(prior, lik, post), type="l", lty=c(2, 1, 1), > xlab="theta", ylab="probability density") > lik <- dbinom(60, 100, thetas) > lik.p <- prior * lik > post <- lik.p / sum(lik.p) > > matplot(thetas, cbind(prior, lik, post), type="l", lty=c(2, 1, 1), > xlab="theta", ylab="probability density") > @ > > \includegraphics[width=\linewidth]{test-binom-sim-fig} > > > \end{document} > ---<--------------------cut here---------------end--------------------->--- > > If the embedded chunks are evaluated directly in an R session, two > different panel data are produced by layout(), as expected. However, > when weaving and latexing the file produces, then the two panels show > the same data, corresponding to the last data set. This doesn't happen > if the data are much simpler, say using matplot() with simple sequences > of numbers. Any ideas what is causing this and how to get around it?I was very confused, too when I first had this happen to me. The reason is that chunks with fig=TRUE are executed three times by default: once for the eps file, the pdf and the default device. Accordingly, whenever you modify data in such a code chunk, the results change with each round of execution. The solution to the problem is either - separating the manipulations from the plotting in two code chunks - or keeping the modified values in a separate variable instead of modifying the original. In your example you are modifying 'lik' and 'post'. Just call the modified versions likMod and postMod or something like this and your problem will go away. cu Philipp -- Dr. Philipp Pagel Lehrstuhl f?r Genomorientierte Bioinformatik Technische Universit?t M?nchen Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel