From: Jean-Christophe BOUETTE <jcbouette_at_gmail.com>

Date: Mon 13 Feb 2006 - 23:05:04 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon Feb 13 23:19:49 2006

Date: Mon 13 Feb 2006 - 23:05:04 EST

*> From: Göran Broström <goran.brostrom@gmail.com>
**> To: r-help@stat.math.ethz.ch
**> Date: Mon, 13 Feb 2006 11:16:14 +0100
**> Subject: [R] Sweave, mle and curve
*

> I am trying to write a lesson on maximum likelihood with Sweave. I get

*> a surprising result with the following code, lec4.Snw:
**>
**> \documentclass[a4paper,12pt]{article}
**> \usepackage[latin1]{inputenc}
**>
**> \title{Maximum likelihood}
**>
**> \author{Göran Broström}
**>
**> \begin{document}
**>
**> \maketitle
**>
**> <<fig=TRUE>>=
**> ## Simulate Y:
**> n <- 25
**> Y <- sum(rpois(n, lambda = 1))
**> Y
**> ## Define minusloglik:
**> minusloglik <- function(theta) n * theta - Y * log(theta)
**> curve(minusloglik, 0.2, 2, xlab = "theta")
**>
**> library(stats4)
**> cat("Y is now ", Y, "\n")
**> fit <- mle(minusloglik, start = list(theta = Y/n))
**> summary(fit)
**> @
**>
**> \end{document}
**>
**> In R, I get:
**>
**> > Sweave("lec4.Snw")
**> Writing to file lec4.tex
**> Processing code chunks ...
**> 1 : echo term verbatim eps pdf
**> Y is now 27
**> Y is now 24
**>
**> You can now run LaTeX on 'lec4.tex'
**> >
**>
**> and the latex document will have two different mle's, one in the
**> figure, and another one from 'mle'. One uses Y = 27 and the other Y =
**> 24!
**>
**> I can save the situation by moving "Y <- ..." to a separaye "code chunk".
**> Does 'fig=TRUE' imply that the code chunk is run twice?
**>
**> --
**> Göran Broström
*

Which figure did you use ? The .eps or the .pdf ? I guess one of them has Y=24.
The problem is that Sweave runs the code twice, to get the .eps plot
and the .pdf plot.

The solution is to isolate the "random" code in a separate chunk. I
think this issue was adressed some time ago in this list.

**HTH,
**

Jean-Christophe Bouëtté.

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon Feb 13 23:19:49 2006

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