[R] Sweave, mle and curve

[Jean-Christophe BOUETTE]

> From: Göran Broström <goran.brostrom at gmail.com>
> To: r-help at 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{Göran Broström}
>
> \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?
>
> --
> Göran Broström

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 Bouëtté.