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Sweave, mle and curve

2 messages · Göran Broström, Friedrich Leisch

Göran Broström
# 
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Ã¶ran BrostrÃ¶m}

\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:
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Ã¶ran BrostrÃ¶m
Friedrich Leisch
# 
> 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??ran Brostr??m}

  > \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?

Yes, once to get all textual output, and then once for each graphics
format requested.

Best,