Hi all
I am preparing a document using Sweave; a really useful tool. But I am having
a problem.
Consider this toy example Sweave file:
\documentclass{article}
\begin{document}
<<echo=TRUE,results=verbatim>>=
options(width=40) # Set width to 40 characters
hide <- capture.output(example(glm)) # Create an example of the problem, but
hide the output
summary(glm.D93) # This is where the problem is evident
@
\end{document}
The intent of the options(width=40) command is to ensure the output does not
extend to far to the right of the page, as per the Sweave manual Section A.14.
And in most cases, this does the job.
Now, I run Sweave on the above file, run pdflatex. Feel free to run the above
code to see the actual result, but here is an edited text version of the output:
> options(width = 40)
> hide <- capture.output(example(glm))
> summary(glm.D93)
Call:
glm(formula = counts ~ outcome + treatment, family = poisson())
Deviance Residuals:
1 2 3 4
-0.67125 0.96272 -0.16965 -0.21999
5 6 7 8
-0.95552 1.04939 0.84715 -0.09167
9
-0.96656
Coefficients:
Estimate Std. Error
(Intercept) 3.045e+00 1.709e-01
outcome2 -4.543e-01 2.022e-01
outcome3 -2.930e-01 1.927e-01
treatment2 8.717e-16 2.000e-01
treatment3 4.557e-16 2.000e-01
z value Pr(>|z|)
(Intercept) 17.815 <2e-16 ***
outcome2 -2.247 0.0246 *
outcome3 -1.520 0.1285
treatment2 4.36e-15 1.0000
treatment3 2.28e-15 1.0000
The final pdf output file is mostly fine: but not all of the output of
print.summary.glm obeys the width=40 command.
The middle parts of the output are suitable wrapped (the coefficients, std
error, z and P-value bit), but the bits at the end (not shown) and the start
are not; for example, look at the Call: section of the output above.
I'd be expecting the initial part of the output to appear something like this,
suitably wrapped:
> summary(glm.D93)
Call:
glm(formula = counts ~ outcome +
treatment, family = poisson())
As far as I can recall, print.summary.glm and print.summary.lm are the only
times I have seen this behaviour. I found a similar thread posted June 2009
("overshoot of formula line in summary output of Sweave"); there appeared no
resolution in that thread, or after contacting the originator of the post.
So my question:
* What can I do to ensure my output is not extending too far to the right with
print.summary.glm?
Thanks as always.
P.
> sessionInfo()
R version 2.9.0 (2009-04-17)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GLMsData_0.7
loaded via a namespace (and not attached):
[1] tools_2.9.0
>
Peter Dunn: Biostatistician
School of Health and Sport Science
Faculty of Science, Health and Education ML-34
University of the Sunshine Coast, Locked Bag 4
Maroochydore DC Qld 4558
Tel: +61 7 5456 5085
Fax: +61 7 5430 2896
Email: pdu...@usc.edu.au
www.usc.edu.au ( http://www.usc.edu.au/ )
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This communication is intended for the recipient only and should not be
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