Oops
I forgot to mention ?xtable and ?latex in Frank Harrell's Hmisc or Design
packages (I cannot remember)
Duncan
Hi Peter
If all else fails you can make the space between the columns smaller by
changing the column spacing in latex
by:
\setlength\tabcolsep{3pt}
The default is 7pt. You may have to go a little higher if it looks cramped.
I have gone down as far as 2pt using a small font size
Also changing the fontsize for the chunk can work wonders eg for small
\begin{small}
<< >>==
R code
@
\end{small}
HTH
Duncan Mackay
Department of Agronomy and Soil Science
Univeristy of New England
ARMIDALE NSW 2351
Email: home : mac...@northnet.com.au
At 10:10 19/08/2009, you wrote:
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/ )
CRICOS Provider Number: 01595D
This communication is intended for the recipient only and should not be
forwarded, distributed or otherwise read by others without express
permission. The views expressed in this email are not necessarily those of
the University of the Sunshine Coast.
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