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: pdunn2@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.

-- 
This message has been scanned for viruses and\ dangerous...{{dropped:8}}


