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}}
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 : mackay at 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: pdunn2 at 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}}
>
>______________________________________________
>R-help at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
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 : mackay at 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: pdunn2 at 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}}
>
>______________________________________________
>R-help at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
Hi Peter Sorry I must have been reading too much into your email. I had thought that either latex or xtable packages handled summaries effectively. I have not really got into summaries in Sweave. I do not know whether SweaveListingUtils may help. I had a look at it but I did not have the time to properly set it up so have left it for another time. There was one post about the querieng the length of the verbatim text in Sweave being cut off or not wrapping but I did not see a reply. I would like to know too Regards Duncan At 12:16 19/08/2009, you wrote:>Thanks Duncan > >Yes, I use xtable and co. > >But here, I am talking about the verbatim output from R, no LaTeX code at >all. That is, my LaTeX document contains the R output >(from print.summary.glm), which I want to include verbatim in the final >document, but it is too wide, and option(width=) doesn't seem to help. > >P. > >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: <mailto:pdunn2@usc.edu.au>pdunn2@usc.edu.au >www.usc.edu.au > > > >>> Duncan Mackay <mackay@northnet.com.au> 19/08/2009 12:14 pm >>> >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 : mackay@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.UT > F-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/>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}} > > > >______________________________________________ > >R-help@r-project.org mailing list > ><https://stat.ethz.ch/mailman/listinfo/r>https://stat.ethz.ch/mailman/lis > tinfo/r-help > >PLEASE do read the posting guide > <http://www.R>http://www.R-project.org/posting-guide.html > >and provide commented, minimal, self-contained, reproducible code. > > >-- >This message has been scanned for viruses and >dangerous content by MailScanner, and is >believed to be clean. > > >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 content by <http://www.mailscanner.info/>MailScanner, and is >believed to be clean.[[alternative HTML version deleted]]