Re: [R] Sweave bug? when writing figures / deleting variable in chunk
On Thu, 28 Jun 2007 08:14:44 -0400, D G Rossiter (DGR) wrote: Thanks to the four distinguished R'ers who answered. I have used Sweave intensively for over a year, and have poured through all the doc. as well as the help archives, and could find nothing on this. It is now well known to me! since it bit me, but it did cost me a day of head-scratching and putting it in the shortest possible form for the list (the original example where this happened was a lot more complicated). Sorry! Perhaps it could be documented in Sweave- manual-20060104.pdf or its successor? Yes, I'll put it in ASAP. Best, Fritz -- --- Prof. Dr. Friedrich Leisch Institut für Statistik Tel: (+49 89) 2180 3165 Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308 Ludwigstraße 33 D-80539 München http://www.stat.uni-muenchen.de/~leisch __ R-help@stat.math.ethz.ch 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.
Re: [R] How to extract R codes that embedded in a HTML file
Original Message
Subject: Re: [R] How to extract R codes that embedded in a HTML file
using Stangle?
Date: Thu, 17 May 2007 17:01:30 +
From: Tao Shi [EMAIL PROTECTED]
To: [EMAIL PROTECTED], [EMAIL PROTECTED]
CC: r-help@stat.math.ethz.ch
: [EMAIL PROTECTED]
Hi Uwe,
Thanks for the answer, but I still need a bit more clearification. I
always
thought that a .rnw or .snw file is a file mixing word processing markup
(e.g. tex or HTML) and R/S code using noweb syntax. Is the reason for
'Stangle' is not working with .rnw file with HTML due to there is no proper
driver available (like RweaveHTML driver for Sweave)? If yes, does R2HTML
package have plans to provide a such driver?
Tao
The following does the trick for me:
R mytangle - function ()
list(setup = RtangleSetup, runcode = utils:::RtangleRuncode,
writedoc = RtangleWritedoc,
finish = utils:::RtangleFinish, checkopts = RweaveHTMLOptions)
R Stangle(/PATH/TO/R/SITE-LIBRARY/R2HTML/samples/example1.snw,
driver=mytangle)
Writing to file example1.R
Best,
Fritz
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Re: [R] Issues with Sweave and inclusion of graphics from nlme
On Fri, 27 Apr 2007 07:15:22 -0400,
Duncan Murdoch (DM) wrote:
On 4/27/2007 5:39 AM, [EMAIL PROTECTED] wrote:
Dear all,
I'm using the nlme package. I would like to introduce the plot of my
groupedData object in my latex report using Sweave but it doesn't work.
I have no error message in R (Sweave(my.file_Rnw)) and the plot is
generated in R, but when I want to see the pdf (I'm using TexnicCenter) of
my report, there is an error message and no pdf file is generated. It seems
that the plot generated by plot.nmGroupedData is not found by TexnicCenter.
Does anyone have an idea on how to solve this problem?
If the dot in the filename is real, I'd guess that's your problem. To
confirm, take a look at the .tex file produced by Sweave. Find the line
corresponding to this figure. It will be an \includegraphics call,
something like
\includegraphics{my.file_Rnw-fig}
Your TeX is probably interpreting this as the file my.file_Rnw-fig
rather than automatically adding the .pdf file extension, because it
thinks you've specified the extension to be file_Rnw-fig.
Another reason could be that many nlme plots are using lattice, see
http://www.ci.tuwien.ac.at/~leisch/Sweave/FAQ.html#x1-9000A.7
Best,
--
---
Prof. Dr. Friedrich Leisch
Institut für Statistik Tel: (+49 89) 2180 3165
Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308
Ludwigstraße 33
D-80539 München http://www.stat.uni-muenchen.de/~leisch
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Re: [R] Sweave question: prevent expansion of unevaluated reused code chunk
On Wed, 14 Mar 2007 10:39:43 -0500, Kevin R Coombes (KRC) wrote: Hi, I don't know of a standard way to indicate this; I would have suggested combined,expand=FALSE (with expand=TRUE the default), except for the fact that Seth Falcon already suggested the same notation in his response...so I can only second the motion. Sounds like a good idea. Currently this is not possible, but it shouldn't be too hard to add the feature. Best, Fritz __ R-help@stat.math.ethz.ch 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.
Re: [R] Sweave, Xfig, pdflatex and \setkeys
On Wed, 13 Dec 2006 12:38:04 +0100,
David Lindelöf (DL) wrote:
On Tue, 2006-12-12 at 13:22 -0500, Kevin E. Thorpe wrote:
Trouble is that Sweave defines (with \setkeys) the default width of
\includegraphics to be 0.8 times the \textwidth. The result is that the
graphic is scaled, but not the text.
I was looking for a way to temporarily undefine the default width of
included graphics, but without success. Does anyone know how to undo a
definition that has been set with \setkeys?
If you knew what setting you needed, you could try
\setkeys{Gin}{width=whatever}
before your include, and set it back to the default afterward with
\setkeys{Gin}{width=0.8\textwidth}
Yes, but the trouble is that for arbitrary figures created with Xfig I
cannot know what the correct width is going to be. And I could not find
any help on how to undefine variables set with \setkeys.
Yes, I should document Sweave.sty much better ...
\usepackage[nogin]{Sweave}
in your .Rnw file will do the trick, i.e., not set any Gin keys.
HTH,
Fritz
--
---
Prof. Dr. Friedrich Leisch
Institut für Statistik Tel: (+49 89) 2180 3165
Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308
Ludwigstraße 33
D-80539 München http://www.stat.uni-muenchen.de/~leisch
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Re: [R] Sweave, R and complex latex projects
On Sat, 14 Oct 2006 23:00:27 +0100,
Mark Wardle (MW) wrote:
Hello all,
I've been able to use R very successfully to run simple statistics and
generate the plots I require.
I've been evaluating Sweave, and have hit upon a small problem that I
don't seem to be able to workaround. Sweave runs very well for single
file latex documents, but I have a complex thesis made up of several
parts and chapters. These are arranged with a master latex file and
subdirectories with \include-ed latex fragments representing those
parts/chapters, and I don't seem to be able to get Sweave to work properly.
I've tried a number of approaches, including converting the master
document into a Snw file itself, or even generating chapters manually
chapter by chapter using Sweave and then \includeing the result into
the master tex file. Unfortunately for the latter attempt, the the latex
generated doesn't prepend the required path to the filename, and so
latex looks for the pdfs and tex files in the wrong place - it looks in
the root directory (where the master tex file is located) rather than
the chapter subdirectory where all the files have been generated.
I hope I'm not missing something obviously documented, but I can't see
it in the Sweave docs. Is there an option to prepend a pathname to the
filename of Sweave generated TeX and PDF documents?
Yes, simply set prefix.string to a path, not only a filename. E.g.,
\SweaveOpts{prefix.string=figs/myfile}
will place all figures in subdir figs (you have to create the
directory first manually) and call the separate files myfile-XXX
where XXX is number or name of the chunk.
Do people use Sweave for complex multi-file latex projects, and what is
the best approach? I'm almost tempted to keep R and Latex separate, and
continue to run a R script to generate all of the dynamic tables/charts
which are then \inputed, but I was rather attracted to the whole
Sweave approach.
I personally mostly use Makefiles as suggested by Deepayan.
In addition there is \SweaveInput{} which works similar to Latex's own
\input{} command. There currently is no equivalent of \include{}.
HTH,
Fritz
--
---
Prof. Dr. Friedrich Leisch
Institut für Statistik Tel: (+49 89) 2180 3165
Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308
Ludwigstraße 33
D-80539 München http://www.stat.uni-muenchen.de/~leisch
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Re: [R] Sweave, R and complex latex projects
On Sat, 14 Oct 2006 16:04:50 -0700,
Deepayan Sarkar (DS) wrote:
%.tex: %.Rnw
echo library(tools); Sweave('$') | ${R_PROG} --vanilla --silent
Note that we now have R CMD Sweave (new in R 2.4.0) for this purpose.
Best,
Fritz
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Re: [R] Sweave and the [ function
On Tue, 05 Sep 2006 20:56:33 +1000, Ross Darnell (RD) wrote: Hi Vincent This would seem logical but in this case doesn't work. It doesn't seem to be a Sweave problem (feature) at all but within R as Hadley stated. Yes, Sweave parses deparses the code in oreder to make full expressions out of lines of text, i.e., to know where open parentheses are closed etc. This is necessary in order to know where to insert output when multiple lines are contained in one code chunk, but unfortunately looses the original formatting as has correctly been explained earlier in this thread. Best, Fritz -- --- Prof. Dr. Friedrich Leisch Institut für Statistik Tel: (+49 89) 2180 3165 Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308 Ludwigstraße 33 D-80539 München http://www.stat.uni-muenchen.de/~leisch __ R-help@stat.math.ethz.ch 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.
Re: [R] issues with Sweave and inclusion of graphics in a document
On Fri, 25 Aug 2006 11:05:48 -0700 (PDT),
Thomas Harte (TH) wrote:
--- Prof Brian Ripley [EMAIL PROTECTED] wrote:
savePlot is just an internal version of dev.copy, part of the support for
the menus on the windows() graphics device.
It is described in `An Introduction to R' (the most basic R manual).
the most basic R manual doesn't quite answer my question.
by itself, dev.copy doesn't copy the width and height of the device whereas
savePlot
copies whatever is displayed on the screen giving me
what-you-see-is-what-you-save
capabilities (but only under the Windows OS).
i can get pretty close to this in linux by writing a function to save the
plot to a pdf device:
label=first.ar.1, results=hide=
# no savePlot in Linux ... so write my own function
savePlotAsPdf- function(pdfname, from=dev.cur()) {
from- from
pdf(pdfname, width=width, height=height)
to- dev.cur()
dev.set(from)
dev.copy(which=to)
dev.off()
}
# a long AR process is best viewed in a wide window ...
# width height are now variables
width- 20; height- 5
x11(width=width, height=height)
sp- make.ar.1(alpha=.5, n=800)
plot(sp, type=l, col=blue)
# width height via dynamic scoping in savePlotAsPdf
savePlotAsPdf(ar.pdf)
@
Umm, maybe I don't get your point, but in what way does the complicated
code above do anythingdifferent from
**
results=hide=
sp- make.ar.1(alpha=.5, n=800)
@
ar,fig=true,width=20,height=5,include=false=
plot(sp, type=l, col=blue)
@
\begin{figure}
\includegraphics[width=14.5cm]{myprefix-ar}
\end{figure}
**
???
Best,
--
---
Prof. Dr. Friedrich Leisch
Institut für Statistik Tel: (+49 89) 2180 3165
Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308
Ludwigstraße 33
D-80539 München http://www.stat.uni-muenchen.de/~leisch
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] issues with Sweave and inclusion of graphics in a document
On Sat, 26 Aug 2006 05:38:58 -0700 (PDT), Thomas Harte (TH) wrote: hallo, friedrich, and thanks for your reply. if i Stangle your code i get: sp- make.ar.1(alpha=.5, n=800) plot(sp, type=l, col=blue) whereas if i Stangle my code, i get: width- 20; height- 5 x11(width=width, height=height) sp- make.ar.1(alpha=.5, n=800) plot(sp, type=l, col=blue) savePlotAsPdf(ar.pdf) this, i think, is the problem in a nutshell. i want my R code to look like this because i (often) want to open a separate device (for example, to have specific dimensions as above) and i may wish to save its contents. on the other hand, i may not wish to save a device's contents: i may wish to open several devices for comparison purposes and i may wish to save only certain devices, in keeping with the Sweave options echo=false and results=hide. if i use your, admittedly uncomplicated, code chunk, then i am limited to seeing the output in the final document. i can't cut and paste the code chunk into an R session and see the results as i wish to see them before saving. currently for each project i work on, i usually end up with a very lengthy .R file with all the code (and embedded mathematical annotation in LaTeX), and then i have to write a set of notes or a report in LaTeX duplicating or expanding on the mathematics. i'm hoping to supplant this, rather inefficient, method with a single .Rnw file and the use of Sweave. this, i believe, is what Sweave was designed to do. but i do wish to write my R code (warts and all) the way that i want to in the .Rnw file and only include the output (graphics or text) of certain parts of that code in the document. i hope that seems reasonable. perhaps i was not clear, or succinct enough, in my original post (i tried to get the point across by providing example .Rnw files, but i'm aware that it's asking a lot to wade through a lengthy example to retrieve a point). OK, no I think I understand what you want: running the *tangled* code should open windows with the same height/width ratio as in the Latex document, right? Your first posting suggested to me more the other way round ... No, what you want is currently not directly possible with Sweave, you will have to use workarounds like the one you posted. You can even easily write your own tangle function doing it automatically (Rtangle is really trivial can be easily adjusted to ones personal needs). Best, Fritz __ R-help@stat.math.ethz.ch 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.
Re: [R] Sweave and multipage lattice
On Wed, 19 Jul 2006 11:01:02 -0500,
Sundar Dorai-Raj (SD) wrote:
Dieter Menne wrote:
Dear R-Listeners,
as the Sweave faq says:
http://www.ci.tuwien.ac.at/~leisch/Sweave/FAQ.html
creating several figures from one figure chunk does not work, and for
standard graphics, a workaround is given. Now I have a multipage trellis
plot with an a-priori unknown number of pages, and I don't see an elegant
way of dividing it up into multiple pdf-files.
I noted there is a page event handler in the ... parameters, which would
provide a handle to open/close the file.
Any good idea would be appreciated.
Dieter
Hi, Dieter,
I haven't seen a reply to this and I don't know Sweave. However, will
the following example work? It does require you know the layout for one
page.
--sundar
library(lattice)
trellis.device(postscript, file = barley%02d.eps,
width = 5, height = 3, onefile = FALSE,
paper = special)
## from ?xyplot
dotplot(variety ~ yield | site, data = barley, groups = year,
key = simpleKey(levels(barley$year), space = right),
xlab = Barley Yield (bushels/acre) ,
aspect=0.5, layout = c(1, 1), ylab=NULL)
dev.off()
files - list.files(pattern = glob2rx(barley*.eps))
for(file in files)
cat(\\includegraphics{, file, }\n\n, sep=)
Yes, doing the above embedded in a chunk with results=tex should do
the trick. You may need to enclose the call to dotplot() in print()
though.
Best,
Fritz
--
---
Prof. Dr. Friedrich Leisch
Institut für Statistik Tel: (+49 89) 2180 3165
Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308
Ludwigstraße 33
D-80539 München http://www.stat.uni-muenchen.de/~leisch
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Re: [R] cclust causes R to crash when using manhattan kmeans
On Fri, 07 Apr 2006 09:02:46 +0200, Timo Becker (TB) wrote: Dear R users, When I run the following code, R crashes: require(cclust) x - matrix(c(0,0,0,1.5,1,-1), ncol=2, byrow=TRUE) cclust(x, centers=x[2:3,], dist=manhattan, method=kmeans) While this works: cclust(x, centers=x[2:3,], dist=euclidean, method=kmeans) I'm posting this here because I am not sure if it is a bug. I've been searching for a manhattan kmeans method and I found a solution by using the package amap: require(amap) Kmeans(x, x[2:3,], method=manhattan) This works for me, so I don't need the cclust package anymore. Anyway, I wanted to report the cclust behaviour. R version 2.2.1, 2005-12-20, i386-pc-mingw32 Thanks, this is indeed a bug, and has not been noticed yet because it seems to apply only for very small data sets like your example, for larger data sets it seems to works fine: R require(cclust) Loading required package: cclust [1] TRUE R x=matrix(rnorm(100), ncol=2) R cclust(x, centers=x[2:3,], dist=manhattan, method=kmeans) Clustering on Training Set Number of Clusters: 2 Sizes of Clusters: 33 17 Algorithm converged after 4 iterations. Changes: 12 3 1 1 2 side notes: * cclust is no longer actively maintained, the code has been integrated in my more general package flexclust, see also http://www.ci.tuwien.ac.at/~leisch/papers/Leisch-2006.pdf (but cclust in flexclust has the same bug, so thanks a lot for reporting it). * r-help is not really the correct place to report bugs, please try to contact the package maintainer first, or use r-devel (but only if the maintainer does not respond to a direct email). This is not because we want to hide bugs from the public, but simply to reduce traffic on the lists. Best, Fritz -- --- Prof. Dr. Friedrich Leisch Institut für Statistik Tel: (+49 89) 2180 3165 Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308 Ludwigstraße 33 D-80539 München http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] partitioning cluster function
On Wed, 5 Apr 2006 12:58:00 -0700, Linda Lei (LL) wrote: Hi All, For the function bclust(e1071), the argument base.method is explained as must be the name of a partitioning cluster function returning a list with the same components as the return value of 'kmeans'. In my understanding, there are three partitioning cluster functions in R, which are clara, pam, fanny. Then I check each of them to see which of them can get same components as the return value of kmeans, by using the following codes: The functions in the cluster package will not work, because they have different interface (names of arguments and return values). cclust from the package of the same name can be used together with kmeans, but note that that is no longer actively maintained (see my email to r-help from a few minutes ago). Best, Fritz -- --- Prof. Dr. Friedrich Leisch Institut für Statistik Tel: (+49 89) 2180 3165 Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308 Ludwigstraße 33 D-80539 München http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] about clustering method
On Mon, 27 Feb 2006 11:09:24 -0800, Linda Lei (LL) wrote: Hi there, I'm doing some clustering analysis and try to find all the algorithms related to clustering in R. Here is the list of the algorithms I found. But I'm not sure if It's the complete list. Could you please check it and see if there're other ones? You may want to have a look at the CTAN Task View about Clustering at http://cran.r-project.org/src/contrib/Views/ HTH, Fritz Leisch -- --- Friedrich Leisch Institut für StatistikTel: +49 89 2180 3165 Ludwig-Maximilians-UniversitätFax: +49 89 2180 5308 Akademiestraße 1 D-80799 München http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Question about Sweave
On Mon, 27 Feb 2006 11:34:00 -0800,
Elizabeth Purdom (EP) wrote:
Hi,
I'm not sure if Sweave questions should go to the general list, but it
seems to be part of the core R package without a separate maintainer.
I am writing a tutorial for R in a latex file. I'd like to use Sweave,
since this seems its ideal usage. The problem is that I want to
purposefully put errors in and then the output that comes with it in the
text of my tutorial. However the errors kill the function Sweave() in R
when what I would like is for Sweave to just run it and include the error
message as part of the output.
I have set options(error=NULL). It doesn't seem that the error options
would affect Sweave in the right way, since an error in my .Rnw file causes
an error in Sweave() itself, not just in the processing of the code, but
maybe there's an error-handling system I don't know about that would do it.
(I tried error=expression(NULL) but Sweave couldn't finish regardless). I
don't see any options in the documentation of Sweave that allow this
behavior, either.
There is no direct support, but fortunately R is a full-featured
programming language ;-)
I usually do something along the lines of
**
\documentclass[a4paper]{article}
\begin{document}
errchunk,eval=false=
x=sin(a)
echo=false=
cat(try({
errchunk
}))
@
\end{document}
**
which of course only helps if you know where the error will happen,
but in your application this seems to be the case.
Best,
Fritz Leisch
--
---
Friedrich Leisch
Institut für Statistik Tel: (+49 89) 2180 3165
Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308
Akademiestraße 1
D-80799 München http://www.ci.tuwien.ac.at/~leisch
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Re: [R] Sweave, mle and curve
On Mon, 13 Feb 2006 11:16:14 +0100,
Göran Broström (GB) wrote:
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{Göran Broström}
\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,
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] Sweave: skip if figure exists
On Mon, 23 Jan 2006 16:41:09 +0100, Dieter Menne (DM) wrote: Dear RWeavers, to speed up report generation with Sweave, I am looking for an option skipifexists for figures. A named figure chunk should not be executed if the file to be produced already exists. I know that this could be done with hooks, but I want to avoid to re-invent this wheel. I have plans to implement something like this for a very long time now, but no code yet. Contributions are of course more than welcome. Best, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Downloads -- possible bug?
On Thu, 19 Jan 2006 18:55:03 +0100, Uwe Ligges (UL) wrote: Elizabeth Purdom wrote: Hi, When I go to the CRAN page to download a new version of R, there are not the same versions available depending on which mirror I pick. When I go to http://cran.cnr.berkeley.edu/, for example, I get 2.2.1, but if I go http://cran.stat.ucla.edu/ the option is 2.2.0 (I'm downloading the Windows base file). Neither refreshing nor clearing my cache changes it. For future reference, I'd like to know if this is a mistake or if different mirrors are just updated at different times? Looks like http://cran.stat.ucla.edu/ has not been synced for a couple of months, since Kurt Hornik's *daily* check has the date 08-Oct-2005 on that mirror. Fritz? Yes, I will contact the admins. -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Bookmarking a page inside r-project.org
On Tue, 3 Jan 2006 07:29:27 +, hadley wickham (hw) wrote: A solution would be a content-management system that produced the HTML of the site from some other form of input. Only the output HTML would need to be mirrored. Care to put together such a thing, and import all the existing pages into it? One way to get around the offline problem is to have a dynamic copy somewhere and then spider and save it (eg. with wget -r). This would (obviously) require a server somewhere - but with a post-commit svn hook could be kept up to date easily. However, it is still difficult to view changes to the page immediately. What assumptions can I make about what tools are available to the editors? Can I assume the standard unix tool chain? Yes. What assumptions can I make about the people doing the editing? How many people edit the pages? For www.R-project.org all of R core have write access, but only a few actually do it ;-) How familiar with html are they? Hard to tell, let's assume at least basic familiarity with HTML (but very good familiarity to the concept of markup laguages per se). You say many of the pages are manually edited, which ones aren't? Under www.r-project.org I think all are manual. How are they generated? on CRAN all package listings are of course auto-generated (mostly using perl scripts), the mirror list is created using R. Are all the pages under https://svn.r-project.org/R-project-web/trunk/ ? No, CRAN is not, as it is pulled together from various sites where maintainers of binary distributions etc. create their parts - the CRAN master itself is mirror for the pits and pieces (e.g., windows R base binaries are mirrored from Duncan Murdoch, windows packages from Uwe Ligges, etc. etc.). Best, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave: How can I include S input in paragraph mode
On Fri, 02 Dec 2005 10:38:21 +1000, Ross Darnell (RD) wrote: Sweavers As the title suggests I would appreciate any help to include S code in ordinary paragraph mode. I can use the textsl font but is isn't the same. You can always renew the Sinput and Soutput environments to whatever you like. Sweave.sty provides a default setting, but you are free to modify them as you like. E.g., for slides I redefine them such that input and output have different colors. HTH, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R Hierarchical clustering leaf node
On Thu, 01 Dec 2005 11:34:01 -0600, Qunfeng (Q) wrote: Hello, I am new to the R package. After I use R to perform the hierarchical clustering, I am only interested in retrieving the leaf nodes that share the last common ancestors. As illustrated below, I'd like to retrieve (B, C) as a cluster and then (D, E) as another cluster.Any chance to do this in R? Thanks! BTW, I just subscribed to this list (not sure if the subscription is succeeded), please copy your anser to my personal email ([EMAIL PROTECTED]) -- Qunfeng Knowing what the internal structure of an hclust object is makes it actually quite easy for groups of two (getting triplets or higher would require a little bit more code): As an example we can use R set.seed(1) R x=rnorm(5) R h=hclust(dist(x)) R str(as.dendrogram(h)) --[dendrogram w/ 2 branches and 5 members at h = 2.43] |--leaf 4 `--[dendrogram w/ 2 branches and 4 members at h = 1.17] |--[dendrogram w/ 2 branches and 2 members at h = 0.146] | |--leaf 2 | `--leaf 5 `--[dendrogram w/ 2 branches and 2 members at h = 0.209] |--leaf 1 `--leaf 3 The key is the merge element of the reurn object, from that cou can extract the two pairs by R -h$merge[apply(h$merge,1,function(x) all(x0)),] [,1] [,2] [1,]25 [2,]13 HTH, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] SWeave - can I see output in the source?
On Sat, 19 Nov 2005 09:52:22 -0500, Duncan Murdoch (DM) wrote: On 11/19/2005 6:13 AM, [EMAIL PROTECTED] wrote: On Fri, 18 Nov 2005 13:49:36 -0500, Duncan Murdoch (DM) wrote: I'm working on a Latex document with lots of R code in it, so naturally enough it would be a good idea to use SWeave. But then I don't get to see the output as I'm editing. Or do I? Is there a tool to process a .Rnw file and incorporate the output from the commands into it (in a form that is not used for producing the output .tex file, but which is updated each time I process the file)? I'm not sure if I understand the question correctly, but if you edit Sweave files in Emacs using ESS you can send the code lines to a running R process, and there you see the output. At least that's how I write my Sweave files. When I want to see all at once I typically do a tangle source. That's bad news for me, because I'm allergic to Emacs. Well, the origin of Sweave is that I found Tony Rossini's ESS-noweb mode for Emacs really neat and started to explre what you can do with it ... What I had in mind was this: In my .Rnw file, I enter: echo=true= 1:3 @ Then I pass it to some tool, which modifies the .Rnw file, changing it to something like echo=true= 1:3 @ % 1:3 % [1] 1 2 3 (My editor will notice that the tool has changed the file and offer to load the new version at this point. I think that's a reasonably common editor option.) Then I can see what I'm writing about when I describe the results. If I later come along and edit the source to change it to echo=true= 1:4 @ % 1:3 % [1] 1 2 3 then the next time I run the file through the tool it will delete the stale output and modify my file to look like this: echo=true= 1:4 @ % 1:4 % [1] 1 2 3 4 Shouldn't be too hard to code (apart from the fact that you cannot insert figures as easily as text), but I personally am unlikely to do it because it is completely orthogonal to my style of interacting with Sweave documents. When I edit them I always want them to be connected to a running R process to easily try out modifications etc. Ad emacs vs other editors: well, we just would need another editor that is connected to a running R process, i.e., can easily send code lines to R, and there are a couple of those. Emacs will know when you are in a code chunk and when you are in a doc chunk, and lets you execute code only in those cases (including sending all of the current chunk to R). It also does syntax highlighting (R vs LaTeX) in dependence on the But if the user knows when to press the corresponding button a simple solution might be to simply turn of the R connection for LaTeX files in another editor than Emacs. Besides the advantage that I had in mind (being able to see the output as I'm editing, and being confident that it will match the output in the final document), this will mean that I'll have a versionable record of what the output looked like (so I'll be alerted to changes in it caused by updates to R or some package I'm using). I could get this by saving the .tex output, but to me this seems preferable. But I don't have a lot of experience with SWeave yet, so maybe there's a better workflow. That is something I have alraqdy thought a little bit about, i.e., to have mechanisms for easily comparing the processed versions of Sweave files and see if something has changed. The tricky bit are (as always with regression tests) the figures, and I have no simple solution for that yet. Started playing with Paul's GraphicsQC package, but found no time for serious coding yet. Without checking figures a simple diff on the .tex files so far worked fine for me ... Best, Fritz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] SWeave - can I see output in the source?
On Fri, 18 Nov 2005 13:49:36 -0500, Duncan Murdoch (DM) wrote: I'm working on a Latex document with lots of R code in it, so naturally enough it would be a good idea to use SWeave. But then I don't get to see the output as I'm editing. Or do I? Is there a tool to process a .Rnw file and incorporate the output from the commands into it (in a form that is not used for producing the output .tex file, but which is updated each time I process the file)? I'm not sure if I understand the question correctly, but if you edit Sweave files in Emacs using ESS you can send the code lines to a running R process, and there you see the output. At least that's how I write my Sweave files. When I want to see all at once I typically do a tangle source. Best, Fritz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave (R?) font encoding problems
On Mon, 31 Oct 2005 16:46:24 +0100,
Luís Torgo (LT) wrote:
Dear R list,
I'm having some problems with font encodings when using R+Sweave+Latex in
my
native language: Portuguese.
My environment:
Kubuntu 5.10 Linux
$ uname -a
Linux nassa 2.6.12-9-686 #1 Mon Oct 10 13:25:32 BST 2005 i686 GNU/Linux
R R.version
_
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status
major2
minor1.1
year 2005
month06
day 20
language R
R Sys.getlocale()
[1]
LC_CTYPE=pt_PT.utf-8;LC_NUMERIC=C;LC_TIME=pt_PT.utf-8;LC_COLLATE=pt_PT.utf-8;LC_MONETARY=pt_PT.utf-8;LC_MESSAGES=pt_PT.utf-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=C;LC_IDENTIFICATION=C
R localeToCharset()
[1] ISO8859-1
Here is a small example trying to replicate my problems:
File:exp.Rnw
\documentclass[10pt,twoside]{article}
\usepackage[dvips]{graphicx}
\usepackage[portuges]{babel}
\usepackage[latin1]{inputenc}
\usepackage[T1]{fontenc}
You use a UTF-8 locale but load latin1 input encoding in latex - that
cannot work.
Try
\usepackage[utf8]{inputenc}
and no special fontenc setting - works for me for Austrian German.
HTH,
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] setkeys and Sweave
On Fri, 16 Sep 2005 10:38:51 +0200,
Christian Hoffmann (CH) wrote:
Hi there:
Using
\setkeys{Gin}{width=1.0\textwidth}
\setkeys{Gin}{height=10cm}
\setkeys{Gin}{height=0.8\textwidth}
all seem to work under R-2.1.1 under sparc, solaris2.9, but
\setkeys{Gin}{scale=0.3}
\setkeys{Gin}{angle=90}
do not work. I have not been able to find relevant information, googling
on setkeys proved confusing, at best.
http://cnlart.web.cern.ch/cnlart/218/node85.html states:
---
Setting key values globally
If you want to specify a global value for a set of keys, then you can
use the \setkeys command defined in the keyval package (described below).
As an example let us consider the case where you would like your figure
to be scaled to the width of the line. Then you could specify the following:
\setkeys{Gin}{width=\linewidth}
The first argument Gin of the \setkeys command refers to the
\includegraphics command. The result will be that all images include
with this command (when the graphicx is loaded) will be set to the
desired width inside the current group or environment.
In the similar way one could specify any of the possible arguments of
the \rotatebox command by using the Grot specifier, e.g.,
\setkeys{Grot}{origin=tc}
---
Question:
Which variants of \setkeys are there? Is there a list stating these?
That's not really an R question, but a LaTeX question. Maybe you have
more luck on a LaTeX list. I always use the grfguide.ps manual that
comes with the graphics package (at least on my Debian Luinux box) as
reference, or the LaTeX companion.
Can several \setkeys{of the same sort} be used inside one document?
Yes, I regularly do that. Every \setkeys{} sets the value from the
point in the LaTeX document where it appears, i.e.,
\setkeys{Gin}{width=1.0\textwidth}
fig1
\setkeys{Gin}{width=0.5\textwidth}
fig2
does the expected.
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Long lines with Sweave
On Thu, 15 Sep 2005 09:35:25 +0200,
Martin Maechler (MM) wrote:
Jan == Jan T Kim [EMAIL PROTECTED]
on Wed, 14 Sep 2005 14:46:20 +0100 writes:
Jan On Wed, Sep 14, 2005 at 02:49:56PM +0200, Henrik Andersson wrote:
Jan T. Kim wrote:
On Wed, Sep 14, 2005 at 10:14:59AM +0200, Henrik Andersson wrote:
I have used Sweave a lot the latest year, but never really used any
long
function calls.
If I have code which look like this
-
gof - benthic.flux(ID=Gulf of Finland,
meas.conc=conc,
bw.conc=bw.conc,
time=times,
substance=expression(DIC~(mmol~m^{-3}))
)
-
I get the output by Sweave in my pdf file, like this:
---
gof - benthic.flux(ID = Gulf of Finland, meas.conc = conc,
+ bw.conc = bw.conc, time = times, substance = expression(DIC ~
+ (mmol ~ m^{
+ -3
+ })))
I can understand that it will not look exactly as entered but why is
the
'-3' on a line of it's own?
Can anyone suggest a idea to how I can make this more readable.
It seems you've been thinking LaTeX rather than R ;-) :
The exponent -3 in the expression should be enclosed by parentheses
rather than by curly braces.
The code formatting done by the print method inserts the newline after
{ and before }.
Best regards, Jan
If you look at demo(plotmath), I get the impression that m^(-3) does not
give me the desired behavior.
I want to have -3 in superscript without visible parentheses.
Tricky!
Jan Ok, I see.
Jan It seems to me that you could omit the curly braces in the example, I
Jan don't see any differences between the title in the plots produced by
Jan plot(1:10, main = expression(DIC~(mmol~m^-3)))
Jan and
Jan plot(1:10, main = expression(DIC~(mmol~m^{-3})))
Jan For more complex exponents, you could try plain() to prevent them from
Jan being wrongly grouped by operator precedence, as in
Jan plot(1:10, main = expression(DIC~(mmol~m^plain(-3 + t
neat idea, but
Jan Not exactly ideal for readability, however...
indeed. And really only a workaround:
You shouldn't have to uglify your R code in order to work around
Sweave pecularities.
Hmm, it's not really an Sweave peculiarity, but one of the R
parser. After saving Henrik's code in file test.R I get
R x = parse(test.R)
R x
expression(gof - benthic.flux(ID = Gulf of Finland, meas.conc = conc,
bw.conc = bw.conc, time = times, substance = expression(DIC ~
(mmol ~ m^{
-3
}
R deparse(x)
[1] expression(gof - benthic.flux(ID = \Gulf of Finland\, meas.conc = conc,
[2] bw.conc = bw.conc, time = times, substance = expression(DIC ~
[3] (mmol ~ m^{
[4] -3
[5] }
and the latter is used by Sweave. The code chunks need to be parsed,
because otherwise there is no way how to know where to insert
output. A source(..., echo=TRUE) will suffer from the same problem.
Best,
Fritz
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Setting width in batch mode
On Thu, 8 Sep 2005 15:01:23 -0400 (EDT), Jonathan Dushoff (JD) wrote: As instructed, I have spent a long time searching the web for an answer to this question. I am trying to use Sweave to produce lecture slides, and have the problem that I can't control the formatting of my R source. Setting options(width), as recommended in this forum, works fine on the R _output_, but seems to have unpredictable effects on the echoing of the source code. If I try setting options(width) directly in R, I note that it has _no_ effect on echoed source code, whereas Sweave does sometimes break source code, but not predictably, and not to the same width as output code. I would be happy with any method of manually or automatically controlling the line width of Sweave source, using R, Sweave or LaTeX options. Making the font smaller does not count, though; I want to break the lines. Any help is appreciated. An example of Sweave input and output is appended. The last break is right, while the others are too late. The deparser of R only *tries* to break lines at the given cutoff (Sweave uses 0.75*getOption(width) for input lines), so you soemtimes have to play a little bit, and yes, results are somewhat unpredictable. After storing your code in file ex1.R I get: R expr=parse(ex1.R) R length(expr) [1] 5 R for(n in 1:length(expr)) print(deparse(expr[[n]], width.cutoff=.75*55)) [1] options(width = 55) [1] data(state) [1] data.frame(area = mean(state.area), pop = mean(state.pop), [2] hop = mean(state.area)) [1] c(medianarea = median(state.area), medianpop = median(state.pop)) [1] c(medianarea = median(median(state.area)), [2] medianpop = median(state.pop)) R for(n in 1:length(expr)) print(deparse(expr[[n]], width.cutoff=.75*45)) [1] options(width = 55) [1] data(state) [1] data.frame(area = mean(state.area), [2] pop = mean(state.pop), hop = mean(state.area)) [1] c(medianarea = median(state.area), [2] medianpop = median(state.pop)) [1] c(medianarea = median(median(state.area)), [2] medianpop = median(state.pop)) I know that's not exactly the answer you were looking for, but that's the way it is. I'll add a sentence or two to the FAQ. Best, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to read individual values from a pixmap object
On Thu, 4 Aug 2005 18:02:55 +1000, Tony Gill (TG) wrote: [...] Now I would like to read individual pixel values and store them in a separate vector. However I have not found a straight-forward way to do this. I thought that something like: x - xGrey[1,1] would return the pixel value, but it seems to return a pixmap object with dimension 1x1 (i.e. only one pixel in size) xGrey[1,1] Pixmap image Type : pixmapGrey Size : 1x1 Resolution: 1x1 Bounding box : 1 0 2 1 Any ideas on how to get the actual pixel value from a pixmap? (Note I could output to an ascii file and then read the file back in as text - but not nice!) getChannels(xGrey) will get you the matrix of pixel values. HTH, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] LyX and Sweave
On Mon, 25 Jul 2005 14:12:41 +0200, Gorjanc Gregor (GG) wrote: Hello R-users! I have tried to use Sweave within LyX* and found two ways to accomplish this. I have attached LyX source file for both ways as well as generated PDFs. I have copied Gregor's files at http://www.ci.tuwien.ac.at/~leisch/Sweave/LyX for those who didn't get the attachments. LyX looks actually much better and stable then when I last had a look a couple of years ago. To add to the discussion: One might even get better integration between Sweave and LyX because LyX allows specification of file converters: Edit-Preferences-Converters Edit-Preferences-File Formats After registering .Stex as a file format for Sweave I can import .Stex files using conversion command reLyX -f $$i mv $$i.lyx $$o and the move is necessary only because reLyX produces foo.Stex.lyx rather then foo.lyx. Using an Sweave shell script like Gregor's in combination with lyx -e latex might do the trick to have direct conversion to PDF from the LyX GUI. Best, Fritz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] LyX and Sweave
On Wed, 27 Jul 2005 15:28:54 +0200, Gorjanc Gregor (GG) wrote: [...] Nope. That's what I also thought, but I was really amaized when discovered that there is no need for this. You only need to set up noweb stuff as mentioned at http://thread.gmane.org/gmane.editors.lyx.general/18847 and use article(noweb) for document style. Then everything (export and view directly from LyX GUI) just works. As I said I was really surprised with it. Try with SweaveNoweb.lyx and you will see. This way, one can skip my silly Sweave.sh ;) Ahh, now I get it. Still it needs some polishing, because after configuring LyX that way regular noweb will no longer work, but it shouldn't take too much of an effort to duplicate the noweb configs in LyX to recognise Sweave. That certainly looks like the way to go, might give Sweave another strong push because people do no longer have to learn all of LaTeX ... If we make a clean solution then I think it shouldn't be too hard to convince the LyX guys to include it in their distribution - that would make an out-of-the-box solution. But it certainly looks very promising. Best, Fritz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave with layout() and loop
On Sun, 26 Jun 2005 11:36:14 -0700 (PDT),
Mikkel Grum (MG) wrote:
When I try the following code with the Windows
graphics window, a new window is opened for each
multiple of four images I produce.
par(layout(matrix(c(1,2,3,4), 2, 2, byrow = TRUE)),
mar = c(2, 3, 2, 3))
for (i in 1:n) {
image(... )
}
When I try to do the same with Sweave to produce a pdf
document, I only get one graphic with the first four
graphs. How do I get the rest when n is greater than
four?
Plots, fig=TRUE, eps=FALSE, echo=FALSE,
results=hide, width=6.8, height=9.8=
par(layout(matrix(c(1,2,3,4), 2, 2, byrow = TRUE)),
mar = c(2, 3, 2, 3))
for (i in 1:n) {
image(... )
}
Any ideas?
FAQ A.8:
A.8 Creating several figures from one figure chunk does not work
Consider that you want to create several graphs in a loop similar to
fig=TRUE
for (i in 1:4) plot(rnorm(100)+i)
@
This will currently not work, because Sweave allows only one graph per
figure chunk. The simple reason is that Sweave opens a postscript
device before executing the code and closes it afterwards. If you need
to plot in a loop, you have to program it along the lines of
results=tex,echo=FALSE=
for(i in 1:4){
file=paste(myfile, i, .eps, sep=)
postscript(file=file, paper=special, width=6, height=6)
plot(rnorm(100)+i)
dev.off()
cat(\\includegraphics{, file, }\n\n, sep=)
}
@
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] mlbench xor
On Fri, 17 Jun 2005 13:28:21 +0200, Thorstensen Nicolas (TN) wrote: HI! I have 2D feature vectors and 2 classes. I want to solve this classification problem with SVM. I create an object XOR of the mlbench library. Then I replace the values of the XOR object with my values. Then I do a plot and I have my data plotted and coloured with the labels from the XOR object. So I replace the class labels in the xor object with my class labels. But when I do a plot with the new class labels every object is coloured in one colour. But half of the points should be in different colour(because different class label). As well when I apply svm on the xor object with th replaced data it finds just one class. It is not the purpose of the r-help mailing list that undergraduate students ask questions about their classwork. We have a lab session scheduled for next Wednesday where you can ask questions like this in person. My apologies to the list for the noise that has been generated. Best, Fritz Leisch -- --- Friedrich Leisch Institut fr Statistik Tel: (+43 1) 58801 10715 Technische Universitt WienFax: (+43 1) 58801 10798 Wiedner Hauptstrae 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Hclust question
On Fri, 03 Jun 2005 12:22:52 -0400, Mike Schuler (MS) wrote: Hey, I am running hclust on several different distance matrices and I have a question thats more about labeling. I've been looking for a way to label the edge values on the graph with their distances between them. I've been looking through the documentation and I haven't found anything yet. Anyone know if there is a way to plot 'hclust' graphs with such edge values? Or convert it to another type that can have its edge values labeled? And to clarify what I mean by edge values, I have two pictures describing what I mean. First, http://clavius.bc.edu/~schulerm/images/test.gif [3.8k] is what I currently have. What I'm looking for is something similar to this: http://clavius.bc.edu/~schulerm/images/test2.gif [5.1k]. I arbitrarily put in values on the edges with the Gimp but I'm looking for some way to do that on my plots of 'hclust'. help(dendrogram) example(dendrogram) should give you a start. -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] input line length in Sweave
On Tue, 24 May 2005 16:23:31 -0400 (GMT-04:00), Woodrow Setzer (WS) wrote: I am having trouble in Sweave with input line lengths. For example, I may have in my input file the chunk [...] Is there a way to get Sweave to wrap long input lines better, or get it to use my own formatting of the input? I realize I can edit the output tex file, but that is impractical in my application (too many). I am using R version 2.0.1 Patched (2005-01-26) on a Linux system (so, I suppose one possible answer is that this is fixed in 2.1.0; I cannot switch right now). No, no changes in 2.1 with respect to that problem. I have plans for a solution for this problem, but won't have time for it before summer break - in 2.2 there should be a fix for it. Best, Fritz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave and paths
On Tue, 17 May 2005 14:31:53 -0400,
Bill Rising (BR) wrote:
Is there some way to encourage \SweaveInput{foo} to find foo in a
subdirectory of a file tree?
Sure: Write some code doing it ;-)
Something along the lines of the
behavior of list.files(stuff, recursive=TRUE). This would be very
helpful at calling small modular files, such as solution sets and the
like.
I couldn't see anything in the documentation, and I looked in the
source code, but it seems that SweaveReadFiledoc() wants to look only
in the directory which contains foo.
Well, if you know where it is you can always use the path in the
\SweaveInput{} statement, i.e.,
\SweaveInput{foo/bar}
works for me.
Best,
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] Avoiding Sweave formula cut's?
On Wed, 04 May 2005 13:40:18 +0200, christian schulz (cs) wrote: Hi, anybody know a possibilities how i could avoid less nicely cut's in function calls with sweave like: randomForest(x = RELSHIP ~ ., data = R_RELSHIP[splitR_RELSHIP == 1, ], importance = T, n(*here is the cut in the pdf*) tree = 1000, na.action = na.omit) Until now i add expost linebreaks in the *.tex file, but with dozend of models it might be painfuel for my hands. Currently there is no way of doing this, because the code you see is the result of a parse() and deparse() and I need the parse() step to know where to insert output, i.e., where expressions are complete. I have ideas about chunks where the code is exactly as in the source file, but no time to implement them yet. what you always can do is to write the code in a separate source file, include that with, e.g., latex's listings package and do a source() on it with echo=FALSE. If you want code and output mixed one needs to parse() - you loose the original formatting. .f -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] pstoedit
On Wed, 13 Apr 2005 09:36:21 +0100 (BST), (Ted Harding) ((H) wrote: On 13-Apr-05 Prof Brian Ripley wrote: On Wed, 13 Apr 2005, BORGULYA [iso-8859-2] Gábor wrote: Has onyone experience with pstoedit (http://www.pstoedit.net/pstoedit) to convert eps graphs generated by R on Linux to Windows formats (WMF or EMF)? Does this way work? Is there an other, better way? You can only do that using pstoedit on Windows. ^^ Well, I have pstoedit on Linux and with pstoedit -f emf infile.eps outfile.emf I get what is claimed to be Enhanced Windows metafile and which can be imported into Word (though then it is subsequently somewhat resistant to editing operations, such as rotating if it's the wrong way up). I always use pstoedit -f xfig $1 $figfile fig2dev -L emf $figfile $outfile on Linux (Debian's pstoedit seems not to support emf). Doesn't work for all graphics, but in most cases it does, and when it works I get something I can fully edit in Word, i.e., I can change the text of axis labels, move points etc. HTH, Fritz -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R Package: mmlcr and/or flexmix
On Tue, 12 Apr 2005 00:44:17 -0400, Geller, Scott (IHG) (GS() wrote: Greetings I'm a relatively new R user and I'm trying to build a latent class model. I've used the 'R Site Search' and it appears there's not much dialogue on these packages [...] libray(flexmix) m1-flexmix(nts ~ first_brand_HOLIDAY+ perc_zone1+ perc_Group_nights+ perc_num_asian+ DaysBetweenStays+ CROStays+ DaysSinceLastStay+ wghtmean_median_age_pop100+ perc_num_white+ perc_num_hispanic+ perc_CROStays+ numMonthsActive+ WEBStays+ property_loyalty+ perc_NoZone+ rho+ PCR_Dummy_class+ ltgold1+ ltgold3+ p_hat_PCR, data = data, k = 2, model = FLXglm(family = poisson)) rm1-refit(m1) summary(rm1) [ Scott sent me in private a subset of the data ] For me this seems to work fine: R set.seed(123) R m1-flexmix(nts ~ first_brand_HOLIDAY+ perc_zone1+ perc_Group_nights+ + perc_num_asian+ DaysBetweenStays+ CROStays+ DaysSinceLastStay+ + wghtmean_median_age_pop100+ perc_num_white+ perc_num_hispanic+ + perc_CROStays+ numMonthsActive+ WEBStays+ property_loyalty+ perc_NoZone+ + rho+ PCR_Dummy_class+ ltgold1+ ltgold3+ p_hat_PCR, data = data, k = 2, model + = FLXglm(family = poisson)) R m1 Call: flexmix(formula = nts ~ first_brand_HOLIDAY + perc_zone1 + perc_Group_nights + perc_num_asian + DaysBetweenStays + CROStays + DaysSinceLastStay + wghtmean_median_age_pop100 + perc_num_white + perc_num_hispanic + perc_CROStays + numMonthsActive + WEBStays + property_loyalty + perc_NoZone + rho + PCR_Dummy_class + ltgold1 + ltgold3 + p_hat_PCR, data = data, k = 2, model = FLXglm(family = poisson)) Cluster sizes: 1 2 93 906 convergence after 49 iterations R rm1-refit(m1) R R summary(rm1) Call: refit(m1) Component 1 : Estimate Std. Error z value Pr(|z|) (Intercept) 1.0108e+00 6.4399e-01 1.5696 0.1164971 first_brand_HOLIDAY-9.3504e-01 4.6151e-01 -2.0261 0.0427594 perc_zone1 1.3936e-01 7.4383e-01 0.1874 0.8513845 ... - Component 2 : Estimate Std. Error z value Pr(|z|) (Intercept) 1.00799714 0.39133294 2.5758 0.01000 first_brand_HOLIDAY-0.07928984 0.15935997 -0.4976 0.61880 perc_zone1 0.01208886 0.42596711 0.0284 0.97736 ... So I cannot reproduce the problem. Is maybo one cluster in your solution empty? The EM algorithm can end up in a local optimum with one cluster empty ... either run flexmix() several times by hand or use stepFlexmix() to do so automatically. HTH, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] sweave bwplot error
On Thu, 07 Apr 2005 13:24:42 +0200,
Christoph Lehmann (CL) wrote:
Hi
I use sweave and have a problem with the following figure, but not with
other figures:
tt - data.frame(c(a, b, c), c(1.2, 3, 4.5))
names(tt) - c(x1, x2)
bwplot(x2 ~x1, data = tt)
ok now in sweave:
\begin{figure}[H]
\begin{center}
echo=FALSE, fig=TRUE, height=5, width=10=
lset(col.whitebg())
bwplot(x2 ~x1, data = tt)
@
\caption{xxx}
\end{center}
\end{figure}
PROBLEM:
the pdf of the figure is not correctly created (neither the esp) and the
error I get from sweave is:
pdf inclusion: required page does not exist 0
From the Sweave FAQ:
A.6 Why do R lattice graphics not work?
The commands in package lattice have different behavior than the
standard plot commands in the base package: lattice commands return an
object of class trellis, the actual plotting is performed by the
print method for the class. Encapsulating calls to lattice functions
in print() statements should do the trick, e.g.:
fig=TRUE=
library(lattice)
print(bwplot(1:10))
@
should work.
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] plot(bclust) what is the 2nd plot?
On Wed, 9 Mar 2005 10:36:49 -,
Jacqueline Hall (JH) wrote:
Hi everyone,
Currently i'm trying to understand the bagged clustering algorithm, bclust
{e1071}.
When I run the given example in the help file (as below)
data(iris)
bc1 - bclust(iris[,1:4], 3, base.centers=5)
plot(bc1)
and plot the bclust object, 2 graphs are produced.
The first is a dendrogram, but what is the second plot? The axes are not
labelled and what do the two lines represent?
The monotonic decreasing line gives the relative height of the split
of tyhe tree into 2, 3, etc. branches, the second line is the first
differences of the first. A peak in the differencescan be used as a
crude estimation for the number of clusters.
I tried looking in the URL
given in the references but that didn't help.
Look at Section IV.A of the working paper.
HTH,
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] Putting different colors on labels in plot (hclust)
On Thu, 3 Mar 2005 11:00:10 +0100, JSPC (Jeppe Skytte Spicker) (J(SS) wrote: Hi All R-helpers This is my first (but probartly not last ;-) mail to R-help, so hello to everybody. My problem: Is there a way to give colors to the labels (sample labels) in plots for a hclust object for better visualization? I have looked through plot, points, hclust and more but cannot find anything on label color. Anybody know if this is doable? Have a look at example(dendrogram). Hth, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave and \input or \include LaTeX commands
On Tue, 01 Mar 2005 07:53:47 +0100,
Gregor GORJANC (GG) wrote:
Hi!
What is wrong if there would be the same command?
2 reasons:
1) I try to keep the Sweave and LaTeX namespaces disjunct, i.e., I
currently do not overload regular LaTeX commands with a different
meaning, and I want to keep it that way.
2) If it is the same command, then I you can already take bets on
the date of the first bug report claiming that Sweave's \input{}
command behaves differently that LaTeX's, e.g., by not searching
.Rnw files along the TEXINPUTS path, etc.
I currently also plan only a \SweaveInput{}, but no \SweaveInclude{}
(the former is much easier to implement, because I don't have to
switch output files in the middle of operation).
Recall my example from
previous posts and at the end of this mail. If I have a file a.Rnw and this
one inputs file a1.Rnw. My idea was that Sweave would check \input{a1} or
\include{a1} statements. If file a1 would have extension .Rnw it would
parse it otherwise (i.e. having .tex) it would skip it. Sweave would just
parse .Rnw files, while latex would put all of them in one file during
typesetting.
Example:
- we have files
a.Rnw, which has \input{a1} or \include{a1}
a1.Rnw
Note that theese are *not* the same under LaTeX
- run Sweave(a.Rnw) and you get
a.tex
a1.tex
Nope, for \input{a1} you would get only a.tex. From the LaTeX
documentation:
**
`\input{file}'
The `\input' command causes the indicated `file' to be read and
processed, exactly as if its contents had been inserted in the current
file at that point. The file name may be a complete file name with
extension or just a first name, in which case the file `file.tex' is
used.
**
That is easy to implement, because I read the .Rnw file, replace
(recursively) all \SweaveInput{} statements with their contents until
no more \SweaveInput{} statements are found (here the unique name
comes in handy ;-) and then process as usual.
If you want a fancier system with include statements I am happily
waiting for your code implementing it.
Best,
Fritz
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] Sweave and \input or \include LaTeX commands
On Tue, 1 Mar 2005 12:08:25 + (UTC),
Gabor Grothendieck (GG) wrote:
Friedrich.Leisch at tuwien.ac.at writes:
I currently also plan only a \SweaveInput{},
I agree that its clearer to keep the two systems distinct rather
than having subtle changes in functionality depending on the
extension of the file in \input.
While we are discussing I just wanted to bring two related points up
regarding how Sweave and R CMD interact.
1. As mentioned in a previous post in this thread, if I don't
want R CMD CHECK to process a certain portion of my vignette
(since its involves lengthy processing or software that might not
be available on other systems) I place that portion into a file
called sub, say, with no extension so that R CMD CHECK does not know
its a Sweave file (and therefore automatically process it). I then
process it manually with Sweave: Sweave(sub) and in my main file,
main.Rnw, have an input statement
\input{sub.tex}
The only thing that's a bit confusing is that sub has no extension
but otherwise this has the intended effect of letting me circumvent
the R CMD CHECK for sub. This is all ok, it works fine, but I
was just wondering if there are any clearer ways of achieving this
effect. I guess I could use an extension such as .Rnw-hide or
use the .Rbuildignore file to mask it (although using .Rbuildignore
in that way has the disadvantage that it would be entirely excluded
from the build) but was just wondering if there is some standard way
of dealing with this situation.
Both R and TeX are programming languages, and both feature if/else
statements, so you can easily do
if(FAST){
load(pre-computed-results.RData)
}
else{
res = compute.results()
save(res, file=pre-computed-results.RData)
}
But note that vignettes are meant as introductionary material
containing user-runnable examples, so putting lengthy computations in
there might not serve that purpose too well (depends on the packages
and application, of course).
2. A second problem that is related is that I think there should
be an easy way to include a .pdf vignette that was not generated
by Sweave or even latex. Currently, as I under it, one must use
Sweave since the package building process uses the \VignetteIndexEntry
and associated commands to know how to process the build. If this
is already possible then can someone indicate how its done. Some
time ago I raised this point but no one responded at that time.
Packages already can have documentation in arbitrary formats (although
we strongly recommend PDF) in the inst/doc directory and many packages
on CRAN do have non-Sweave docs. The directory is linked into the
help.start() version of the help system (HTML help in the Windows
Help menu). If inst/doc contains a file index.html that is used as a
TOC for the package docs. I decided to call those other documentation
objects user guides mostly because I had no better idea.
I think we should not call them vignettes for several reasons. Users
should be able to expect that they can easily get and execute the code
contained in a vignette. r-devel contains a poor man's non-gui
version of Bioconductor's vExplorer() where the edit() method for
vignette objects opens the code in an editor. It would be absolutely
fine with me to use alternative methods for vignettes than Sweave (I
am unlikely to implement any ;-), but code extraction for testing and
learning is a key concept.
So a PDF file at the moment does not qualify as a vignette, and that
is not because of missing \VignetteIndexEntry{} statements, but
because you cannot extract the code from the file. The vignette
concept of documents where you can do computations on the code
contained in the document is by no means limited to Sweave, but
currently we do not have any other implementation which can be
installed on all key platforms without too much difficulty.
BTW, I think this discussion is getting way too technical for the
r-help list - if this thread goes on it should do so on r-devel.
Best,
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] Sweave and \input or \include LaTeX commands
On Sun, 27 Feb 2005 12:32:44 + (UTC),
Gabor Grothendieck (GG) wrote:
[...]
Since this might not be desirable in all instances,
if Sweave were to have an include facility then it should
not be implemented in such a way that the latex include facility
can no longer be used. The point was just that it should be possible
to do the include at the Sweave or at the latex level.
I agree that it should not be the same command. I have put an
\SweaveInput{} on my 2do list, should be doable for R 2.1.0.
Best,
Fritz
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Re: [R] Re: Run Sweave and LaTeX directly from command line
On Tue, 22 Feb 2005 20:21:46 -0600,
Dirk Eddelbuettel (DE) wrote:
On 22 February 2005 at 14:58, [EMAIL PROTECTED] wrote:
| side note 2: For make afficionados the follwing 2 rules in combination
| with the Sweave script from the FAQ do almost the same (that's what I
| use :-)
Sure, but it requires a (arguably small) Makefile in every sweave project
directory.
Not really, the way I do it is that I have a $HOME/etc/Makeconf with a
lot of personal rules like those for .Snw files, and in my .bashrc I
define
fmake ()
{
make -f ~/etc/Makeconf $*
}
such that calling fmake instead of make gives me my private rules in
every place I need them :-)
Would you consider integrating Gregor's script (or a suitable
modification) instead?
Yes, sure, that's why I made him aware of texi2dvi: At least on Unix
systems we make sure that that is always available, while rubber might
not be. On the other hand, the R 2-liner I mentioned in an earlier
mail might be the better way to go. I always use the make rules I
described, hence had no need for either one of them - none is in the
R sources (yet).
Best,
Fritz
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RE: [R] Run Sweave and LaTeX directly from command line
On Tue, 22 Feb 2005 20:46:01 +0100, Gorjanc Gregor (GG) wrote: Gabor, I definitely agree about use of R, however I am not so much in R as I am in Bash. It took me less than two hours to write this script. At home I use R under windows and I solve problem of portability with Cygwin. I know that this is not optimal solution for everyone but ... Can you provide me some insights/thoughts how this script might be written in R? I am open for discussion and cooperation on this script. What do you think Friedrich? I must look at this texi2dvi. I didn't hav any experience with it jet. I will look at it. Well, I didn't know about rubber before I read your script ... seems like the 2 do the same job. Some windows installations have a tool called texify which again does the same: run latex, bibtex, etc. as many times as needed. Ad shell vs. R: In R we already have almost all that is needed: example(Sweave) library(tools) texi2dvi(Sweave-test-1.tex) should do what you want ... and a Snw2dvi function is the corresponding 2-liner. If there is need for it I'm happy to include it in package utils. HTH, Fritz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: Run Sweave and LaTeX directly from command line
On Tue, 22 Feb 2005 14:29:00 +0100, Gregor GORJANC (GG) wrote: Hello! Those of you, who use Sweave a lot, will probably find my shell script usable. You can get it at: http://www.bfro.uni-lj.si/MR/ggorjan/programs/shell/Sweave.sh No warranty, however don't hesitate to contact me if you find an error or have a patch! Very nice! Side note 1: R ships a version of texi2dvi, hence you might use that one in case rubber is not found. side note 2: For make afficionados the follwing 2 rules in combination with the Sweave script from the FAQ do almost the same (that's what I use :-) %.tex: %.Rnw Sweave $ %.pdf : %.tex texi2dvi --clean --pdf $ Best, Fritz Leisch -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave and connections
On Mon, 7 Feb 2005 12:32:13 +0100, Göran Broström (GB) wrote: I'm learning to use Sweave (it's really great!) and everything works fine, except that occasionally I get, after having sweaved many times, -- Sweave(report.Snw) Writing to file report.tex Processing code chunks ... 1 : term hide Error: chunk 1 Error in file(file, encoding = encoding) : All connections are in use -- This is no big problem, since it helps to close and reopen the R session, but I wonder if I can avoid this, by closing connections or something similar. (I really have no idea of what is going on!) This should happen only if you have errors in the Sweave document: then Sweave may have no chance to close the output file properly. showConnections() lists all open connections, and you may guess what closeAllConnections() does :-) HTH, Fritz -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] autoscaling plot font size in Sweave output possible?
On Sat, 08 Jan 2005 03:59:14 +0100,
Patrick Drechsler (PD) wrote:
Hi Friedrich,
Friedrich Leisch wrote on 07 Jan 2005 09:49:04 MET:
thanks for taking the time!
On Thu, 06 Jan 2005 23:56:31 +0100,
Patrick Drechsler (PD) wrote:
I was wondering if it's possible to have fonts in plots to be
autoscaled to the same font size used by LaTeX in a
surrounding Sweave document.
Not using the standard mechanism, because there figures are
rescaled *after* they are created, and the font is rescaled
together with the rest.
..I was afraid of that...
What yoy have to do is:
1) Create your own Sweave.sty file
[...]
Ok...
2) Explicitly set height and width of each figure chunk to what
it should be in the final document. Unfortunately you cannot
use any fractions of \textwidth or the like because Sweawe has
no means to know what that might be.
see below...
3) Set the font size to what you use in the tex document using
ps.options().
see below...
Could you or somebody else enhance my OP in this sence to
demonstrate the effect intended? I've fiddled around with
`postscrict' and `ps.options' all day long but haven't reached a
working file. The problem is most likely sitting in front of the
keyboard.
It is because of 2) that I didn't follow this route for the
current defaults, and I haven't found a really convincing
alternative which works in most situations ...
Not knowing if it's actually going to help me: Can you point me
to the file which does the conversion to the *.tex file? I've
tried `locate sweave' on my linux box and there wasn't anything
in the results concerning the conversion to TeX.
???
Sweave is part of package utils (which the help page clearly
indicates), the particular driver for Latex is called RweaveLatex and
referenced in the Sweave help page. If you want to have a look at the
source code the easiest thing is to get the R sources and browse in
the sources of package utils ... I'll leave it to you to figure out
which of the files contains the Sweave R code.
I'm one of those guys that wants to have nice looking results at
the end with all plots having the same layout.
To me it sounds much more like you're one of those guys who like it
when others solve their problems for free. I gave you an IMO perfectly
working cookbook recipe and you didn't even bother to tell me what did
not work out for you, only a see below to completely different
things (export from MATLAB isn't exactly helping me in guessing what
went wrong for you).
As christmas present (mostly to other who bother to follow the thread)
attached a solution that has exactly the same font in plots and normal
text (and was obtained by simply following the recipe I gave in my
earlier email step by step).
Best,
Fritz
* file.Rnw *
\documentclass{article}
\newcommand{\mytext}{some x label --- some y label --- some x label
--- some y label}
\usepackage{MySweave}
\usepackage{times}
\begin{document}
\mytext
results=hide,echo=false=
ps.options(pointsize=10,family=Times)
test0,echo=F,fig=T,width=2,height=2=
x - 1:10
y - sin(x)
plot(x,y,
xlab=some x label,
ylab=some y label
)
@
\mytext
test1,echo=F,fig=T,width=4,height=4=
plot(x,y,
xlab=some x label,
ylab=some y label
)
@ %def
\mytext
\end{document}
* MySweave.sty ***
\RequirePackage[T1]{fontenc}
\RequirePackage{graphicx,ae,fancyvrb}
\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
\newenvironment{Schunk}{}{}
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Re: [R] autoscaling plot font size in Sweave output possible?
On Thu, 06 Jan 2005 23:56:31 +0100,
Patrick Drechsler (PD) wrote:
Hi,
I was wondering if it's possible to have fonts in plots to be
autoscaled to the same font size used by LaTeX in a surrounding
Sweave document.
Not using the standard mechanism, because there figures are rescaled
*after* they are created, and the font is rescaled together with the rest.
What yoy have to do is:
1) Create your own Sweave.sty file, say MySweave.sty which is a copy
of the ofiginal one *without* the \setkeys{Gin} line and insert a
\usepackage{MySweave}
in the .Rnw document.
2) Explicitly set height and width of each figure chunk to what it
should be in the final document. Unfortunately you cannot use any
fractions of \textwidth or the like because Sweawe has no means to
know what that might be.
3) Set the font size to what you use in the tex document using
ps.options().
It is because of 2) that I didn't follow this route for the current
defaults, and I haven't found a really convincing alternative which
works in most situations ...
Hth,
Fritz
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] Sweave and transparent PDF?
On Thu, 04 Nov 2004 14:20:21 +0100,
Benno Pütz (BP) wrote:
Hello,
I have run across the following problem:
Creating PDF files manually by using
pdf(version=1.4)
I can make graphs using the new transparency feature of R2.0. If,
however, I try to create the same graphs with Sweave, all transparent
stuff is gone. This os likely due to the default version parameter in in
pdf().
How can I tell Sweave to use the newer PDF version? The parameter seems
to be hard-coded (not via some option) and I could not come up with some
kind of hook ...
Good point, currently I see no way short of directly creating the PDF
file and manually including it in latex, i.e., do
**
fig=false=
pdf(file=foo.pdf, version=1.4)
myplot(...)
dev.off()
@
\incudegraphics{foo}
**
But we should think about a more general mechansim to specify defaults
for the PDF device (not only for Sweave).
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] unable to open connection
On Mon, 25 Oct 2004 10:10:06 +0200, Uwe Ligges (UL) wrote: Prof Brian Ripley wrote: Actually, you are unable to connect to the Internet from R on your computer. Perhaps you are not connected, or need to set a proxy? Please read the rw-FAQ, as the posting guide asks. Note that right now you there are no packages on CRAN and Bioconductor has not yet released packages for R 2.0.x. The first is a short-term problem, Yes, unfotunately, there was a network breakdown caused by a broken router (that one that connects the whole building with the world) over the weekend - and our department has no access to that machine. The problem is solved now. Windows binaries will soon be back on CRAN. They are now on the CRAN master site, mirrors may take a day or two to recover. Best, Fritz Leisch -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Pixmap problem
On Wed, 25 Aug 2004 21:42:55 +0200 (CEST), Roger Bivand (RB) wrote: On Wed, 25 Aug 2004, Benjamin Lloyd-Hughes wrote: Hi, I'm having trouble writing .pnm images which I think is due to a problem with my colour space. The pixmap object seems to be looking for 72 of 8 colours (one per cell?) which doesn't seem healthy... library(pixmap) x - pixmapIndexed(rep(1:8, 9), nrow=6, col=rainbow(8)) x Pixmap image Type : pixmapIndexed Size : 6x12 Resolution: 1x1 Bounding box : 0 0 12 6 Nr. of colors : 72 of 8 write.pnm(x, file=D:/Temp/output.pnm) Error in options(x) : evaluation nested too deeply: infinite recursion / options(expression=)? This one is in: x - pixmapIndexed(rep(1:8, 9), nrow=6, col=rainbow(8)) as(x, pixmapRGB) Error in options(x) : evaluation nested too deeply: infinite recursion / options(expression=)? Actually that was a bug in the methods package of R which was triggered by pixmap, i.e., no pixmap problem. It has been fixed in the soon to be released version 2.0.0 of R. Sorry for the late answer, I have been travelling for most of the last month and didn't have Internet access all the time, hence the pile of unanswered emails got larger and larger. Best, Fritz -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [Rd] Re: [R] Sweave echoing comments (again)
On Wed, 08 Sep 2004 17:46:51 +0200, Wolski (W) wrote: Hi! I observed it also. There are cases where it is not desirable. It will be quite helpfull, if possible, to have a parameter that allows one to switch of removing the #comments. The problem is that the parser does not keep the comments, and I need to parse deparse the source in order to know when expressions are complete, such that I can insert the ourtput in the right places. Currently there is no way of keepng the comments in Sweave code chunks. Best, Fritz PS: I am promising a workaround for quite some time now, but haven't had the time to code that yet, so don't hold your breath. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Apparent conflict between \Sexpr in Sweave and R2HTML
On Mon, 05 Jul 2004 09:08:38 -0700,
Scott Waichler (SW) wrote:
I have come across an apparent bug in the operation of Sweave. If I
load the package R2HTML then execution of \Sexpr{} in an *.Rnw file no
longer works. The \Sexpr{} code is simply written to the *.tex file.
Below are my *.Rnw file, commands, and output.
R2HTML registers another Sweave driver for HTML files, and after that
the Syntax for HTML is in the search list before the default syntax.
options(SweaveSyntax=SweaveSyntaxNoweb)
or calling Sweave like
Sweave(..., syntax=SweaveSyntaxNoweb)
should do the trick. I'll add this to the Sweave FAQ.
Best,
Fritz
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Re: [R] Sweave and echoing R comments
On Sun, 20 Jun 2004 20:34:50 +, Frank E Harrell (FEH) wrote: Charles H. Franklin wrote: Is there any way to echo comments from an R source file into an SWeave- LaTeX document? Example: # Npop is population total # Npoph0..Npoph2 are stratum totals # Npoph is vector of stratum totals Npop-sum(to2000) Npoph0-sum(to2000[bg==0]) Npoph1-sum(to2000[bg==1]) Npoph2-sum(to2000[bg==2]) Npoph-c(Npoph0,Npoph1,Npoph2) In the final LaTeX document, I'd like the comments to be echoed so readers other than me have guidance about variable names etc. I suppose advocates of literate programming might argue that if the comment is important it should be in the body of the .snw file, not merely as R comments. Still... it seems easier to use brief comments in the code itself and more explanatory text in the body of the document. Searches of Sweave and comment in the list and documentation didn't turn up anything about echoing comments in either R or Sweave. Thanks. Charles I agree that it would be nice to see comments in the output. I hope that Fritz Leisch will consider adding a hook that is a user-provided R function that take vectors of character strings representing a chunk of code and generating any desired LaTeX markup for pretty printing of the code. The function would return character vectors in LaTeX format. I like comments to appear in a smaller font, and for certain character translations, such as - being replaced with a left arrow. I agree that it would be nice, and it is on my list of things I want to do over the summer ... Best, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave and R output: possible to suppress Schunk tags in *.tex file output?
On Fri, 12 Mar 2004 08:38:53 -0800,
Waichler, Scott R (WSR) wrote:
Hello,
I would like to fill the rows of a Latex tabular environment with output from
R, as in
\begin{table}
\caption{Table caption.}
\label{tab:events}
\begin{tabular}{c r r r r r}
\hline
echo=false,results=tex=
fill.my.table.rows()
@
\end{tabular}
\end{table}
Sweave produces the output inside \begin{Schunk} and \end{Schunk} commands,
which latex doesn't tolerate within a table. I would prefer to avoid writing all
of
the Latex table code from R. Is my only other option to produce a separate
text file, e.g. under Sweave with results=hide, then use \input{}
on the file?
Oops, that's a bug in Sweave ... the Schunk shouldn't be there in that
case. I will fix it for 1.9.0.
Best,
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED]
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] Sweave and R output: possible to suppress Schunk tags in *.tex file output?
On Fri, 12 Mar 2004 08:38:53 -0800,
Waichler, Scott R (WSR) wrote:
Hello,
I would like to fill the rows of a Latex tabular environment with output from
R, as in
\begin{table}
\caption{Table caption.}
\label{tab:events}
\begin{tabular}{c r r r r r}
\hline
echo=false,results=tex=
fill.my.table.rows()
@
\end{tabular}
\end{table}
Sweave produces the output inside \begin{Schunk} and \end{Schunk} commands,
which latex doesn't tolerate within a table. I would prefer to avoid writing all
of
the Latex table code from R. Is my only other option to produce a separate
text file, e.g. under Sweave with results=hide, then use \input{} on the file?
results=tex will do what you want, i.e., produce no Soutput and Schunk
environments. you may also want to look at package xtable.
best,
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED]
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
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Re: [R] RE: system.time(), sys.time() etc
On Thu, 26 Feb 2004 10:08:36 -0500, Liaw, Andy (LA) wrote: From: Spencer Graves [mailto:[EMAIL PROTECTED] Martin says, This is another instance of S-Plus following R behind and doing it incompatibly [with a reason?] ... . This is one example of a major issue in how to wage and win a standards war, discussed by Shapiro and Varian (1998) Information Rules (Harvard Business School Press). Whether you're Bill Gates or Larry Ellison, you want to make it easy for people to move to your product from a competitor but expensive for your current customers to escape to the competition. Spencer Graves But I believe neither Insightful nor R-core would want to see each other as competitor. (Reality might be quite different.) It would not be in the best interest of either party. (Apologies for putting words in R-Core's mouth. As for Insightful, at least that's David Smith's word when he talked about `Future of S-PLUs' at the 2002 Insightful Technology Conference.) I never saw R about trying to be a competition or replacement for Splus, in fact many of us in R Core think that it is an advantage for R that there also is a commercially supported version of S. I personally would rather like to see if S (i.e. R and Splus combined) gain market share at the cost of certain other statistical software packages (e.g., ones matching the regular expression S..?S :-) Best, Fritz __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] latex problem with Sweave output file under Debian
On Wed, 18 Feb 2004 18:19:48 -0600 (CST), Dan Davison (DD) wrote: Could someone tell me how to end the trouble I'm encountering when running latex on the .tex file produced by Sweave()? Sweave() seems to process the example file (http://www.ci.tuwien.ac.at/~leisch/Sweave/example-1.Snw) without problems, and the file example-1.tex produced is the same as in the Sweave manual. However, when I run latex on example-1.tex, many error messages and requests for user input are generated (below). And when I view the .dvi that eventually results with xdvi it is empty apart from a small graphic containing the box plot that shouldbe there; there is no text. latex produces apparently perfect .dvi files when the .tex files are not produced by Sweave. [...] ! LaTeX Error: File `ae.sty' not found. Type X to quit or RETURN to proceed, or enter new name. (Default extension: sty) Enter file name: ! LaTeX Error: File `fancyvrb.sty' not found. Type X to quit or RETURN to proceed, or enter new name. (Default extension: sty) Enter file name: Well, both ae.sty and fancyvrb.sty seem not to be installed on your system ... probably you don't have the tetex-extra package installed. .f -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R News Volume 3/3
We have published the 2003/3 issue of R News on http://cran.R-project.org/doc/Rnews where you can download the newsletter as PDF or Postscript file. It will propagate to the CRAN mirrors within a day or two. Contents of this issue: Dimensional Reduction for Data Mapping R as a Simulation Platform in Ecological Modelling Using R for Estimating Longitudinal Student Achievement Models lmeSplines Debugging Without (Too Many) Tears Th R2HTML Package R Help Desk: Package Management Programmer's Niche: Regular Expressions Recent Events Upcoming Events Changes in R 1.8.1 Changes on CRAN R Foundation News For the editorial board, Fritz Leisch -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch ___ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-announce __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave and X11 on OSX 10.3
On Tue, 6 Jan 2004 23:44:42 -0700 (MST), Kieran Healy (KH) wrote: Hi - I'm running R 1.8.1 (compiled from source) on Mac OS X 10.3 (Panther). I find that, if Apple's X11 application is not running, Sweave gives an error when it wants to create a pdf or eps figure. E.g., in the package's own example-1.Snw file a boxplot is created at chunk 2: fig=TRUE,echo=FALSE= boxplot(Ozone ~ Month, data = airquality) @ Normally this will create a pdf and an eps version of the boxplot. I get: Sweave(example-1.Snw) Writing to file example-1.tex Processing code chunks ... 1 : echo term verbatim 2 : term verbatim eps pdf Warning message: unable to open connection to X11 display`' Error: chunk 2 Error in X11(display, width, height, pointsize, gamma, colortype, maxcubesize, : unable to start device X11 If I start the X11 application, Sweave runs as normal but displays any figures on an x11() device in addition to creating the eps / pdf files. I don't remember this happening before and experience teaches me to assume the issue is with my own setup rather than Sewave. Maybe there's a problem with the DISPLAY variable, or something that I did while upgrading to Panther -- but I can't see what it is. Has anyone else had this issue? Your R session has obviously x11() as the default plotting device ... e.g., plot(1:10) at the prompt should also give an error, if no graphics device is open. I don't know too much about MacOS X, but having the DISPLAY variable set without having an X11 server surely means asking for trouble on Linux, and I guess MacOS X is not different ... -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Sweave and X11 on OSX 10.3
On Wed, 7 Jan 2004 08:30:04 -0800 (PST), Thomas Lumley (TL) wrote: On Wed, 7 Jan 2004 [EMAIL PROTECTED] wrote: open. I don't know too much about MacOS X, but having the DISPLAY variable set without having an X11 server surely means asking for trouble on Linux, and I guess MacOS X is not different ... Yes, except there is no excuse for doing this under Linux and there are good reasons for doing it on OS X. Under Linux, if you are running X then all your terminals were probably started after the X server, and they are usually children of the X root window. Under OS X the terminals are usually started independently of X11 and may have been running before the X server was started. I don't know any automatic way to have DISPLAY set correctly when the server is running and unset when it isn't. The result is that you either need to have DISPLAY set in .tcshrc or equivalent, or remember to set it when needed. I see, could in this case R for the Mac be smarter about what the default graphics device should be? This is not an Sweave issue, it simply means that under the setup described above any call to plot() ---without actively opening a device first---will fail ... .f __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] passing par() options to pdf under Sweave
On Thu, 4 Dec 2003 15:58:32 -0800 (PST), Anne York (AY) wrote: I'm using Sweave to generate LaTeX output from R. Thank-you very much for this capability. It is very useful. Could someone please tell me how to pass non-default graphics parameters from par() to the pdf driver when it is called by Sweave? (I need to change some of the margin defaults. ) Hoping there is an easy solution to this question, Yes, simply define a hook function for figure chunks: The effect of options(SweaveHooks=list(fig=function() par(bg=red, fg=blue))) should be easy to see :-) The hook function will be executed at the beginning of each chunk where fig=true (i.e., all figure chunks). What you want is something like options(SweaveHooks=list(fig=function() par(mar=c(1,2,3,4 Hope this helps, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Fwd: License Agreement
On Mon, 17 Nov 2003 14:01:17 -0500, Sigrid Volko (SV) wrote: Dear Mr. Leisch, [don't know why you assume that I'm behind r-help ... but anyway ... I was asked by one of our faculty members at Johns Hopkins University to = assist him in licensing a software application that he has developed. This = package is based on R, the statistical software that is distributed as = freeware. In the course of my due diligence analysis, I reviewed the = official R web page which states that R is an official part of the Free = Software Foundation's GNU project. However, it does not explicitly state = under which License Agreement R is made available. Reviewing the GNU = official web page, I assume that R is made available under the GNU General = Public License. I would, however, appreciate if you could confirm that = this information is correct.=20 I think the web page clearly states that R is indeed distributed under the terms of the GPL ... and if you use R you get a pointer to the GPL every time you start it. -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] R News Volume 3/2
We have published the 2003/2 issue of R News on http://cran.R-project.org/doc/Rnews where you can download the newsletter as PDF or Postscript file. It will propagate to the CRAN mirrors within a day or two. Contents of this issue: R Help Desk Integrating grid Graphics Output with Base Graphics Output A New Package for the General Error Distribution Web-based Microarray Analysis using Bioconductor Sweave, Part II: Package Vignettes R Foundation News Recent Events Book Reviews Changes in R 1.8.0 Changes on CRAN Crossword Solution Correction to ``Building Microsoft Windows Versions of R and R packages under Intel Linux'' For the editorial board, Fritz Leisch -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch ___ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-announce __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] CRAN down on Sunday, 26.10.2003
Due to construction work in a neighboring building there will be a power outage in our offices for the complete day of Sunday, 26.10.2003 which means we will shut down all our computers some time tomorrow and reboot them Monday morning (central European time). This includes the server for www.R-project.org cran.R-project.org cran.at.R-project.org Please a mirror site on this day (and do not flood us with bug reports stating that CRAN is down :-). Best, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch ___ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-announce __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] using identify() together with plot () and pixmap()
On Tue, 30 Sep 2003 10:16:11 +0200, Christoph Lehmann (CL) wrote: Dear R users I have a two-dimensional array, whose values I want to plot, using the pixmapGrey class. Plotting works fine, and now I would like to be able to identify some of the points in the plot using identify(). But I get the following message while pressing the left mouse button: plot(pixmapGrey(fmri.vtc[,,slice,volume])) identify(fmri.vtc[,,slice,volume]) warning: no point with 0.25 inches identify() needs x and y values, you are passing it the z values of the image. Maybe you want to use locator()? .f __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] using identify() together with plot () and pixmap()
On Tue, 30 Sep 2003 09:38:31 +0100, Barry Rowlingson (BR) wrote: Christoph Lehmann wrote: plot(pixmapGrey(fmri.vtc[,,slice,volume])) identify(fmri.vtc[,,slice,volume]) warning: no point with 0.25 inches pressing the right mouse button I get: numeric(0) what is the problem here and how can I solve it? The problem is that there is no method for identifying points on a pixmap (and anyway, you are feeding identify() a matrix). You'll need to write an identify.pixmapGrey function. This would do something like use the 'locator()' function to get clicks on the screen, and then it would compute which grid cell the coordinates of those clicks were in. pixmap objects store enough information for you to work this out from the attributes - look at the 'bbox' attribute for example. It would make a nice addition to the pixmap library. Although one thing that just suprised me was that the different flavours of pixmap - pixmapGrey, pixmapIndexed, pixmapRGB - dont all inherit from a 'pixmap' class, But they do, and class pixmap has the necessary geometry information, i.e., size, bounding box and resolution of the image. which might make it easier to write a single identify function for all the types. yes, shouldn't bbe too hard (all contributions welcome). .f __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] allShortestPath function in e1071 package
On Thu, 25 Sep 2003 13:04:21 -0400, Bing Zhang (BZ) wrote: Hi All, I am using the allShortestPath function based on Floyd's algorithm in e1071 package. It runs great when I have less than 5000 nodes. But when I tried to work on more than 5000 nodes, I ran into memory problem. The problem I really want to solve has 1-15000 nodes. Does anybody know how to deal with this problem? Are there any other packages in R that can handle this problem? Thanks! The e1071 implementation uses NxN matrices (where N is the number of nodes), hence it does not scale well with the number of nodes as memory consumption is N^2. From Bioconductor you get package graph which represent the graph using lists of nedges and edges, and needs much fewer memeory if the graphs is sparsely connected. Package RBGL (also from Bioconductor) has shortest paths for such graph objects. .f __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] overlay two pixmap
On Fri, 26 Sep 2003 10:32:21 +0200, Christoph Lehmann (CL) wrote: Hi I need to overlay two pixmaps (library (pixmap)). One, a pixmapGrey, is the basis, and on this I need to overlay a pixmapIndexed, BUT: the pixmapIndexed has set only some of its pixels to an indexed color, many of its pixels should not cover the basis pixmapGrey pixel, means, for this in pixmapIndexed not defined pixels it should be transparent. What would you recommend me to do? Should I go for another solution than pixmap? There is no method for doing this in pixmap yet ... but if you write one (shouldn't be too much code) I'd be happy to include it in the package such that others can use it in the future. -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Re: Tutorial docs: Vignettes! {was searching R-help ..}
On Thu, 25 Sep 2003 16:11:57 +0200, Martin Maechler (MM) wrote: I'd recommend taking one of these (or the Bioconductor ones if you are using some of them!) as an example to follow. And many more packages have other *.pdf documents in their installed ./doc/ directories. However, currently this is not shown in library(help = package) --- nor anywhere on CRAN's package-source page (which may be worth improving ...) Yes (in the long run we want a web page where you can access vignettes directly). BTW [shameless advertising]: there will be an article in the next issue of R News on package vignettes (no vaporware, finished it yesterday). Best, Fritz __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] R News: Call for Papers
R News (see http://CRAN.R-project.org/doc/Rnews/) is running low on submissions lately. If you are the author of a package on CRAN or Bioconductor and want to attract a larger audience to your software, you should consider writing a short article introducing the package. Another typical kind of R News article is to describe a data analysis application using R (not necessarily using software you have written). We are looking forward to all contributions! For the editorial board, Fritz Leisch -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch ___ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-announce __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] CRAN package orphanizing process
As the list of packages on CRAN becomes longer almost on a weekly basis, we need a formal mechanism to handle the case when somebody wants to resign from maintaining a package. Possible reasons for orphanizing a package: 1) The current maintainer actively wants to orphanize the package, e.g., because he has no longer the time or interest to act as package maintainer. 2) The current maintainer does not answer to emails by the CRAN admins for longer periods of time. The orphanizing process: 1) The package gets the special keyword ORPHANED as maintainer in the DESCRIPTION file, the patch level of the version number is increased. 2) The package is moved from $CRAN/src/contrib to $CRAN/src/contrin/Orphaned. 3) As long as the package passes R CMD check for the current release version of R, it additionally remains in $CRAN/src/contrib/. Everybody is more than welcome to take over as maintainer of an orphaned package. Simply download the package sources, make changes if necessary (respecting original author and license!) and resubmit the package to CRAN with your name as maintainer in the DESCRIPTION file of the package. For the CRAN admins, Fritz Leisch ___ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-announce __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Bagged clustering and fuzzy c-means
On Thu, 26 Jun 2003 14:43:41 +0100, Xu Yun (XY) wrote: Dear All: I'm a newbie to R and chemometrics. Now I'm trying apply bclust on fuzzy c-means like this: bc1 - bclust(iris[,1:4], 3, base.centers=20,iter.base=100, base.method=cmeans) Committee Member: 1(1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)Erro r in bclust(iris[, 1:4], 3, base.centers = 20, iter.base = 100, base.method = cmeans) : Could not find valid cluster solution in 20 replications I can't get any valid result with many parameter adjustments, such as iter.base, base.centers etc. But I think fcm should return similar result just like k-means (e.g. centers, cluster size) plus fuzzy membership information. Can anyone explain this for me? cmeans expects a matrix as input, iris[,1:4] is a data.frame. bc1 - bclust(as.matrix(iris[,1:4]), 3, base.centers=5,iter.base=100,base.method=cmeans) works for me. But I agree that this behaviour is not desirable, I'll add an x=as.matrix(x) at the beginning of both bclust and cmeans Besides, I'm not quite understand the meaning of bootstrap. In my view, it might means independent, am I correct? No, a bootstrap sample is a sample drawn from the empirical distribution of a data set, i.e., drawing with replacement from the original data. There are heaps of books explaining what bootstrapping is, simply search for books with bootstrap in the title in your library :-) Best, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] dendrograms
On Wed, 25 Jun 2003 06:31:49 -0400, Edoardo Airoldi (EA) wrote: Hello all, I am using libraries (mva,cluster) to produce dendrograms. With 1000 examples the dendrogram gets too crowded, and i am wondering whether there is an option (which i cannot find) to set the number of leaf nodes, like in matlab, and return the plot and the assignment map examples - leaf nodes. Any suggestion is appreciated. Thanks Just wondering: did you try help(dendrogram) before sending an email to r-help with subject dendrogram? The examples show you how to cut a dendrogram at a specified height ... If you want 10 leafs, you just have to get the height of the 9th splitting (in element height of hclust objects). help(cutree) might also be of interest ... -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] R News Volume 3/1
We have published the 2003/1 issue of R News on http://cran.R-project.org/doc/Rnews where you can download the newsletter as PDF or Postscript file. It will propagate to the CRAN mirrors within a day or two. Contents of this issue: Name Space Management for R Converting Packages to S4 The genetics Package Variance Inflation Factors13 Building Microsoft Windows Versions of R and R packages under Intel Linux Analysing Survey Data in R Computational Gains Using RPVM on a Beowulf Cluster R Help Desk Book Reviews Changes in R 1.7.0 Changes on CRAN Crossword Recent Events For the editorial board, Fritz Leisch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Re: About ability of allShortestPaths function in e1071 package
On Thu, 27 Mar 2003 23:49:04 +0900, Hisaji Ono (HO) wrote: Hello. R's e1071 package has allShortestPaths function using Floyd's algorithm. It is very useful for road network analysis. I'll try to analyze facility allocation programs using this. I'd like to know how much nodes this function can deal with? And for larger nodes(for example million nodes), allShortestPaths employs graph partition algorithm? no, the current implementation uses matrices to represent the graph, hence it can only handle several thousand nodes depending on thje amount of memory your computer has. millions of nodes is currently impossible. best, -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED] A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch --- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] multinomial conditional logit models
On Wed, 29 Jan 2003 11:57:20 -0800 (PST), John Hendrickx (JH) wrote: A multinomial logit model can be specified as a conditional logit model after restructuring the data. Doing so gives flexibility in imposing restrictions on the dependent variable. One application is to specify a loglinear model for square tables, e.g. quasi-symmetry or quasi-independence, as a multinomial logit model with covariates. Further details on this technique and examples with several packages are on my homepage at http://www.xs4all.nl/~jhckx/mcl/ I've been trying to implement an MCL model in R and have been mostly succesful. However I'm still stuck on a few points and I'm hoping someone can point out how to do fix them. To estimate an MCL model, the data must be restructured into a person-choice file. * Each case must be duplicated ncat times (ncat is the number of categories of the dependent variable) * Each case must be identified by a strata variable (id) * Each duplicate must be identified by a variable indexing the choices (newy) * A dichotomous variable must indicate which duplicate corresponds with the respondent's choice (didep) I'm not completely sure if I understand your target format completely, but it sounds like reshape() could do all you want: R df3 id age dose1 dose2 dose4 1 1 40 1 2 3 2 2 50 2 1 3 3 3 60 1 2 3 4 4 50 2 1 3 R reshape(df3, direction = long, idvar=1, varying=list(dose=c(dose1, dose2, dose4))) id age time dose1 1.1 1 401 1 2.1 2 501 2 3.1 3 601 1 4.1 4 501 2 1.2 1 402 2 2.2 2 502 1 3.2 3 602 2 4.2 4 502 1 1.3 1 403 3 2.3 2 503 3 3.3 3 603 3 4.3 4 503 3 which is a (modified) example from help(reshape) ... there you find much more examples. Hope this helps, Fritz -- --- Friedrich Leisch Institut für Statistik DSSTel: (+43 1) 4277 38613 Universität WienFax: (+43 1) 4277 38639 Universitätsstraße 5 [EMAIL PROTECTED] A-1010 Wien, Austria http://www.ci.tuwien.ac.at/~leisch --- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] calling sweave function from latex
On Wed, 29 Jan 2003 14:12:15 +1300,
Sam McClatchie (SM) wrote:
System info:
Mandrake 9.0
R Version 1.6.1
ESS 5.1.21
Emacs 21.2.1
---
Colleagues
I've been calling R-code embedded in my LaTex document using Sweave, but
would like to make things more convenient. At present as I understand it
you first process the R chunks of code using the Sweave function
called from within R to process a precursor file e.g. foo.sw to get a
LaTex file (foo.sw.tex) that you then process with latex foo.sw.tex.
example code segment
%\item {\bf Matched trawl and acoustic data} \label{real data}
\item {\bf Results}
sweave code
echo=false,results=hide=
average.trawl.spp.composition()
@
insert figure generated from sweave code
\begin{figure}
\includegraphics[scale=0.6]{../figures/bycatch_by_weight}
\caption{\label{catch by weight} Proportions of selected species (from
Table \ref{ts length regressions}) in the fish assemblage using
catch rate ($kg\ km{-1}$) as an approximation for fish density
(neglecting variable capture efficiencies). Note: there were no
oblique banded rattails in this dataset, although we have a
\textit{TS-length} regression for them (see Table \ref{ts length
regressions}). Box plot centre line = meadian, box limits are
$25^{th}$ and $75^{th}$ quartiles, whiskers represent 1.5 times the
interquartile range from the median, and points outside the whiskers
are the tails of the distributions.}
\end{figure}
---
This works fine, but it is cumbersome for someone who likes to write a
bit and then latex that additional bit. Of course I can just add the new
LaTex code chunks to the foo.sw.tex and latex that, but I have to
remember to copy the foo.sw.tex back to foo.sw or the versions get mixed
up. Trivial, but annoying.
The question is: can I call the Sweave function from within LaTex so I
just latex the foo.sw.tex and the Sweave chunks will also get processed.
This would be much tidier.
One suspects that the short answer is 'no'.
One way to deal with this is to write several Sweave filew and collect
them into the main latex document using \input{} statements. Then you
can Sweave() only those files which have some changes, makefiles can
automate that easily.
I have some ideas on conditional processing of chunks and re-using
previously saved results in case nothing has changed, but that has not
been implemented yet.
Best,
Fritz
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED]
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
---
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Re: [R] ConTEXT .chl file for R?
On Fri, 24 Jan 2003 04:18:14 +, Andrew C Ward (ACW) wrote: I created one of these a little while ago. If anyone would like it, email me separately and I will send it to you. WinEdt is mentioned on CRAN (under Software/Other) and I believe is quite popular among users of R for Windows. It is shareware, however, whereas ConTEXT is freeware. I don't see much merit in paying for an editor when R itself is free. Others may say Look what I bought with the money I saved on R :-) CRAN carries whatever users submit to it ... the fact that there is a WinEdt configuration file on CRAN is not because it is the officially recommended editor for R, but because Uwe Ligges submitted his code to CRAN and actively maintains it. So if you think ConTEXT is a nice and free editor for writing R code on windows and have already written corresponding configuration maybe you want to share it with the rest of us? I personally use Emacs on Linux ... but would have use for a free and easy-to-use windows editor for teaching (emacs is free, but not easy to use). Best, -- --- Friedrich Leisch Institut für Statistik DSSTel: (+43 1) 4277 38613 Universität WienFax: (+43 1) 4277 38639 Universitätsstraße 5 [EMAIL PROTECTED] A-1010 Wien, Austria http://www.ci.tuwien.ac.at/~leisch --- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Loops Sweave and Many Figures
On Sun, 12 Jan 2003 06:03:41 +0100,
Serguei (S) wrote:
Is it any way?
This code doesn't work:
%%%
\multido{}{10}{
fig=T=
...
@
}
\multido{}{10}{
fig=T,echo=F=
plot(1:10)
@
}
works while the samle with echo=T does not ... seems like multido
cannot hande verbatim enveronments, but that's hardly Sweave's fault.
%%%
Or:
%%%
1, fig=T=
...
@
=
1
@
%%%
what is that supposed to do? if you want a figure also resulting from
the second chunk you need
1, fig=T=
...
@
fig=T=
1
@
or
\SweaveOpts{fig=T}
1=
...
@
fig=T=
1
@
Hope this helps,
--
---
Friedrich Leisch
Institut für Statistik Tel: (+43 1) 58801 10715
Technische Universität WienFax: (+43 1) 58801 10798
Wiedner Hauptstraße 8-10/1071 [EMAIL PROTECTED]
A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch
---
__
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