Re: [R] [ESS] CPU usage on Windows
On 3/19/07, Jonathan Wang [EMAIL PROTECTED] wrote: On 3/16/07, Richard M. Heiberger [EMAIL PROTECTED] wrote: I can't imagine using Windows without Emacs. In particular, the Windows ports of Emacs are very aware of the operating system and usually make the right assumptions. The type of behavior you are noticing can probably be cured by typing C-g in the *R* buffer in emacs. The most likely cause is that the R process in Emacs is waiting for the plot to finish and is querying the plotting device. Most of that excess CPU usage is from the query loop. The C-g tells Emacs and R to stop waiting. If C-g doesn't stop the 100% CPU utilization, then it is most likely something about the specific plot you are drawing. We will need to see a reproducible example to say more. The behavior I'm seeing is different from what you've described. It's reliably reproducible and occurs whenever a plot window is visible, whether using ESS Rterm or Rterm directly. Something as simple as plot(1:10, rnorm(10)) will trigger this behavior. The Windows task manager shows that it's the Rterm process that's spinning and not emacs. I've previously observed the behavior you mention, where ESS gets stuck in a busy loop waiting for the next command prompt from Rterm. This is also (obviously) suboptimal, but isn't the particular issue I'm having. Perhaps it's a graphics driver conflict of some sort? No, it's some weirdness going on with respect to the different threads and blocking (and from a Ripley-esque perspective, the intution I'm presenting is technically wrong). Emacs wants to control certain things from the I/O perspective, and some how doesn't do it right, sending Rterm into 100% CPU utilization. So I think I'm still right, that this is more of an design issue, the conflicting suspects being Emacs' design for controlling Microsoft OS subprocesses (emacs inferior process) and R's design as a subprocess with multiple threads (again, I can't help but think that threads is the wrong word here, I'm sure Duncan knows the right one to use), under Microsoft OSs. (Duncan took this as a cynical backslap, and I can't stay that I wasn't partially intending it, but it's also true at face value without historical baggage of peoples opinions). And again, at this point I firmly believe that it's probably more of an ESS/Emacs issue than a pure R one. best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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.
[R] Editors which have strong/solid support for SWeave?
Greetings! I have a few colleagues who like the idea of Sweave, but have failed to become enlightened monks of the One True Editor (http://www.dina.dk/~abraham/religion/) Are there any other Microsoft-centric editors or IDEs which have solid support for writing SWeave documents (dual R / LaTeX enhancements similar to ESS's support)? Has anyone tried the folding editors which support Noweb? (the alternative would be brainwashing, but that is generally frowned upon ;-). best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] Editors which have strong/solid support for SWeave?
What I'm wondering about is can you have both the LaTeX and R advantages that WinEDT provides available at the same time? (does it handle the modes in a context-sensitive way within the same document, or do you have to use one or the other, or do you just have to be careful?) On 7/5/06, Chuck Cleland [EMAIL PROTECTED] wrote: A.J. Rossini wrote: Greetings! I have a few colleagues who like the idea of Sweave, but have failed to become enlightened monks of the One True Editor (http://www.dina.dk/~abraham/religion/) Are there any other Microsoft-centric editors or IDEs which have solid support for writing SWeave documents (dual R / LaTeX enhancements similar to ESS's support)? Has anyone tried the folding editors which support Noweb? Tony: I don't know what you mean by a folding editor or Microsoft-centric, but I am using R, WinEdt, and MikTeX on WinXP. I have been using Sweave with this setup for several months and have been happy with it. Thanks to Uwe Ligges, the RWinEdt package provides R enhancements to WinEdt, and WinEdt is configured to work with MikTeX by default (can be configured to work with other LaTeX systems). The editor itself is very intuitive - all you really need to know to get started is how to write *.Rnw files (via Sweave documentation and the many examples on can find). I can recommend this setup for anyone working on Windows. http://www.winedt.com/ http://cran.r-project.org/src/contrib/Descriptions/RWinEdt.html hope this helps, Chuck (the alternative would be brainwashing, but that is generally frowned upon ;-). best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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 -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 -- best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). [[alternative HTML version deleted]] __ 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] Editors which have strong/solid support for SWeave?
On 7/5/06, Uwe Ligges [EMAIL PROTECTED] wrote: A.J. Rossini wrote: What I'm wondering about is can you have both the LaTeX and R advantages that WinEDT provides available at the same time? (does it handle the modes in a context-sensitive way within the same document, or do you have to use one or the other, or do you just have to be careful?) No, not at the same time. I planned to add such a feature for the last two years or so, but there were always topics with higher priority on my ToDo list. Anyway, these days Tinn-R seems to be the Windows way to go. It already supports R, LaTeX and SWeave. It definitely has active development. Thanks for the suggestion, Uwe, I'll take a look. best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). [[alternative HTML version deleted]] __ 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] Editors which have strong/solid support for SWeave?
On 7/5/06, Ramon Diaz-Uriarte [EMAIL PROTECTED] wrote: On Wednesday 05 July 2006 10:14, A.J. Rossini wrote: Greetings! I have a few colleagues who like the idea of Sweave, but have failed to become enlightened monks of the One True Editor (http://www.dina.dk/~abraham/religion/) Are there any other Microsoft-centric editors or IDEs which have solid support for writing SWeave documents (dual R / LaTeX enhancements similar to ESS's support)? Has anyone tried the folding editors which support Noweb? Dear Tony, I often use Leo (http://webpages.charter.net/edreamleo/front.html) which is like a literate editor on steroids (folding + outlining, noweb and cweb support, and a _lot_ more), and I use it for all complex/long Rnw documents, including interacting with R ... ...but I cheat, because the editing itself (of the nodes or folds), including submitting code to R from the R chunks, I do in emacs (with ESS). Leo is available for Linux, Win, Mac and is written in Python. I've used Leo a few years ago, and liked it (but not enough to convert). I'll have to try it again. Thanks! best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] ROrca
From: Erin Hodgess [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Date: Mon, 15 May 2006 05:49:11 -0500 Subject: [R] Rorca zip? Dear R People: Is there a Windows binary for ROrca, please? When I did the search on the R site, there were several links to a zip file, but all of the links were broken. Thanks in advance! R Windows R-2.3.0 ROrca works quite well for dynamic multiviews for correlated high-dimensional data under the recent SJava's and R. I think there were a few copies around somewhere on the 'net, I believe the last location might've been on Greg Warnes' WWW site, which I'm not sure was moved completely intact from Yale to Rochester with him. I've got a working copy of the last public release somewhere, of course, but unfortunately, I don't have any means to distribute it. I've even got a much more recent version, but I don't have the legal authority to distribute it, as it was modified at work. best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] [S] S-PLUS 8 beta program [repost]
On 3/31/06, eugene dalt [EMAIL PROTECTED] wrote: In addition, I think people should always explore ways to repackage exclusive S-Plus facilities and libraries into R. By rewritting them or using GPL loopholes. Licenses are important. They state for the author, precisely what the author intends. Just because it's not really what the author might want, is a different story. The GPL has no loopholes. It does precisely what it is supposed to do, which it to provide free-as-in-speech software, which maintains that freedom. Read it; love it; use it :-). I do. Take BioConductor, which isn't GPL (it would've been by my choice, which is what I argued for when we released it the first time). The intent was for others to use it, and not be forced to share the changes. I went along with that, fully aware of what I was going to be contributing to. It seems to me that Insightful is very good at protecting whatever they create and the same time feels very comfortable taking R stuff to keep they clients happy. In essence they are selling free stuff. Packaging is worth something. It's why folks pay for Linux distributions. I'm very happy that Insightful packages up free stuff. I wish they'd do it better and add incredible amounts of value to S-PLUS, so that it could truly compete with R. There are some really nice facilities that R doesn't have, and probably will never have. But it's still missing key features. And I'm happy that they are finally listening to comments (I can't claim to be the only one that suggested this over 7 years ago -- I also can't claim to be a user (again), until my new job; but it's nice that it took them less than a decade). best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] [S] S-PLUS 8 beta program [repost]
On 3/31/06, A.J. Rossini [EMAIL PROTECTED] wrote: There are some really nice facilities that R doesn't have, and probably will never have. But it's still missing key features. It's late, and somewhere in my 18+ hour day today, I spent a miserable evening in Heathrow. Yech. I meant: There are some really nice facilities in S-PLUS that R doesn't have, and probably never will have. But S-PLUS is still missing key features. best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] ESS, transcripts, and such
Work in an inferior R session M-x write-buffer to TonyIsSilly.Rt So now your buffer is associated with a file, TonyIsSilly.Rt M-x R-transcript-mode M-x ess-transcript-clean-buffer and you should be left with a script file, not a transcript file. Enjoy. I'll be talking about such things at useR if enough people show up for the tutorial... On 3/13/06, Kevin E. Thorpe [EMAIL PROTECTED] wrote: A.J. Rossini wrote: SNIP One nice thing about ESS/Emacs is that it will cean a transcript buffer. So if you are working in the inferior process buffer (where you shouldn't be, but that's for another day), then you can write it to disk as a transcript file, and clean it into a script. Okay, I'll bite. Could you ellaborate a bit on your parenthetical comment? best, -tony Thanks, Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.946.3297 -- best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] ESS, transcripts, and such
From: Duncan Murdoch [EMAIL PROTECTED] To: [EMAIL PROTECTED] Date: Fri, 10 Mar 2006 08:33:09 -0500 Subject: Re: [R] To improve my understanding of workspaces Other than Emacs, I use the same work habits as Adai. An advantage of this workflow is that almost everything is stored in text format, so it is easy to compare different versions to see what has changed, and it works very well with version control (I use Subversion). The only thing I'd add to his recommendation is that you be sure to save the scripts that produced the objects in the binary images (his lala.rda), so that they can be reconstructed if necessary. As long as the reconstruction isn't too difficult, this means I don't need to bother to save them in Subversion. Agree with everything that Duncan said, except that I use bzr or darcs instead of subversion, and of course, ESS/Emacs. One nice thing about ESS/Emacs is that it will clean a transcript buffer. So if you are working in the inferior process buffer (where you shouldn't be, but that's for another day), then you can write it to disk as a transcript file, and clean it into a script. best, -tony __ 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] xlispstat and R
From: Wensui Liu [EMAIL PROTECTED] Just curious how xlispstat is used in the industry and what's it strengthen compared with other computing languages such as R or matlab? Almost not at all, though there are a few holdouts. On a related note, I've been doing some interesting things with a branch of LispStat for CommonLisp. It'll be more interesting when R gets embedded (now it's back on topic). Rumor has it that R is embedded within SBCL, which makes for an interesting distributed computing environment. It's a nice system, it still works, it's got some reasonable (though old) tools, numerically it needs a good bit of work and updating, but for a 17-year old program, it works quite nicely. Dynamic graphics are comparable to GGobi's (more flexible, but less scalable). Plus, it truly works cross platform. CommonLispStat is fast (SBCL and CMUCL are compiled, not interpreted, commonlisps), but needs a bit of work with numerics (SBCL isn't stable), and Graphics (CLISP doesn't quite like it yet; though tk and gtk2 supported), and decisions about object systems (the old prototypes vs. CLOS) are still open, both being available at this point. Also back on topic, Duncan T-L had a nice embedding of R/XLispStat that worked nicely, but XLIsp isn't a rapidly evolving language, unlike the OSS common lisps. best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] [ESS] ESS and Emacs
Whoops, sorry John. In the last few months, we took off the XEmacs
packaged ESS since it wasn't keeping up very well with the tarball,
due to complications, mis-matched release schedules/requirements, and
the like.
It now needs to be installed from tarball, though there is some help
for that, I believe. (someone remind me what it is!).
On 12/30/05, John Fox [EMAIL PROTECTED] wrote:
Dear Paul and Mark,
I've just taken a look at the current XEmacs setup program for Windows, and
it has changed significantly since the document to which you referred was
last updated (about a year ago). In particular, the XEmacs setup no longer
gives you the option to install all packages, as I recommended. Among these
is ess, which is not in the small set of packages that XEmacs currently
installs, nor does ess seem to be available via the packages tool in XEmacs.
I'm copying this response to the ESS help list, and will remove the
XEmacs/ESS document on my web site so that people aren't further misled.
Sorry for the problem,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of paul sorenson
Sent: Thursday, December 29, 2005 11:51 PM
To: Mark Leeds
Cc: R-Stat Help
Subject: Re: [R] ESS and Emacs
I tried it with XEmacs on Win XP and I had to install ESS separately.
Mark Leeds wrote:
I have been using the document written by John Fox titled Sn
Introduction to ESS + XEmacs for Windows Users of R.
It's a very nice document and
I went through it carefully but I got
an error when I finished it and launched XEmacs.
The error is cannot open load file : ess-site.
So, I did more investigation
and it seems like there is a folder
Program Files/XEmacs/xemacs-packages/etc/ess
that should have been created when
I downloaded XEmacs but it doesn't exist.
There is a folder called efs ( rather than ess ) but I don't think
that's it.
I tried installing XEmacs again but the same thing happened.
Does anyone know anything about this ?
I am using Windows NT.
Thanks.
Mark
**
This email and any files transmitted with it are
confidentia...{{dropped}}
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--
best,
-tony
[EMAIL PROTECTED]
Muttenz, Switzerland.
Commit early,commit often, and commit in a repository from which we can easily
roll-back your mistakes (AJR, 4Jan05).
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[R] S4 classes: referencing slots with other slots
For those who suggest other ways to do this, I ALREADY HAVE ANOTHER
DESIGN SOLUTION, DESCRIBED AT THE END.
That being said, I want to know if it's possible to reference a slot
in an S4 class from another slot, i.e. I'd like to have the self.*
semantics of Python so that I can reuse a slot. That is, for various
reasons it would be nice to be able to do something like:
setClass(fooWfcn,
representation(dat1=vector,
dat2=vector,
fn1=function,
fn2=function),
prototype=list(dat1=0:10,
dat2=10:20,
fn1=function(x) { return(x - mean(self.dat1)) },
fn2=function() { mean(self.dat2) }))
and in the context of
foo - new(fooWfcn)
have self.dat2 refer to [EMAIL PROTECTED], etc (I.e. in an instantiated object,
have the reference be within the object).
One could easily imagine doing this on the fly, as well, during the new call.
I've looked this up in a number of books, on-line talks/papers, etc,
but havn't managed to find the right page describing it as possible or
impossible. I think it is the latter (impossible), since one could
easily end up with a nasty self-referencing infinite loop (fn1
refering to fn2 refering to fn1). If it's the former, I'd be
interested in knowing about it.
Anyway, here's the DESIGN SOLUTION: write methods which do the
appropriate combination.
Critique:
pro - it works, it's simple, and I've already done it.
con - for the problem I'm looking at, it's not quite so clean, adding
one more layer of indirection that in Python or CLOS I'd not need,
multiplied by a fair number of subclasses.
best,
-tony
[EMAIL PROTECTED]
Muttenz, Switzerland.
Commit early,commit often, and commit in a repository from which we can easily
roll-back your mistakes (AJR, 4Jan05).
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Re: [R] R-help Digest, Vol 33, Issue 27
From: Duncan Murdoch [EMAIL PROTECTED] I'd recommend using the RWinEdt package instead for a different way to integrate winedit with R. winedit and winedt are two different editors, last I checked. best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] Insightful Announces: R and S-PLUS- Panel Discussion at 9th Annual 2005 User Conference
But who is on the panel? On 10/17/05, Michael O'Connell [EMAIL PROTECTED] wrote: Event: 2005 Insightful User Conference Dates: Oct 26-27, 2005 Location: Princeton, NJ URL: http://www.insightful.com/news_events/2005uc/ for details on pricing, hotel accommodations and to register for this event. The Insightful 2005 User Conference is being held October 26th-27th in Princeton, NJ. This year's conference focuses on the techniques and methodologies pivotal to the increased demand for statistics in business organizations. The conference program will include presentations by S-PLUS experts from market-leading companies such as Novartis, Procter Gamble, Amgen, and MCI. Of particular interest to subscribers to r-help is the panel discussion on future plans for compatibility between S-PLUS and R. The panel discussion is on the topic Ensuring Compatibility and Portability Between the Two Prime Dialects of the S Language. Martin DeBono from Insightful will moderate a panel of experts in both S-PLUS and R to discuss plans for a common packaging system and tools to make it easy to convert R packages to S-PLUS. There will also be broader discussion about how the users of each dialect can coordinate efforts to create a vibrant community focused on the continued advancement of the S Language. [[alternative HTML version deleted]] __ 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 -- best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] Insightful Announces: R and S-PLUS- Panel Discussion at 9th Annual 2005 User Conference
So the answer seems to be Insightful folks and industry folks. On 10/17/05, A.J. Rossini [EMAIL PROTECTED] wrote: But who is on the panel? On 10/17/05, Michael O'Connell [EMAIL PROTECTED] wrote: Event: 2005 Insightful User Conference Dates: Oct 26-27, 2005 Location: Princeton, NJ URL: http://www.insightful.com/news_events/2005uc/ for details on pricing, hotel accommodations and to register for this event. The Insightful 2005 User Conference is being held October 26th-27th in Princeton, NJ. This year's conference focuses on the techniques and methodologies pivotal to the increased demand for statistics in business organizations. The conference program will include presentations by S-PLUS experts from market-leading companies such as Novartis, Procter Gamble, Amgen, and MCI. Of particular interest to subscribers to r-help is the panel discussion on future plans for compatibility between S-PLUS and R. The panel discussion is on the topic Ensuring Compatibility and Portability Between the Two Prime Dialects of the S Language. Martin DeBono from Insightful will moderate a panel of experts in both S-PLUS and R to discuss plans for a common packaging system and tools to make it easy to convert R packages to S-PLUS. There will also be broader discussion about how the users of each dialect can coordinate efforts to create a vibrant community focused on the continued advancement of the S Language. [[alternative HTML version deleted]] __ 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 -- best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). -- best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] log4j
no, there isn't a general logging package. On 10/12/05, Spencer Graves [EMAIL PROTECTED] wrote: I just got 145 hits from RSiteSearch(debugger). Does this help? spencer graves Omar Lakkis wrote: Is there a log4j, or similar, package for R? __ 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 -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ 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 -- best, -tony [EMAIL PROTECTED] Muttenz, Switzerland. Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). __ 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] Digest reading is tedious
Trevor - There's a wonderful feature in gnus (the emacs information (including mail) reader), that bursts digests into subparts for reading (and hence, easy access). I think there are other similar tools as well for other mail readers. best, -tony On 8/9/05, Trevor Hastie [EMAIL PROTECTED] wrote: Like many, I am sure, I get R-Help in digest form. Its easy enough to browse the subject lines, but then if an entry interests you, you have to embark on this tedious search or scroll to find it. It would be great to have a clickable digest, where the topics list is a set of pointers, and clicking on a topic takes you to that entry. I can think of at least one way to do this via web pages, but I bet those with more web skills than me can come up with an elegant solution. --- Trevor Hastie [EMAIL PROTECTED] Professor, Department of Statistics, Stanford University Phone: (650) 725-2231 (Statistics) Fax: (650) 725-8977 (650) 498-5233 (Biostatistics) Fax: (650) 725-6951 URL: http://www-stat.stanford.edu/~hastie address: room 104, Department of Statistics, Sequoia Hall 390 Serra Mall, Stanford University, CA 94305-4065 [[alternative text/enriched version deleted]] __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Eclipse, R, plug-in?
On 04 Aug 2005 10:26:40 +0200, Peter Dalgaard [EMAIL PROTECTED] wrote: I seem to recall that there is an S-PLUS plugin in the latest version, but we haven't received it yet. I believe it's in the enterprise edition (which is the version with large datasets, etc), not the more common and less expensive professional version. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] chocolate [was Re: calling R from C or C++]
On 7/24/05, David Whiting [EMAIL PROTECTED] wrote: Dirk Eddelbuettel wrote: On 23 July 2005 at 20:18, Bahoo wrote: [...] Dirk, who still wants chocolate to grow on trees, preferably in his backyard Well, it does, sort of. To have it in your backyard you are going to have to move nearer the equator though :) I'll keep it in the grocery store. Nothing like a whole aisle or 2 of quality chocolate, instead of having to make it yourself. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Chemoinformatic people
Just with R, or via another tool integrating R, such as Pipeline Pilot? best, -tony On 7/20/05, Frédéric Ooms [EMAIL PROTECTED] wrote: Dear colleague, Just an e-mail to know if they are people working in the field of chemoinformatic that are using R in their work. If yes I was wondering if we couldn't exchange tips and tricks about the use of R in this area ? Best regards Fred Ooms [[alternative HTML version deleted]] __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Chemoinformatic people
I know of a good number of companies who use R via pipeline pilot (and have looked into it a bit recently), but not R by itself. One of the big I wish items that I've got is seemless handling of large data. Some of the RDBMS will do it, but not quite seemlessly. SPLUS 7.0 does it for a limited class, but in a painful (very non-seemless) manner. This would be required to use R in this context, at least for what I've seen. best, -tony On 7/21/05, Frédéric Ooms [EMAIL PROTECTED] wrote: I am looking for both. Fred -Original Message- From: A.J. Rossini [mailto:[EMAIL PROTECTED] Sent: Thursday, July 21, 2005 3:36 PM To: Frédéric Ooms Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Chemoinformatic people Just with R, or via another tool integrating R, such as Pipeline Pilot? best, -tony On 7/20/05, Frédéric Ooms [EMAIL PROTECTED] wrote: Dear colleague, Just an e-mail to know if they are people working in the field of chemoinformatic that are using R in their work. If yes I was wondering if we couldn't exchange tips and tricks about the use of R in this area ? Best regards Fred Ooms [[alternative HTML version deleted]] __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Chemoinformatic people
Sure, but Luke, I DO NOT currently use R at work... (now, that's not to say I won't be using it in a few months, but currently...). best, -tony On 7/21/05, Luke Tierney [EMAIL PROTECTED] wrote: I don't. THere is an address an email at novartis in the ASA directory ID 068970 NameAnthony J. Rossini Company Novartis Pharma AG Address Biostatistics WSJ-27.1.012 City State Zip CH-4002 Basel Country Switzerland Phone (206) 543-2005 Email [EMAIL PROTECTED] luke On Thu, 21 Jul 2005, A.J. Rossini wrote: Just with R, or via another tool integrating R, such as Pipeline Pilot? best, -tony On 7/20/05, Frédéric Ooms [EMAIL PROTECTED] wrote: Dear colleague, Just an e-mail to know if they are people working in the field of chemoinformatic that are using R in their work. If yes I was wondering if we couldn't exchange tips and tricks about the use of R in this area ? Best regards Fred Ooms [[alternative HTML version deleted]] __ 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 -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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 GUI for Linux?
If you really want something closer to an IDE, add ECB to that mix (Emacs Code Browser). ESS does some minimal connections to it, for code browsing between functions, data.frame creations, and S4 class constructions. On 5/31/05, Jari Oksanen [EMAIL PROTECTED] wrote: On Tue, 2005-05-31 at 10:43 +0100, Ernesto Jardim wrote: ESS looks very good but why should I load more than 30MB on the memory to work on a text file ? and why do I need to lear all the tricks and features of emacs just to edit a text file ? With emacs tricks you perhaps refer to four-finger key combinations that even gave name to emacs: it's supposed to be an acronym for Esc-Meta- Alt-Ctrl-Shift (say the enemies). However, you don't need those tricks. The only ones you need are Alt-x R to start R in ESS, and Esc-p to go back in command history -- these at least are the only ones I use, although I know people who really like acrobatic key combinations (I don't). All the rest is in the menus -- even in ordinary GNU Emacs (and also in its MacOS X and Windows ports). Installing ESS may be more trouble with GNU Emacs, but if you use Debian based distributions (like Ubuntu), you can directly install a deb package for ess (I once found an rpm for ESS as well, but that's not official nor standard). I avoid XEmacs, but people say things are even easier there. I'd suggest you try Emacs + ESS + R. It is really good and likable. Emacs is much more user friendly than it used to be some decade ago. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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 commandline editor question
Of course it should be in ESS. In fact, it is for me, anyway
(different colors depending on whether they match or not).
Check out the paren-hilit or paren-match (or something like that)
customize options.
I.e.
M-x customize-groups ret paren spc
(which ought to complete on names of groups/options starting with
paren) or blink-paren.
(I'm not on an Emacs-enabled computer right now).
On 5/27/05, Robin Hankin [EMAIL PROTECTED] wrote:
Hi Ajay
well ESS has such a facility.
However, I think Mathematica has a super scheme: unbalanced brackets
show up
in red, making them obvious.
This is particularly good for spotting wrongly interleaved brackets, as
in
([ blah di blah )]
note bracket closure is out of order
in which case both opening braces are highlighted in red: and the
system won't
accept a newline until the closures are all correctly matched.
Would anyone else find such a thing useful?
Could the ESS team make something like this happen?
On May 27, 2005, at 12:11 pm, Ajay Narottam Shah wrote:
I am using R 2.1 on Apple OS X.
When I get the prompt, I find it works well with emacs commandline
editing. Keys like M-f C-k etc. work fine.
The one thing that I really yearn for, which is missing, is bracket
matching When I am doing something which ends in it is really
useful to have emacs or vi-style bracket matching, so as to be able
to visually keep track of whether I have the correct matching
brackets, whether ( or { or [.
I'm sure this is possible. I will be most grateful if someone will
show the way :-) Thanks,
--
Ajay Shah Consultant
[EMAIL PROTECTED] Department of Economic Affairs
http://www.mayin.org/ajayshah Ministry of Finance, New Delhi
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tel 023-8059-7743
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best,
-tony
Commit early,commit often, and commit in a repository from which we can easily
roll-back your mistakes (AJR, 4Jan05).
A.J. Rossini
[EMAIL PROTECTED]
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Re: [R] Can simulation involving random number generation be segmented?
You might consider the rlecuyer package, which provides parallel streams and avoids the potential worst case scenario from arbitrary seed setting. On 5/25/05, Dr L. Y Hin [EMAIL PROTECTED] wrote: Dear all, Apologies for this pedantic question that only arise when there is hardware limitation. Setting: R 2.1.0 for windows xp sp2. Scenario: To generate 1000 samples using rnorm for a simulation activity. Background: The simulation activity requires so much memory resources that generating 200 samples clogs up the PF usage as indicated in the Windows Task Manager. Therefore, short of implementing the simulation on a computer with more resources, the alternative is to generate the 1000 samples in 5 separate runs, each generating 200 samples, closing the R window and re-opening between runs. Question to be addressed: To maintain consistency and ensure reproducibility of the simulation results, the 1000 samples generated in one single run should be indentical to the 5x200 samples generated on 5 separate runs. While such consistency can be ensured using set.seed() in the case of one single run, in the case where 5 separate runs are performed, can we do the following to ensure identical samples being generated? 1. In the first run, specify the seed by, say, set.seed(1) 2. At the end of the first run, store the .Random.seed by the following manner: saved.seed.1-.Random.seed 3. At the beginning of the second run, assign the saved.seed.1 to .Random.seed as follows: .Random.seed-saved.seed.1 4. At the end of the first run, store the new .Random.seed by the following manner: saved.seed.2-.Random.seed 5. At the beginning of the second run, assign the saved.seed.2 to .Random.seed as follows: .Random.seed-saved.seed.2 This is repeated until 5 runs are completed. Will the paths of random number generation be identical in these two approaches? If not, is there a way to ensure this? Apologies again for this long-winded inquiry. Thank you. Best Lin __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Is anyone working on an S4 classes for dummies book/paper? If so, please contact me off-list
Is anyone working on an S4 classes for dummies book/paper/package? If so, please contact me off-list. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] 21 CFR Part 11 Compliance and R
21 CFR Part 11 is mostly about data audit trails (tracking changes and electronic signatures) and validation of software. Most of this involves documentation and the creation of documentation LOCALLY at YOUR site, regarding YOUR processes and operating procedures. R satisfies most of what is needed, depending on who you are. If you happen to be working for a large Pharma, it comes up slightly short, but not too short; I happen to know of 2 pharmas very interested in getting the gaps filled, and an analysis suggests that this is simple, though time consuming, of course. Hopefully, the missing pieces will exist soon (mostly traditional vendor documentation for validation). If you happen to be working in an nonprofit/academic setting, R is probably fine (again depending on your SOPs, data transport audit trail, etc). best, -tony On 5/23/05, Richard Haney [EMAIL PROTECTED] wrote: I have used S-PLUS, R, MATLAB and SAS for many years, and I am actually quite happy to use any of these four languages. The reason may in part involve my using the various languages for the purposes to which they seem most suited. Hence there are many things for which I would not use SAS or MATLAB, but for which I would greatly prefer to use R instead. On the other hand ( to take one of a couple of examples), in the past I have not even been permitted to use R whatsoever in clinical trials applications, which also typically involve a need for CFR Part 11 compliance. In this context, though, may I ask if there are people who have recently been able to use R for clinical trials work that is done within an FDA-approved 21 CFR Part 11-compliant framework? Thanks very much. Rich Haney [EMAIL PROTECTED] Duke Comprehensive Cancer Center [[alternative HTML version deleted]] __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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.batch (Was: Re: [R] Calling R from R and specifying wait until script is finished)
On 5/22/05, Henrik Bengtsson [EMAIL PROTECTED] wrote: -- very interesting package description deleted -- Future: Recently, I have been working on adding dependency control between jobs so certain jobs are processed before others. This is not included in the current version. Some kind of mechanism to restarting interrupted jobs where they where interrupted would also be very nice, but this is very tricky and will propably require modification of the R engine, which is beyond my skills. For the latter, probably the best approach would be to employ a job/grid/queueing engine which does this (i.e. grid-enabling R with a grid approach which has checkpointing). I've been looking at this at work in a different context. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Does R have a command for sending emails?
On 5/10/05, Barry Rowlingson [EMAIL PROTECTED] wrote: Hoping this helps! (Of course, if you're not a unixoid, this is probably no use to you at all, and I have no idea how to do anything similar in Windows). How about an R package to talk to google's gmail service, perhaps leveraging an existing API, such as: http://libgmail.sourceforge.net/ this is written in pure python, so not only is it cross-platform but it should be possible to write one in pure R using HTTP calls and the like. you could then do statistical analysis of your gmail spam purely in R. or am I now getting too silly? Not yet. However, one could just connect via sockets to port 25 (smtp port) and do an appropriate mail sending dialog. Not too hard, provided that you get the details right and handle any security issues. -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Maximum # of predictors?
Your data won't support it. It has nothing to do with R or any other decent linear regression fitting software. I've seen up to 60 indep variables, with a data set for which it almost made sense. best, -tony On 5/8/05, Jim BRINDLE [EMAIL PROTECTED] wrote: Hello, Is there anyway one can have more than 11 independent variables in a regression model? To hopefully illustrate: with 13 predictors in my model, the last 2 coefficient estimates are NA. When I view the summary, it indicates that 2 coefficients are not defined because of singularities. I am using the command: mod - lm(y ~ ., data = volumes[,3:22]) I am fairly new to R so I don't know if my issue is something inherent to R or my modeling approach. Any insight would be most appreciated... Thanks in advance __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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 for HTS data analysis
Define HTS please -- if you mean HCS/HTS, then there are a few packages in BioConductor which will help (prada, rflowcyt). On 5/6/05, Frédéric Ooms [EMAIL PROTECTED] wrote: Hello, I am looking for any packages, tutorials, documents,... about the use of R for the analysis of HTS data. Thanks for your help Fred [[alternative HTML version deleted]] __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Classes and methods
On 5/3/05, Rolf Turner [EMAIL PROTECTED] wrote: Sean Davis wrote: I just did some of this learning myself. Here are a couple of links that I found useful: http://www.stat.auckland.ac.nz/S-Workshop/Gentleman/S4Objects.pdf http://eeyore.ucdavis.edu/stat250/OOP.html I found the first particularly easy reading and it got me going quickly with S4 methods, which it seems to me are the way to go in most cases. If you want to simultaneously handcuff yourself, strap yourself into a strait jacket, and tie yourself in knots, and moreover write code which is incomprehensible to the human mind, then S4 methods are indeed the way to go. Which humans? I know quite a few for which the above isn't true. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] good editor for R sources ?
On 4/26/05, Paul Smith [EMAIL PROTECTED] wrote: On 4/26/05, Liaw, Andy [EMAIL PROTECTED] wrote: (Sorry if the question has already been answered.) Could someone please suggest a good text editor for writing R sources ? (I know emacs exists ... but I find it a bit heavy). I use crimson (http://www.crimsoneditor.com) which is small and simple, but the R syntax seems not to be supported. See http://www.sciviews.org/_rgui/projects/Editors.html The page tells us that there is support for Crimson editor. And for Linux, what do you recommend? Tere are suggestions on that page that Uwe mentioned above for Linux! First choice would be (X)Emacs/ESS. Then there are also vim, kate, bluefish, ... Thanks, Andy. Does somebody know how to install ess on xemacs? It comes with ESS built-in if you get the full distribution. But this would be better asked on the ess-help list. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] A question about function behavior
Perhaps by using apply?
What do you think that
max(0,c(1,2,3,4)+1)
should return?
On 4/20/05, Jorge Ahumada [EMAIL PROTECTED] wrote:
Hello,
I have been trying to figure this one out, but don't seem to go
anywhere. I have a function like this:
a = function(t) {
max(0,t+1)
}
very simple, but if I pass a vector of n values to this function I
expect n evaluations of max and instead I get only one value (the
largest value of them all..). Is there anyway to do this without
invoking a for loop?
thanks,
Jorge
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-tony
Commit early,commit often, and commit in a repository from which we can easily
roll-back your mistakes (AJR, 4Jan05).
A.J. Rossini
[EMAIL PROTECTED]
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Re: [R] Running scripts and the console
You can do it the same way that I do it for both R and S-PLUS -- use Emacs/ESS. There are sensibly reasons to use cross-platform tools, even if they are a bit harder to get used to (being a compromise between many systems). On 4/15/05, Stephan Tolksdorf [EMAIL PROTECTED] wrote: Hi, is there any way to execute scripts in R (Windows) without the script being copied to the console, so that only error messages are reported? Or to have a second console in parallel? Please. Not being able to hit the F10 button like in S-Plus seriously impairs my productivity (not only because it is slow and clutters my console history). And totally unrelated: Is there any chance that R is renamed to something searchable on Google? R-Minus could do the trick... ;-) Besides these minor nuisances I'd like to thank the developers for a great product. Ciao, Stephan __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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 4/13/05, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Wed, 13 Apr 2005 [EMAIL PROTECTED] 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). Maybe, but the URL quoted says pstoedit 3.40 # Windows Meta Files (WMF) (Windows 9x/NT only) # Enhanced Windows Meta Files (EMF) (Windows 9x/NT only) so the quoted URL claims otherwise for the current version. If you follow the link for exact support, you find out that it supports EMF using a wemf - Wogls version of EMF wemfc - Wogls version of EMF with experimental clip support wemfnss - Wogls version of EMF - no subpathes which is apparently different than the MS Windows EMF support. How, it isn't clear from the documentation. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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 as programming language: references?
On Apr 12, 2005 11:54 AM, Duncan Murdoch [EMAIL PROTECTED] wrote: - Original Message - From: Federico Calboli [EMAIL PROTECTED] To: r-help r-help@stat.math.ethz.ch Sent: Tuesday, April 12, 2005 5:14 PM Subject: [R] R as programming language: references? Hi All, I am looking for references on R as a programming language (apart form the standard R-lang.pdf and the other manuals), reference that would cover _in_depth_ things like loops, code optimisation, debugging tools etc... and is as up-to-date as possible. Can anyone suggest any book or other reference apart from the green book and the VR S-programming? I think you've already got the best references. There is always the source. In a sense, it IS the most in-depth and up-to-date description of the intricacies of using the language, though it isn't as easy to read as VR's S Programming. In-depth and up-to-date are tradeoffs rather than being complementary. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] build rpvm under cygwin
Read the FAQs, etc, about building R on Windows. Summary: stay away from Cygwin when it comes to R. On Apr 7, 2005 11:34 AM, Lars Schouw [EMAIL PROTECTED] wrote: I tried ot build rpvm in my own makefile. But runs into some linker errors like e.g. undefined reference to `_R_alloc' My enviornment looks like this: CYGWIN pvm 3.4 compiled under cygwin myself R installed from the rw2001.exe setup file. I guess that the R under rw2001.exe was build with some other compiler? I then tried to compile R myself under CYGWIN but runs into the following problem: building from src typing make gcc -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CON FIG_H -D__NO_MATH_INLINES -g -O2 -c dynload.c -o dynload.o In file included from dynload.c:35: ../../src/include/Defn.h:60:22: psignal.h: No such file or directory I found the psignal.h header file under gnuwin32/fixed/h/psignal.h how do incoperate this udner cygwin? I also tried to type build under src/gnuwin32 but get another error: $ make make: ./Rpwd.exe: Command not found make[1]: ./Rpwd.exe: Command not found make --no-print-directory -C front-ends Rpwd make -C ../../include -f Makefile.win version make[3]: Nothing to be done for `version'. make Rpwd.exe gcc -O2 -Wall -pedantic -I../../include -c rpwd.c -o rpwd.o rpwd.c:22:20: direct.h: No such file or directory rpwd.c: In function `main': rpwd.c:38: warning: implicit declaration of function `chdir' rpwd.c:41: warning: implicit declaration of function `getcwd' make[3]: *** [rpwd.o] Error 1 make[2]: *** [Rpwd] Error 2 make[1]: *** [front-ends/Rpwd.exe] Error 2 make: *** [all] Error 2 Ideas would be appreciated. Regards Lars Schouw --- Lars Schouw [EMAIL PROTECTED] wrote: Dear Professor Ripley The good news is that I fot PVM up and running one two Windows nodes now. I had to connect them with each other manually . for now not using rsh or ssh. Now building RPVM for Windows might not be so easy as it sounds. Did anyone try this out before successfully? Also the SNOW package but that did not look so bad. Regards Lars --- Prof Brian Ripley [EMAIL PROTECTED] wrote: On Thu, 24 Mar 2005, A.J. Rossini wrote: Looks like you are trying to install source tarball on Windows without the relevant toolset (compiler, etc)? To save further hassle, rpvm is not going to build on Windows unless you have PVM installed and working on Windows. If that is the case, this looks like the use of the wrong make, with the wrong shell (that message is coming from a Windows shell, not sh.exe). Do see the warnings in README.packages about the MinGW make. On Thu, 24 Mar 2005 00:11:34 -0800 (PST), Lars Schouw [EMAIL PROTECTED] wrote: I am trying to install the rpvm package doing this: C:\R\rw2000\binrcmd install rpvm_0.6-2.tar.gz '.' is not recognized as an internal or external command, operable program or batch file. '.' is not recognized as an internal or external command, operable program or batch file. make: *** /rpvm: No such file or directory. Stop. make: *** [pkg-rpvm] Error 2 *** Installation of rpvm failed *** Removing 'C:/R/rw2000/library/rpvm' What does this error message tell me? -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ Show us what our next emoticon should look like. Join the fun. http://www.advision.webevents.yahoo.com/emoticontest __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] off-topic question: Latex and R in industries
Ha -- that's a good one, Roger. Which demonstrates that most industrial people don't bother to read EULA's :-). (of course, it depends on which industry, and for some industries, which segment you are in ). On Apr 6, 2005 6:05 PM, roger koenker [EMAIL PROTECTED] wrote: my favorite answer to this question is because there is no one to sue. url:www.econ.uiuc.edu/~rogerRoger Koenker email [EMAIL PROTECTED] Department of Economics vox:217-333-4558University of Illinois fax:217-244-6678Champaign, IL 61820 On Apr 6, 2005, at 10:38 AM, Wensui Liu wrote: Latex and R are really cool stuff. I am just wondering how they are used in industry. But based on my own experience, very rare. Why? How about the opinion of other listers? Thanks. __ 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-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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] RE: Gmail invitation
Heck, if anyone cares, I've got 50 or so. Just drop an email. It's not a bad service. On Sat, 26 Mar 2005 15:19:04 +0100, Gorjanc Gregor [EMAIL PROTECTED] wrote: I still have 40 invitations! Do not hesitate ;) This is last remainder on r-help. -- Lep pozdrav / With regards, Gregor Gorjanc University of Ljubljana Biotechnical Faculty URI: http://www.bfro.uni-lj.si/MR/ggorjan Zootechnical Departmentemail: gregor.gorjanc at bfro.uni-lj.si Groblje 3 tel: +386 (0)1 72 17 861 SI-1230 Domzalefax: +386 (0)1 72 17 888 Slovenia __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] build failed of package
Looks like you are trying to install source tarball on Windows without the relevant toolset (compiler, etc)? On Thu, 24 Mar 2005 00:11:34 -0800 (PST), Lars Schouw [EMAIL PROTECTED] wrote: I am trying to install the rpvm package doing this: C:\R\rw2000\binrcmd install rpvm_0.6-2.tar.gz '.' is not recognized as an internal or external command, operable program or batch file. '.' is not recognized as an internal or external command, operable program or batch file. make: *** /rpvm: No such file or directory. Stop. make: *** [pkg-rpvm] Error 2 *** Installation of rpvm failed *** Removing 'C:/R/rw2000/library/rpvm' What does this error message tell me? Regards Lars Schouw __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Package vignette and build
Yes, you need the package installed first. Something like: R CMD build --no-vignettes DLM R CMD install DLM. R CMD build DLM R CMD install DLM. At least you had to do this with 1.9.1, can't recall looking again since then. On Tue, 22 Mar 2005 11:23:36 -0600 (CST), Giovanni Petris [EMAIL PROTECTED] wrote: Hello, I am writing a package called 'DLM' containing a vignette. The vignette contains a chunck with the function call 'library(DLM)'. This worked fine with 'R CMD check DLM', but when it comes to building the package with 'R CMD build DLM' I get the following error message: * creating vignettes ... ERROR Error: chunk 1 Error in library(DLM) : There is no package called 'DLM' Error in buildVignettes(dir = .) : Error: chunk 1 Error in library(DLM) : There is no package called 'DLM' Execution halted It looks to me as if I should have the package already installed before building it... I have read the article by F. Leisch on package vignettes in R News 3/2 and looked at the source for 'strucchange', but I can't figure out what I am doing wrong. Any suggestions you can provide are more than welcome! Thank you in advance, Giovanni version _ platform sparc-sun-solaris2.8 arch sparc os solaris2.8 system sparc, solaris2.8 status major2 minor0.1 year 2004 month11 day 15 language R -- __ [ ] [ Giovanni Petris [EMAIL PROTECTED] ] [ Department of Mathematical Sciences ] [ University of Arkansas - Fayetteville, AR 72701 ] [ Ph: (479) 575-6324, 575-8630 (fax) ] [ http://definetti.uark.edu/~gpetris/ ] [__] __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] CDISC tools for R?
Has anyone hacked up tools for reading/writing CDISC applications (ADaM, SEND, SDTM, ODM) files or using/verifying vocabulary with R? (i.e. via the XML, ontoTools, and similar packages)? (I'd be interested in hearing privately from any consultants/vendors who have been working on this as well; S-PLUS would be a related/relevant target). best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Interval censoring in Survival analysis
On Thu, 10 Mar 2005 08:01:57 -0800 (PST), Thomas Lumley [EMAIL PROTECTED] wrote: On Thu, 10 Mar 2005, AMOROS NAVARRO, ALEX wrote: I am not aware of any package that allows semiparametric regression modelling of interval censored or doubly censored data. I'm aware of 2 such packages, but the one that is more accurate won't be published due to licensing restrictions on one of the subcomponents (nonlinear programming with nonlinear constraints optimizer), and the other is less accurate (a profiling approach) and shouldn't be. That being said, I'm sure others have tried. -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] write a **package** under 2.0.1 version
Yet again, yet again, Martin. I told you... On Tue, 1 Mar 2005 17:28:04 +0100, Martin Maechler [EMAIL PROTECTED] wrote: marta == marta [EMAIL PROTECTED] on Tue, 1 Mar 2005 16:23:17 +0100 (CET) writes: marta Hi there, marta I had written a library under R 1.9.0 and now I would like to import that marta library under R 2.0.1 package, package, package -- a library is something really different! marta Apparently it does not work; I can install the marta package, but when I try to read it the error is the marta following: marta Error in library(compvar) : 'compvar' is not a valid package -- installed marta 2.0.0 so you haven't really installed in the sense of Rcmd INSTALL pkgname [ You didn't tell us, but you probably are using Micro$oft Windows? On other platforms its R CMD INSTALL pkgname ] and you (or whoever provided the ``pre-compiled'' package to you) must run Rcmd INSTALL on that package where 'Rcmd' is any R version 2.x.y (2.0.1, typically). However, this won't work easily for you if you are on Windows, since you need to first install quite a few tools before you can build and install packages ```from source'' -- read the 'rw-faq' i.e. R for windows Frequently Asked Questions (and answers) that is accessible from the [Help] menu on Windows. marta I have checked other libraries in R 2.0.1 and I other packages marta noticed that there is a new folders (Meta) that were marta not present under R 1.9.1 as well as a file marta (MD5). Moreover, under R folders there are files with marta .rdx and .rdb extensions that were not present marta before. these are rather in connection with Lazyloading and other features that more packages are using, but you shouldn't have to know about. marta I was wondering how I can built these files for the library to be marta importable under 2.0.1 version. marta Any suggestion? Rcmd INSTALL (but see above) Regards, Martin Maechler, ETH Zurich __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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: Packages and Libraries
Hm. Everyone else got it (the reasons for the change). The reason is that beginners often fail to get it (package vs. library), and one of the contributing factors is the naming approach, which isn't clear. Certain people are rather sensitive to mistakes of this nature, so we end up with 2-3 messages expressing frustration because some people (who are sometimes asking otherwise reasonable questions) aren't detail-oriented enough to suit. Please read the rest of the thread, where the questions you ask are covered (though whether on r-devel or r-help, I'm not sure, since my mail is completely threaded). On Wed, 09 Feb 2005 17:32:15 -0800, Spencer Graves [EMAIL PROTECTED] wrote: The reasons to 'introduce package() and deprecate library()' may be OBVIOUS to you, but they completely escape me. Could you please clarify why that's obvious? I've seen many admonitions on this list that the term is package NOT library, but I don't recall ever seeing any explanation of why the term package is more appropriate than library. I suspect there may be some rationale that package seems more appropriately descriptive. However, is it so much more precise that it justifies creating a distinction between S-Plus and R? Or is it your intention to make it harder for people who have to use S-Plus to also use R? Or do you want to make it more difficult for people to write code that will work in both S-Plus and R or for people to migrate from S-Plus to R or vice versa? Unless that is your intent, I'd like to know why you don't make the complementary change, namely globally replace package with library everywhere in the documentation -- or at least deprecate its future use. R is a marvelous creation, a solid contribution to the advancement of science and through that human knowledge and eventually even the ability of people everywhere to live more comfortably, longer. spencer graves p.s. I'm told that the French Royal Academy delayed the introduction in France of a product marketed by a US company. The product couldn't be sold in France without a French language manual. The translation could not be published until the French Royal Academy officially provided or blessed new French words for new technical terms. Similarly, Le Monde Diplomatique recently carried an article proposing A polyglot world to escape the English dictatorship. (January 2005, pp. 22-23: Un monde polyglotte pour echapper a la dictature de l'anglais'; someone may wish to correct my translation.) We could require all r-help subscribers to learn enough French, German, Spanish AND Portuguese to be able to read posts in those languages, but that might be counterproductive. Peter Dalgaard wrote: A.J. Rossini [EMAIL PROTECTED] writes: For OBVIOUS reasons, is there any chance that we could introduce package() and deprecate library()? usepackage() or usePackage() has been suggested, but someone got ambitious and wanted it to be different from library(), and it sort of didn't get any further. We still have some time before feature freeze for 2.1.0 though. (well, I'll also ask if we could deprecate = for assignment, but that's hopeless). You're not *forced* to use it... -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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
Packages and Libraries (was: Re: lme4 package etc {Re: [R] lme4 -- GLMM}
For OBVIOUS reasons, is there any chance that we could introduce package() and deprecate library()? (well, I'll also ask if we could deprecate = for assignment, but that's hopeless). best, -tony On Tue, 8 Feb 2005 11:49:39 +0100, Martin Maechler [EMAIL PROTECTED] wrote: Pavel == Pavel Khomski [EMAIL PROTECTED] on Tue, 08 Feb 2005 10:20:03 +0100 writes: Pavel this is a question, how can i specify the random part Pavel in the GLMM-call (of the lme4 library) for compound Pavel matrices just in the the same way as they defined in Pavel the lme-Call (of the nlme library). ``twice in such a short paragraph -- yikes !!'' ... I'm getting convulsive... There is NO lme4 library nor an nlme one ! There's the lme4 *PACKAGE* and the nlme *PACKAGE* -- please -- (If the nlme package is built, it will rely on a nlme.so or nlme.dll (or nlme.dylib ...) *library* of compiled C code, and if packages are installed, they are installed into a library of packages; typically into one of the libraries in .libPaths() ) whooh Martin __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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 on Beowulf cluster?
That's a shell/R script issue. I've come across it before, but I've no longer got access to any clusters of that form (yet :-). Depending on the jobs, it's not clear to me that you want a truly interactive process on a subnode, but the idea is the same as the chicanery we used to have a remote R process. best, -tony On Mon, 7 Feb 2005 14:59:33 -0500, Liaw, Andy [EMAIL PROTECTED] wrote: Dear R-help, Has anyone tried running R on a Beowulf-type cluster? I can get R to run in batch (using R CMD BATCH) on a cluster, but am wondering if it is possible to get an interactive R session on a compute node. Right now, if I run: beorun --nolocal R I just get the R start-up message and back to the shell prompt. If I try bpsh 0 R I can get R started (but the R prompt does not appear) and do computations, but no access to an x11() device. I'd very much appreciate any pointer. Best, Andy Andy Liaw, PhD Biometrics Research PO Box 2000, RY33-300 Merck Research Labs Rahway, NJ 07065 andy_liaw at merck.com 732-594-0820 __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] A rude question
How do you know that any results from any software package are trustable? I'm not sure that the number of authors has anything to do with it. If you are extremely paranoid, you can reprogram everything you do a few times in a large number of completely different languages written by different people, and top it off with hand calculations. Then you should do this across 4-5 operating systems with different core libraries. I'm somewhat joking in the second paragraph, but very serious in the first. How and why do YOU trust software? What criteria fit? Perhaps a better question would be to ask by what criteria people use to trust software, using R as an illustration. best, -tony p.s. R does satisfy a good part of the second paragraph, at least for a critical subset of the language. On Wed, 26 Jan 2005 23:09:51 -0600, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear all, I am beginner using R. I have a question about it. When you use it, since it is written by so many authors, how do you know that the results are trustable?(I don't want to affend anyone, also I trust people). But I think this should be a question. Thanks, Ming __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] empirical (sandwich) SE estimate in lme ()?
Right, but you still can sandwich them if you want. (I recently did that in Proc MIXED, but Michael, I'm not sure how to do it using lme). best, -tony On Fri, 14 Jan 2005 11:16:10 -0800, Berton Gunter [EMAIL PROTECTED] wrote: ??? correlated within group errors are explicitly modeled by corStruct classes. See ?lme and Chapter 5.3 in Bates and Pinheiro. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Na Li Sent: Friday, January 14, 2005 8:42 AM To: r-help@stat.math.ethz.ch Subject: [R] empirical (sandwich) SE estimate in lme ()? Is it possible to get the empirical (sandwich) S.E. estimates for the fixed effects in lme () (thus allowing possibly correlated errors within the group)? In SAS you can get it by the 'empirical' option to PROC MIXED. Cheers, Michael -- Na (Michael) Li, Ph.D. Division of Biostatistics A443 Mayo Building, MMC 303 School of Public Health420 Delaware St SE University of MinnesotaMinneapolis, MN 55455 Phone: (612) 626-4765 Email: [EMAIL PROTECTED] Fax: (612) 626-0660 http://www.biostat.umn.edu/~nali __ 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-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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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 classification
But similar to Jon's issue, one might imagine the following future scenario, in 10 years, after R dominates statistics: but it's not in R's biostat task list, so I don't have to know about it! (I am NOT being serious, but I've heard similar justifications in the past, i.e. it's not part of the curriculum, it wasn't explicit in the syllabus,etc, etc) best, -tony On Fri, 14 Jan 2005 19:11:35 +0100 (CET), Achim Zeileis [EMAIL PROTECTED] wrote: On Fri, 14 Jan 2005, Jonathan Baron wrote: I worry about this proposal because of the following example. I don't think you will get something that satisfies everyone in all cases...and not doing it for the reason will result in still having 400 unsorted packages on CRAN. One of the packages I use a lot (because it solves a problem I've been mulling for 10 years about how to test individual subjects) is multtest. That is part of Bioconductor, and the original purpose of it was (apparently) for DNA stuff. I doubt I ever would have thought to look there. I don't really see the point here: if there were, say, a DNA analysis view and multtest were a part of it, how could that be a problem? If there were another view social sciences or psychology, say, then multtest could, of course, also be part of it. The point of task views would be to have maintained lists of packages that are useful for a certain taks. And there will obviously be packages that are suitable for several views and there might be some that are suitable for not a single one. That said, I actually found it by using my own search engine and looking for multiple tests or something like that. So I guess this proposal isn't so bad, so long as people know about search. It is not meant to replace any search facilities! It should help users who come to CRAN and say: I want to do biostatistics with R, which of the 400 packages do I need to look at? Z Jon On 01/14/05 18:08, Achim Zeileis wrote: We are currently playing around with a concept of task views for CRAN. The idea is that there are maintained views on CRAN that highlight which CRAN packages are useful for, say, biostats, econometrics, machine learning, etc. So there should be a web page giving a summary and a package list that could also be queried for automatic package installation. -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] [survey] R for Reporting - the R Output MAnager (ROMA) project
complicated tables, with merged cells, embedding lists, eventually sub-tables Importance: __ 6. Here are some conceptual objects that a report may contain. Are there any more you can think to which may be important? Tables (containing Rows and Cells), Lists, Titles, Footnotes, Comment, Abbreviations / Acronyms, Code, Links, Graphs, Layout (to have 2 or 3 columns), Mathematics (equations), Table of Contents, Index Other that could be added: 7. Two different tools allow to create dynamic or alike documents: Sweave (for LaTeX and HTML) and Rpad (HTML, with a server). I would be interested in beeing able to describe the structure of a document that would be exportable to: 7.1 - Sweave [ ] Yes[ ] No 7.2 - Rpad [ ] Yes[ ] No If you are interested in contributing to the project, please let me know also. If many people do need XML representations, I think it would be great to have a guru in XLST abilities in the development team. Thanks for attention, Happy R, Eric Eric Lecoutre UCL / Institut de Statistique Voie du Roman Pays, 20 1348 Louvain-la-Neuve Belgium tel: (+32)(0)10473050 [EMAIL PROTECTED] http://www.stat.ucl.ac.be/ISpersonnel/lecoutre If the statistics are boring, then you've got the wrong numbers. -Edward Tufte __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] Compilation of R code
There was a real compiler which was under development as a MS thesis at Rice U last year, but I'm not sure if it was finished or ever will be released. I actually saw it in action on a small example... best, -tony On Fri, 7 Jan 2005 16:12:56 +0100, Depire Alexandre [EMAIL PROTECTED] wrote: Hello, I'm a newbie on this list. I have a R code but its execution take a very long time. Is it possible to compile it (in C for example) to decrease the execution time ? -- Alexandre DEPIRE INRETS / GARIG __ 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 -- best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] lme: error message with random=~1
On Wed, 05 Jan 2005 13:31:51 +0100, Thomas Petzoldt [EMAIL PROTECTED] wrote: Dimitris Rizopoulos wrote: Hi Thomas, random=~1 works if your data frame is in groupedData format, check this: # Orthodont is in groupedData format fm1 - lme(distance~age+Sex, data=Orthodont, random=~1) # dat - as.data.frame(Orthodont) fm2.1 - lme(distance~age+Sex, data=dat, random=~1) `dat' is an ordinary data.frame and thus random=~1 doesn't work. But this works: fm2.2 - lme(distance~age+Sex, data=dat, random=~1|Subject) # you declare the grouping factor I hope it helps. Best, Dimitris Thank you very much, now I see, why the Orthodont example works. There is however an important difference. In the example the random effects structure is not only ~1 but in reality ~1|Subject, which is inherited from the groupedData object. So ranef(fm1) yields 27 intercepts, but what I want is only one single intercept. Then you don't want a random intercept, right?Those are fitted estimates, if I'm not mistaken. best, -tony Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes (AJR, 4Jan05). A.J. Rossini [EMAIL PROTECTED] __ 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] ess in Windows (newbie Q)
The basic problem is that ESS is not being loaded. To find the init file, pull down the Help menu item and I believe that there is an entry Edit Init File (or similar -- I don't have access to (X)Emacs right now). Alternatively, after starting Emacs, open up: ~/.emacs and put it there (it will select your home directory for you). i.e. C-x C-f ~/.emacs or M-x find-file ret ~/.emacs Apologies for being pedantic, if that happens to be the case. best, -tony On Tue, 07 Dec 2004 00:18:59 -0500, Murray Eisenberg [EMAIL PROTECTED] wrote: I'm a rank beginner with R, and I'm stumped at how to get it to work with Xemacs under Windows XP. I'm afraid there are some VERY basic questions I have here. Yes, I did read http://ess.r-project.org/Manual/readme.html. Both R and Xemacs are installed and working. The current ess files are installed in a subdirectory of my Xemacs directory. I added the R bin directory to my Windows PATH environment variable. But when I start Xemacs and then give command M-x-R what I see in the mini-buffer is M-x-Rd- and it's waiting for more input. So what could be wrong? 1. Where might I find or should I put the requisite Xemacs init.el, in which I'm supposed to enter a line of the form (load /PATH/ess-site) to point to the ess location? I found no such file anywhere on my system, so I created one in each of the _two_ HOME directories I have -- one pointed to by the enviroment system variable HOME and the other pointed to by the user environment variable HOME (which seem to be different -- I don't recall whether that happened automatically when I installed Singular or whether I did it manually). 2. And what should that file actually be called? The ess docs say it should be %HOME%/.xemacs/init.el for Xemacs, but they also say to put it in the .emacs (or _emacs) file or default.el or site-init.el. I'm using init.el. 3. Did I get the form of that line correct for init.el (or whatever it should actually be named)? My file ess-site.el is in D:\WP\XEmacs\ess-5.2.3\lisp so the line I actually put into default.el is: (load /D:/WP/XEmacs/ess-5.2.3/lisp/ess-site) 4. Anything else I should check or do to proceed? -- Murray Eisenberg [EMAIL PROTECTED] Mathematics Statistics Dept. Lederle Graduate Research Tower phone 413 549-1020 (H) University of Massachusetts413 545-2859 (W) 710 North Pleasant Streetfax 413 545-1801 Amherst, MA 01003-9305 __ [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 -- best, -tony --- A.J. Rossini [EMAIL PROTECTED] __ [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: Reasons not to answer very basic questions in a straightforwa rd way; was: Re: [R] creating a sequence of object names
lots of good points from Andy and Uwe deleted and perhaps the most important reason for the particular socratic form of teaching on this list are the number of to-be, current, and former faculty members who feel compelled to teach general solutions to the problems (reading the FAQ is a rather general solution, eh?) rather than spoonfeed answers. This is a bit unlike some of the program language mailing lists where the care and feeding of personal egos is also part of the scene. (of course, I'm not referring to the wizards lists...!). best, -tony --- A.J. Rossini [EMAIL PROTECTED] __ [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] help with glmmPQL
For better or worse, it's holidays in the states. Very amusing for me being in a non-Thanksgiving celebrating country. In addition, it's not a problem. The complaint is valid. Probably no one has coded up the right solution yet for comparison. I can't recall if one would want those statistics for a binomial random effects model, but I do recall some issues with model comparison in that setting, though they are a bit dated (say, 2 years or so). On Fri, 26 Nov 2004 09:31:40 +0700, Andrew Criswell [EMAIL PROTECTED] wrote: Hello: Will someone PLEASE help me with this problem. This is the third time I've posted it. When I appply anova() to two equations estimated using glmmPQL, I get a complaint, anova(fm1, fm2) Error in anova.lme(fm1, fm2) : Objects must inherit from classes gls, gnls lm,lmList, lme,nlme,nlsList, or nls The two equations I estimated are these: fm1 - glmmPQL(choice ~ day + stereotypy, +random = ~ 1 | bear, data = learning, family = binomial) fm2 - glmmPQL(choice ~ day + envir + stereotypy, +random = ~ 1 | bear, data = learning, family = binomial) Individually, I get results from anova(): anova(fm1) numDF denDF F-value p-value (Intercept) 1 2032 7.95709 0.0048 day 1 2032 213.98391 .0001 stereotypy 1 2032 0.42810 0.5130 anova(fm2) numDF denDF F-value p-value (Intercept) 1 2031 5.70343 0.0170 day 1 2031 213.21673 .0001 envir 1 2031 12.50388 0.0004 stereotypy 1 2031 0.27256 0.6017 I did look through the archives but didn't finding anything relevant to my problem. Hope someone can help. ANDREW _ platform i586-mandrake-linux-gnu arch i586 os linux-gnu system i586, linux-gnu status major2 minor0.0 year 2004 month10 day 04 language R -- Andrew R. Criswell, Ph.D. Graduate School, Bangkok University __ [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 -- best, -tony --- A.J. Rossini [EMAIL PROTECTED] __ [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] UML programming
Sure, you could do it in a UML way. But I know of no tools yet that will, and more importantly, the object-orientation style (generic functions, i.e. similar to CLOS) isn't the easiest to use in that way. On Tue, 16 Nov 2004 11:03:28 +0100, wayne [EMAIL PROTECTED] wrote: hello, I'd like to know if it is possible to use R in a UML way by creating classes, methods,etc... If yes, can you please give me links for documentation and example ? thanks Accdez au courrier lectronique de La Poste : www.laposte.net ; 3615 LAPOSTENET (0,34/mn) ; tl : 08 92 68 13 50 (0,34/mn) [[alternative HTML version deleted]] __ [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 -- best, -tony --- A.J. Rossini [EMAIL PROTECTED] __ [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] R sumo package suggestion
Let them fail. Not all of the elisp code installed is self contained
in the XEmacs bundles, but you won't use or know about them if you
don't care.
That's exactly what that snippet that I wrote before did -- ignored errors.
best,
-tony
On Thu, 11 Nov 2004 15:59:09 -0500, Liaw, Andy [EMAIL PROTECTED] wrote:
Good idea, IMHO, but there are some practical difficulties:
I guess the XEmacs packages are (most, if not all) pure elisp code, and do
not need other stuff to work. However, quite a few CRAN packages depend on
external libraries or programs, and do not necessarily work on all platforms
that R runs on. How would such dependencies be resolved in such a kitchen
sink bundle?
I have a somewhat related idea: Start labelling packages with a set of
pre-defined categories, and a package can be labelled with more than one
categories (especially those *misc type packages). It is then possible to
have facility to let people install all packages that fall in a particular
category (e.g., `spatial statistics'). I believe several systems have such
facilities, Debian being one of them, TeXLive being another.
Just my $0.02...
Andy
From: Rodney Sparapani
r-help:
I have an R package suggestion. After spending
several hours the other day installing about a dozen
packages, I had an idea. In xemacs, there is a
sumo package which allows me to install a large
bundle of xemacs packages at one time (about a 120
modes including ESS). I think R should have a
similar bundle. It would be so much easier than
hunting/downloading/installing. Martin encouraged
me to send this suggestion to r-help. In addition,
he put together a few comments relating to the previous
times that this, or a similar suggestion, has been
brought up here.
Martin wrote:
If you search for install all CRAN packages
on
http://maths.newcastle.edu.au/~rking/R/
(the URL which is quickly found from the [Search] sidebar of
http://www.R-project.org/)
You find things like Greg Warnes 'Makefile'
http://tolstoy.newcastle.edu.au/R/help/04/04/0723.html
and
http://tolstoy.newcastle.edu.au/R/help/04/04/0616.html
which is from Tony and has the following small function:
installNewCRANPackages - function() {
## (C) A.J. Rossini, 2002--2004
test2 - packageStatus()$avail[Status]
install.packages(row.names(test2)[which(test2$Status==not
installed)])
}
--
Rodney Sparapani Medical College of Wisconsin
Sr. Biostatistician Patient Care Outcomes Research
[EMAIL PROTECTED] http://www.mcw.edu/pcor
Was 'Name That Tune' rigged? WWLD -- What Would Lombardi Do
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-tony
---
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Re: [R] R under Pocket PC
One concern I recall from looking into this a while back (hopefully not founded) was the issue with floating point handling on the ARMs and similar PDA CPUs. This was relevant to the familiar/intimate linux distro's around 18-24 months ago, when I was considering an IPAQ or Zaurus to replace my old but not dead yet palm. On 09 Nov 2004 19:06:39 +, David Whiting [EMAIL PROTECTED] wrote: Gabor Grothendieck [EMAIL PROTECTED] writes: David Whiting david.whiting at ncl.ac.uk writes: : It is interesting this has come up at this time. Two days ago I : installed Linux on a Psion 5MX (16Mb RAM) and am tickled pink by : it. Installation is easy. At the moment I only have a small : compactflash disk so I have not been able to install X windows or R : yet. You could see if MacAnova will install -- its an R/S-like package. Its pretty small (even runs on 640K DOS) and is quite portable. Its not as powerful as R but its still amazingly powerful and you might be able to fit it on. Thanks. I took a quick look and I think I would have to cross-compile it (I didn't find an ARM binary). When I get my larger compactflash card I am hoping that I will be able to just get the ARM debian package (and all the assorted dependencies) without having to setup a cross-compiling tool chain---I will have to take a look and see what is involved in doing this. I don't have a compiler installed on the Psion and probably would not have enough room for all the libraries (just guessing here). Dave -- David Whiting University of Newcastle upon Tyne, UK __ [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 -- best, -tony --- A.J. Rossini [EMAIL PROTECTED] __ [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] Creating a text codebook
Something like summary() will produce the start of a codebook for a dataset within a data.frame, but it probably would need to be munged up a bit more. Actually, the first use of literate statistical analysis (noweb-style) was done to produce a codebook. On Thu, 30 Sep 2004 14:35:03 -0400, John Fox [EMAIL PROTECTED] wrote: Dear Harold, I'm not sure what you have in mind, but take a look at the prompt() function, which can create a skeleton .Rd (R documentation) for a data frame. It will distinguish between numeric variables and factors, and will show the various levels of each factor. I don't think that there's any other relevant information in the data frame. I hope that this helps, John -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold Sent: Thursday, September 30, 2004 11:39 AM To: [EMAIL PROTECTED] Subject: [R] Creating a text codebook Is there a currently existing method in an R package for creating a codebook from a dataframe? Preferably, I would like to be able to export to a text file all relevant information. __ [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 -- A.J. Rossini [EMAIL PROTECTED] __ [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] problems with ESS R ...
PLEASE send ESS/R related problems to the ESS list. We just recently answered that one over there. Read the manuals and HELP pages in the doc directory, you aren't using it right. You want to C-c C-d. On Wed, 29 Sep 2004 14:34:59 +0200, Meinhard Ploner [EMAIL PROTECTED] wrote: Hi! I have R 1.9.1, Mac OS X 10.3.5, GNU Emacs 21.2.1 and ESS 5.2.3. I installed today the ESS by not changing ess-site.el, but creating .emacs in $home with the single line: $ cat ~/.emacs (load /usr/local/lib/ess-5.2.3/lisp/ess-site) If I start now emacs and then R (with M-x R) then I get: options(STERM='iESS', editor='emacsclient') but using fix() oder edit() doesn't work: fix(pc) emacsclient: can't find socket; have you started the server? Error in edit(name, file, editor) : problem with running editor emacsclient Maybe I forgot to do some simple steps?? Hope anybody could help me Meinhard __ [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 -- A.J. Rossini [EMAIL PROTECTED] __ [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] using tcltk in R under ESS/XEmacs on Windows
It most likely is Windows specific. It's most amazing that we
actually have ESS/(X)Emacs working under windows in the first place.
Unfortunately, I'm in transit for the next few weeks, but I'll
probably have a windows machine on my desk sometime after that. Argh.
best,
-tony
On Fri, 24 Sep 2004 17:48:18 -0400, Liaw, Andy [EMAIL PROTECTED] wrote:
From: Marc Schwartz
On Fri, 2004-09-24 at 15:02, Liaw, Andy wrote:
Sorry for the cross-post. Not sure where the problem is...
A while back I posted an R function to R-help:
cd - function (dir = tclvalue(tkchooseDirectory()),
saveOld = FALSE,
loadNew = TRUE) {
stopifnot(require(tcltk))
if (saveOld)
save.image(compress = TRUE)
setwd(dir)
rm(list = ls(all = TRUE, envir = .GlobalEnv), envir =
.GlobalEnv)
if (loadNew file.exists(.RData)) {
loaded - load(.RData, envir = .GlobalEnv)
return(invisible(loaded))
}
where the default value for the `dir' argument is to run
the tcltk directory
chooser and get the directory name chosen. (Thanks to
Prof. John Fox for
the tcltk part!!) While this function works fine under
Rgui on Windows, it
doesn't work when running R within ESS (5.2.3) and XEmacs
(21.4.13). The
directory chooser never shows up, and dir just gets the
empty string. Does
anyone have any idea what could be the problem? I'd very
much appreciate
any pointers.
Best,
Andy
Andy,
This works under FC2 using ESS 5.2.3 with XEmacs version 21.4.15, so
presumably there is something specific to the Windows implementation?
Given Prof. Fox's follow-up and your obvservation, I guess the problem _is_
Windows-specific. 8-(
Also, two things:
1. You are missing a closing brace above, which I presume may be a
simple copy and paste issue.
Yes. My apologies.
2. If you successfully change the directory, the cd()
function itself is
deleted from the global environment via your rm(...), as you currently
have it implemented. I am not sure if this is intentional or not.
Well, sort of. I've placed it in a small package along with other handy
stuff, so that won't be a problem.
Best,
Andy
HTH,
Marc
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Re: [R] WARNING: terminal is not fully functional
That looks like what happens if one runs R from one of the older
Emacs sub-shells. (esp the pager bit).
It's possible but unlikely that something wrong with comint. ESS
should have redirected the output of
?sink
to a different buffer.
Another possibility is that you've configured things differently,
i.e. have you a edited any
options()
(prompt, or more likely, pager, or other options?). Emacs/ESS doesn't
like that unless you tell it about them.
Peter Dalgaard [EMAIL PROTECTED] writes:
Thomas Schönhoff [EMAIL PROTECTED] writes:
Hello,
first trials to run R from inside of Emacs repeatedly gives me:
?sink
WARNING: terminal is not fully functional
- (press RETURN)
-
Seems like this is going to happen to all help calls using a questionmark!
Any idea how to change this, maybe this isn't subject to change at all!???
...
emacs2121.3+1-7
ess5.2.2-2
Odd. You'd get that sort of error if you tried to run a pager in a
shell buffer, but ESS should intercept it and dump the help page into
a separate buffer. Any chance you're not actually running ESS?
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Re: [R] WARNING: terminal is not fully functional
Thomas Schönhoff [EMAIL PROTECTED] writes:
Hello,
Peter Dalgaard schrieb:
Thomas Schönhoff [EMAIL PROTECTED] writes:
Hmm, I'm running R within Emacs without calling ESS diretly. Thought,
that ESS is activated by default when invoking R!?
Isn't this true!?
I thought you might think that...
No. Loading ESS creates M-x R, which you should use to start R and
get
all the associated goodies.
Ooops, yes really tricky.. an M-x-ess-imenu-R (Godness, there are
a lot of ess-entries!?) did the trick..
Hmm, by the way, is there any tutorial or something similar point to
how to use Emacs, ESS and GNU R?
There are a few, some at http://ESS.R-Project.org/
I'll put my versions up after I get settled in Basel (mid November).
best,
-tony
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Re: [R] loading error of the Rcmdr library on Debian Sid [SOLVED]
That sounds like the result of having a too-old nvidia-common and
booting between 2.4 and 2.6 kernels.
I believe that nvidia until 2.6 likes the TLS libs, under 2.4 doesn't.
Thomas Schönhoff [EMAIL PROTECTED] writes:
Hello,
hopefully someone will remember my previous problem to load the Rcmdr
library from within GNU R resulting in an error message:
libnvidia-tls.so.1: cannot handle TLS data.
Some suggestions have been raised by Christian Schulz and others that
unfortunately didn't work around this error.
Nevertheless I felt very grateful for your suggestions!
This morning I investigated this problem a bit more in depth. It
turned out that a buggy NVidia driver (libnvidia-tls.so) is loaded by
defualt provoking the reported problem.
After renaming /usrlib/tls/ too /usr/lib/tls_old (can also be entirely
removed!) the problem vanished inmediately and R Commander works
smoothly out of the box!
Just thought this might be of interest in case of someone else is
affected by this NVidia related problem!
regards
Thomas
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Re: [R] loading error of the Rcmdr library on Debian Sid
You can apt-get RGL in sid.
Thomas Schönhoff [EMAIL PROTECTED] writes:
Hello,
I just tried to get Rcmdr package working, resulting in:
--
library(Rcmdr)
Loading required package: tcltk
Loading required package: lattice
Loading required package: foreign
Loading required package: abind
Loading required package: lmtest
Loading required package: multcomp
Loading required package: relimp
Loading required package: effects
Loading required package: rgl
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
/usr/lib/R/site-library/rgl/libs/rgl.so:
libnvidia-tls.so.1: cannot handle TLS data
Error in .C(symbol.C(rgl_quit), success = FALSE, PACKAGE = rgl) :
C function name not in DLL for package rgl
Loading required package: mgcv
This is mgcv 1.1-1
Loading required package: car
Error: Missing packages: rgl
Error: .onLoad failed in loadNamespace
Error in library(Rcmdr) : package/namespace load failed
Missing rgl-package ?
---
thomas dpkg -l |grep r-
r-cran-abind 1.1.0-1
r-cran-car 1.0.13-1
r-cran-foreign 0.7-1
r-cran-lattice 0.9.16-1
r-cran-mgcv1.1.1.1-1
r-cran-rgl 0.64.13-1
r-cran-relimp 0.8.4-1
r-cran-rcmdr 0.9.11-1
r-cran-lmtest 0.9.6-2
r-cran-effects 1.0.5-1
r-cran-multcom 0.4.7-1
r-cran-mvtnorm 0.6.8-1
amongst other R related (basic and specific) packages.
Am I still missing some required packages to run RCommander smoothly?
My system:
Debian Sid (unstable)
GNU R 1.9.1
Xfree 4.3
Anyone else noticed this on Debian Sid whilst trying to run the R
Commander !? So far I didn't find a related bug report for
Linux. Maybe this is a Debian related problem, I really have no clue
at the moment.
Regards
Thomas
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Re: [R] Slightly off-topic --- distribution name.
Have you checked Johnson and Kotz? That's the obvious place to start
looking for distributions beyond the usual.
Rolf Turner [EMAIL PROTECTED] writes:
I've built R functions to ``effect'' a particular distribution, and
would like to find out if that distribution is already ``known'' by
an existing name. (I.e. suppose it were called the ``Melvin''
distribution --- I've built dmelvin, pmelvin, qmelvin, and rmelvin as
it were, but I need a real name to substitute for melvin.)
The distribution is really just a toy --- but it provides a nice (and
``non-obviouse'') example of a two parameter distribution where both
the moment and maximum likelihood equations for the parameter
estimators are readily solvable, but at the same time are
``interesting''. So it's good for exercises in an intro math-stats
course.
The distribution is simply that of the ***difference*** of two
independent exponential variates, with different parameters.
I.e. X = U - V where U ~ exp(beta) and V ~ exp(alpha) (where
E(U) = beta, E(V) = alpha).
This makes the distribution of X something like an asymetric Laplace
distribution, with its mode at 0. (One could shift the mode too, but
that would add a third parameter, which would be de trop.)
Anyhow: Is this a ``known'' distribution? Does it have a name?
(I've never seen it mentioned in any of the intro math-stat books
that I've looked into.) If not, can anyone suggest a good name for
it? (Don't be rude now!)
cheers,
Rolf Turner
[EMAIL PROTECTED]
P. S. To save you putting pen to paper and working it out,
the density function is
{ exp(x/alpha)/(alpha + beta) for x = 0
f(x) = {
{ exp(-x/beta)/(alpha + beta) for x = 0
The mean and variance are mu = beta - alpha and
sigma^2 = alpha^2 + beta^2 respectfully. :-)
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[R] [R-pkgs] Announcing snowFT 0.1
Parallel programming with snowFT
Our package snowFT is now available at CRAN. It is an extention of the
package snow, which adds fault tolerance (in the sense of recomputing
computational units when hardware/network failures occur on compute
nodes) and a tighter notion of reproducibility for computations
running on clusters. It additionally provides tools for flexible
management of cluster size as well as computation transparency.
snowFT is written by Hana Sevcikova and Tony Rossini.
(this tool currently requires rpvm for the SNOW backend, though we are
exploring the possibility of extensions for the Rmpi backend. It is
unlikely that these extensions will be implemented for the socket
backend.
best,
-tony
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Re: [R] Surprise when mapping matrix to image
I think I'd have to respectfully disagree with both Brian and
Deepayan, as to whether it should be obvious. It is reasonable
(principle of least suprise) to expect orientation of the plot to
match the print order of the matrix. I would have expected Brian's
one-liner to be in the help page, with a notice. It's a not-so-rare
activity, being a general matrix visualization that is commonly used
in certain areas of science (whether it ought to be commonly used is a
separate question).
While heatmap might've been perhaps a better pointer, but it doesn't
seem to do the right thing, either. I.e.
myTemp - matrix(c(1,2,3,3,2,3),nrow=2)
heatmap(myTemp,Rowv=NA,Colv=NA)
doesn't look right to me (R Version 1.9.1 (2004-06-21))
I see the pixmap/bitmap issue as a bit of a red herring, in this
case.
best,
-tony
p.s. I seem to get bit by this about once a year for the last few,
hence why I'm speaking up.
Deepayan Sarkar [EMAIL PROTECTED] writes:
Quoting Glynn, Earl [EMAIL PROTECTED]:
Prof Ripley:
Thank you for your prompt reply.
It's pure convention: see below.
Did you try reading the help for image? You don't seem to
understand it
if you actually did. It seems you are looking for
image(t(x)[ncol(x):1, ])
I think you guys are too close to R to understand how hard it is to
use sometimes. What may be blatantly obvious to you is quite a problem
especially to beginners. Some of us may be beginners to R, but we know
math, science, programming, and how to solve problems with other tools
and languages.
I re-read the guidelines before posting fearing condemnation.
Before posting I searched the online R-help Google interface with
keywords image, flip, rotate. A discussion from 1998 touched on
this issue but I was hoping that this was deemed a bug at some point
and fixed -- or had an easy workaround, like some parameter I was
missing.
I read the ?image help before posting. Was the part I didn't
understand buried in this note?
Based on a function by Thomas Lumley [EMAIL PROTECTED]
You seem to be thinking that Prof Ripley's solution had something to do with
image(). It doesn't, it has to do with manipulating a matrix. image()
visualizes a matrix in a particular and well-defined way. You want your matrix
to be shown in a different way, and one (simple) way of doing that is to
convert your matrix into a different matrix, on which calling image would give
you what you want. Why would this be explained in ?image ? This is basic R.
More generally, I think your frustration is caused by your expectation that a
matrix object should behave like a bitmap image. It doesn't. If you want work
with images, use the pixmap package.
Deepayan
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Re: [R] Surprise when mapping matrix to image
Richard A. O'Keefe [EMAIL PROTECTED] writes:
Once you know what image() is _intended_ to do with a matrix,
you can figure out the transposing and reversing you need for any
other view. It's knowing you need to that's the problem.
This is a much better statement of my point, and precisely why it
keeps (though only occassionally) burning me.
best,
-tony
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Re: [R] How generate A01, A02, ..., A99?
Yao, Minghua [EMAIL PROTECTED] writes:
Hi,
Anyone can tell me how to generate A01, A02, ..., A99?
paste(A, 1:99, sep=) generates A1, A2,..., A99. This is not what I want.
c(paste(A0,1:9,sep=),paste(A,10:99,sep=))
?
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Re: [R] Is R good for not-professional-statistician, un-mathematical clinical researchers?
One thought -- the first course I took, I taught physicians
XLispStat. They appreciated it since it allowed them to do logistic
regression without spending large $$$.
Now, that isn't quite true any more. So might depend on how times
have changed.
Jacob Wegelin [EMAIL PROTECTED] writes:
Alternate title: How can I persuade my students that R is for them?
Alternate title: Can R replace SAS, SPSS or Stata for clinicians?
I am teaching introductory statistics to twelve physicians and two veterinarians
who have enrolled in a Mentored Clinical Research Training Program. My course is the
first in a sequence of three. We (the instructors of this sequence) chose to teach
R rather than some other computing environment.
My (highly motivated) students have never encountered anything like R. One frankly
asked:
Do you feel (honestly) that a group of physicians (with two vets) clinicians will
be able to effectively use and actually understand R? If so, I will happily call this
bookstore and order this book [Venables and Ripley] tomorrow.
I am heavily biased toward R/S because I have used it since the first applied
statistics
course I took. But I would love to give these students some kind of objective
information
about the usability of R by non-statisticians--not just my own bias.
Could anyone suggest any such information? Or does anyone on this list use R who is
a clinician and not really mathematically savvy? For instance, someone who doesn't
remember any math beyond algebra and doesn't think in terms of P(A|B)?
Or have we done a disservice to our students by choosing to make them
learn R, rather than making ourselves learn SAS, Stata or SPSS?
Thank you for any ideas
Jake Wegelin
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Re: [R] Rserve needs (but cannot find) libR.a (or maybe it's .so)
Need to install R with the shared libraries (it's a config option).
Paul Shannon [EMAIL PROTECTED] writes:
I have successfully installed Rserv (http://stats.math.uni-augsburg.de/Rserve)
on Mac OS, but I have trouble on two different linux platforms.
R CMD INSTALL Rserve_0.3-10.tar.gz
fails with this message
** libs
gcc -g -O2 -I/usr/local/include -L/usr/local/lib Rserv.c -o Rserve \
-DDAEMON -O -I/usr/local/lib/R/include -Iinclude -I. -lR -L/usr/local/lib/R/bin
-ldl -lcrypt
/usr/bin/ld: cannot find -lR
collect2: ld returned 1 exit status
make: *** [Rserve] Error 1
ERROR: compilation failed for package 'Rserve'
Sure enough, when I look, I cannot find either libR.a or librR.so on either
linus system.
On the Mac, I -do- find libR.dylib.
Can anyone help with this?
Many thanks -
- Paul Shannon
Institute for Systems Biology
Seattle
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Re: AW: [R] built-in Sweave-like documentation in R-2.x
Khamenia, Valery [EMAIL PROTECTED] writes:
I think just smarter C-c C-r would be kind of trade-off here.
hm, maybe there are some other voices here similar to mine?
It would be easier to discuss the subj.
Within ESS, you've got the ess-thread-eval (similar to
ess-chunk-eval), so the guts for cross-chunk evals are there, so the
next part would be as you say, making C-c C-r SWeave-aware.
An simpler alternative to code would be to allow one to
eval-chunk-and-step, stepping through chunks, similar to C-c C-n for
stepping through lines. Would this solve the basic problem? 3 x (2
or 3 keystrokes) for 3 chunks.
I can't imagine an evaluation which would cross chunks but use only
part of chunks (this suggests bad programming design to me), but
perhaps you (or others) have an example of when this functionality
would be useful? (i.e. actual regions to eval which cross code-chunk
boundaries but contain 1 or 2 incomplete code-chunks?).
best,
-tony
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Re: [R] built-in Sweave-like documentation in R-2.x
What exactly do you mean by this?
1. generation of Sweave-style docs from R programs or interaction? A
related approach is the reviveable statistical analysis (the
authors/researchers will have to forgive me for not recalling the WWW
site or their Uni!)
2. tools for doing docs and analysis at the same time? Emacs Speaks
Statistics has supported this with R since last century (1997 or so).
3. the vignettes of Bioconductor?
4. a text book in line with the above?
best,
-tony
Khamenia, Valery [EMAIL PROTECTED] writes:
Hi devels,
i did not find at this page:
http://developer.r-project.org/ideas.txt
any ideas concerning incorporating documentation
possibilities (say, Sweave-based) into R-scripts.
Was it discussed already?
(If discussed, then what is the decision/conclusion then?)
thanks,
Valery
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Re: AW: [R] built-in Sweave-like documentation in R-2.x
If you name chunks that should be run together the same thing
(i.e. similar to how Noweb suggests that you should create documents),
then ess-eval-thread will evaluate all chunks in the thread
(i.e. that noweb would have sent to the same file upon tangling).
This is similar to the ess-eval-chunk ESS function.
Khamenia, Valery [EMAIL PROTECTED] writes:
See the 'Writing R Extensions' manual, specifically
Creating R Packages - Writing package vignettes
thank you, i saw this entry. However, this entry is rather
about how to include documents (in particular Sweave-based)
into a package. But I have meant smth else.
Let me explain in example. Today I use emacs as
environment for my R-sessions. I am quite happy to
use Sweave, but not happy, that there is no good
possibility to run some selected *part* of the R-code.
Indeed, the R-chunks are alternated with
Latex-chunks in Sweave. So, if one would like to
execute, say, three consequent R-chunks (C-c C-r in ESS-mode),
then the corresponding Latex-chunks between the
R-chunks will cause side-effects. Actually, it is
because neither ESS nor R could accept Latex-chunks
and the markup symbols of Sweave. This makes interactive
work in .Rnw files not fully convenient.
Making the above short: would it be a bad idea to
allow Latex-friendly documentation chunks in
R-language?
Thank you.
P.S. I am sorry if i missed something well-known
concerning the subj.
--
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Re: AW: [R] built-in Sweave-like documentation in R-2.x
Deepayan Sarkar [EMAIL PROTECTED] writes:
Is selecting and 'C-c C-r'-ing the 3 chunks separately that bad?
Yes. The UI should take care of it for him.
Others may have better suggestions.
A bit more work on the chunk evaluation approach within Emacs is one;
it almost does what is needed, but not quite.
best,
-tony
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Re: [R] Approaches to using RUnit
Seth Falcon [EMAIL PROTECTED] writes:
Having used JUnit and PyUnit, I was pleased to see the release of the
RUnit package on CRAN.
I'm wondering if there are any RUnit users out there that would be
willing to share some tips on how they organize their code to work with
RUnit.
Specifically, I'm wondering about the best way to load/import/source the
functions to be tested. I would like to end up with a script, testall
or some such, that allows me to run all the unit tests in a given
directory.
Hi Seth -
The version that I was working on (before the other folks released a
less eclectic and more functional/general package) had a
testrunner(test=c(list,of,functions),testall=FALSE)
API, along with a preliminary tcltk
GUIrunner()
with a similar intended API. I've been trying to find the initiative
to integrate (overlay) those tools with the current RUnit as an
add-on, but the difference is that I attached tests as S4 object
instantiations.
Stop by if you want to chat a bit about it.
best,
-tony
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Re: [R] How to import specific column(s) using read.table?
If you've got access to unix tools (i.e. linux or cygwin), consider
the cut command. Great for column selection.
Thomas Lumley [EMAIL PROTECTED] writes:
On Mon, 9 Aug 2004, F Duan wrote:
Dear R people,
I have a very big tab-delim txt file with header and I only want to import
several columns into R. I checked the options for read.table and only
found nrows which lets you specify the maximum number of rows to read in.
Although I can use some text editors (e.g., wordpad) to edit the txt file first
before running R, I feel its not very convenient. The reason for me to do this
is that if I import the whole file into R, it will eat up too much of my
systems memory. Even after I remove it later, I still cant release the memory.
You can't avoid reading the whole file, but you can avoid having it in
memory.
I'll assume you know how many lines are in the file, call it N. (this
isn't necessary but it is tidier) and that you are interested in columns
10 and 110, both numeric
If you do something like
inputfile-file(inputfile.txt,open=r)
result-data.frame(col10=numeric(N), col110=numeric(N))
chunksize-1000
nchunks- ceiling(N/1000)
for(i in 1:nchunks){
chunk-read.table(inputfile,nrows=chunksize)
result[ (i-1)*chunksize+ (1:chunksize),]-chunk[,c(10,110)]
}
close(inputfile)
you can choose the chunk size so that the memory use is not too bad.
There are also more efficient ways that make you do more of the work (eg
read in lines of text with readLines and use regular expressions to
extract the columns you need)
-thomas
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Re: [R] Question on Differentiating Two Populations in R
Sounds like you need a course in statistics. This is a 2-sample
comparison problem. It might be worth finding a local stat
consultant, it shouldn't take much time.
James R. Graham [EMAIL PROTECTED] writes:
Hello All,
Forgive me if this a blatantly newbie question or not germane to the
list, but i was wondering if my current approach to my problem is the
best way in R.
I have two experimental datasets (positive and negative) of differing
lengths and a large number of ways of numerically expressing the data
by using various scales to represent each data point.
I am looking for a scale that will allow me to differentiate between
the positive and negative populations.
Each dataset is simply a list of numbers: 43 numbers in the positive
case and 9 in the negative (small sets, i know, but it's all the data
i currently have) and I have hundreds of scales.
I assign each dataset to a variable using scan() (each are in separate
files).
My initial comparison of the two datasets is simply a boxplot with the
hope that the two do not overlap too much...
Is this the way you would approach this problem? Is there an easier
way of doing this in R?
Any and all help is greatly appreciated!
james
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Re: [R] ERROR: compilation failed for package 'rgl'
OpenGL or MESA librares.
Korponai János [EMAIL PROTECTED] writes:
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Dear All,
I could not install rgl package. What is missing?
daphnia:~# R CMDR INSTALL rgl_0.64-13.tar.gz
* Installing *source* package 'rgl' ...
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for X... libraries /usr/X11R6/lib,
headers /usr/X11R6/include
checking for libpng-config... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/usr/lib/R/include -I/usr/X11R6/include -DHAVE_PNG_H
-mieee-fp -Wall -pedantic -fno-exceptions -fno-rtti -fPIC -g
-O2 -c x11lib.cpp -o x11lib.o
In file included from glgui.h:9,
from gui.h:10,
from x11gui.h:10,
from x11lib.cpp:13:
opengl.h:19:19: GL/gl.h: No such file or directory
opengl.h:20:20: GL/glu.h: No such file or directory
In file included from gui.h:10,
from x11gui.h:10,
from x11lib.cpp:13:
glgui.h:27: error: 'GLuint' is used as a type, but is not defined
as a type.
glgui.h:28: error: 'GLuint' is used as a type, but is not defined
as a type.
glgui.h:29: error: 'GLuint' is used as a type, but is not defined
as a type.
glgui.h: In member function `void GLBitmapFont::enable()':
glgui.h:22: error: `listBase' undeclared (first use this
function)
glgui.h:22: error: (Each undeclared identifier is reported only
once for each
function it appears in.)
glgui.h:22: error: `glListBase' undeclared (first use this
function)
In file included from x11lib.cpp:13:
x11gui.h:13:20: GL/glx.h: No such file or directory
In file included from x11lib.cpp:13:
x11gui.h: At global scope:
x11gui.h:45: error: syntax error before `*' token
x11gui.h:52: error: 'GLXContext' is used as a type, but is not
defined as a
type.
make: *** [x11lib.o] Error 1
ERROR: compilation failed for package 'rgl'
** Removing '/usr/local/lib/R/site-library/rgl'
daphnia:~# version
_
platform i386-pc-linux-gnu
arch i386
os linux-gnu
system i386, linux-gnu
status
major1
minor9.0
year 2004
month04
day 12
language R
--
Dr. Janos Korponai
West-Transdanubian District Environmental and Water Authority,
Dept. Kis-Balaton
H-8360 Keszthely, Csik F. str. 1, Hungary
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Re: [R] keep.source.pkgs()
Thomas Lumley [EMAIL PROTECTED] writes:
Personally, I find this the easiest way to look at the source. You can
browse the source on https://svn.r-project.org/R/ if you are using a
binary distribution, rather than downloading the whole thing.
Except that you probably don't want to, i.e. grab a copy via a
subversion client rather than a WWW-server.
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Re: [R] a question about using nlme
Lijuan Wang [EMAIL PROTECTED] writes:
I am using Splus ...
So why post to an R list?
best,
-tony
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[R] zsh and R
In the process of evaluating new shells, I've run into a few problems
with zsh and the R CMD build, R CMD check scripts.
I'd like to ask a few questions off-line if anyone has experience with
R and the zsh completion/substitution functionality.
Note that bash continues to work as well as ever, just that zsh is
being finicky.
best,
-tony
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[R] Thanks to Dirk for making the parallel R packages available on debian!
For those tracking debian unstable, note that thanks to Dirk E.,
installation is now mostly trivial.
(i.e. for snow, rpvm, rmpi, rsprng, and the sprng libraries).
best,
-tony
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Re: [R] SWIG for R
I like SWIG (well, it facilitates wrappers for Python really well),
but it's not perfect.
I've not delved into the difficulties in any detail yet, but we've had
problems with mixing SWIG and Boost.python for connections with Python
code -- and the Boost.python mechanism feels like DTL's RSyour
language here code, where as SWIG doesn't quite have the same flavor.
(sorry for failing on the details, but I'm doing something else
today).
Duncan Murdoch [EMAIL PROTECTED] writes:
On Wed, 14 Jul 2004 08:01:28 -0700, Duncan Temple Lang
[EMAIL PROTECTED] wrote :
SWIG is an extensible system and so people
other than the SWIG developers can indeed
provide facilities for supporting R.
I am surprised nobody has done it yet
and remember asking you whether you had considered
using SWIG for your OpenGL about 3 years ago.
Sorry, I forgot about that.
I don't think SWIG would be much help with OpenGL, because there the
difficulty is in translating the R ideas of what data is like and what
people want to do with it into corresponding concepts in OpenGL, the
actual calls to the OpenGL API are a pretty easy part of the whole
exercise. In any case, they probably have to be written in compiled
code for performance reasons, since you make so many OpenGL calls
for every frame being drawn.
But I'm sure there are other libraries where this isn't true, and SWIG
would be useful for them. Maybe Hisaji has one, and would want to
tackle the R support.
Duncan Murdoch
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Re: [R] SWIG for R
[EMAIL PROTECTED] (A.J. Rossini) writes:
I like SWIG (well, it facilitates wrappers for Python really well),
but it's not perfect.
I've not delved into the difficulties in any detail yet, but we've had
problems with mixing SWIG and Boost.python for connections with Python
code -- and the Boost.python mechanism feels like DTL's RSyour
language here code, where as SWIG doesn't quite have the same flavor.
(sorry for failing on the details, but I'm doing something else
today).
Argh. To be clear, this is in the context of C++ systems. Which is
relevant but completely different.
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Re: [R] general questions about R on debian/powerpc
I ran Debian/PPC for about a year, 1-2 years ago -- it worked fine at
that point, on a G3 iBook.
Of course, you get weird looks with MacOS / Linux dual boots, but
that's different than whether it functions.
I switched back to intel-based hardware because it was cheaper and
faster, not necessarily better.
best,
-tony
Tamas Papp [EMAIL PROTECTED] writes:
Hi,
I am about to but a laptop, and have narrowed the choices down to a
Dell Latitude 600 and an Apple Powerbook G4 Aluminium (Princeton
provides these models at a discount for grad students).
I am biased towards the Powerbook, and would like to run Debian on it.
I have only used debian on i386 platforms so far. I use R quite
frequently, so I would be interested in your experience of running R
in debian/ppc --- are there any quirks with libraries, any packages
that don't compile, anything that should discourage me from buying a
powerbook or running debian on it, etc.
I would also be interested in your experience with the speed of the
platform. I have never used a RISC processor before, so I don't know
whether the claims that it delivers much more power per MHz are valid.
Please share anything that you consider relevant. If you think that
it's not R-related, please send an e-mail to the either address below
instead of the list.
Thanks,
Tamas
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Re: [R] anti-R vitriol
Barry Rowlingson [EMAIL PROTECTED] writes:
It's not that I think SAS is such great software,
it's not. But I really hate badly designed
software. R is designed by committee. Worse,
it's designed by a committee of statisticians.
They tend to confuse numerical analysis with
computer science and don't have any idea about
software development at all. The result is R.
They'd probably prefer computer scientists and numerical analysts who
confuse data munging with statistical data analysis, a common problem
in mixed departments...
best,
-tony
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Re: [R] Readline on R-1.9.1a
Dirk Eddelbuettel [EMAIL PROTECTED] writes:
On Mon, Jun 14, 2004 at 04:01:02PM -0400, Roger D. Peng wrote:
People who compile from source still need to install the necessary rpms.
Which is why another Linux distribution uses the concept of Build-Depends :)
Which is another reason why I use that other Linux distribution...
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Re: [R] how to initialize random seed properly ?
[EMAIL PROTECTED] writes:
Here is my best solution so far using $RANDOM in bash
or maybe somebody has pure R solution ?
Sure -- use the rsprng or rlecuyer packages from CRAN, which support
(independent?) streams of random numbers from a common set of seeds.
best,
-tony
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Re: [R] Building package on Windows: No rule to make target '-llapack'
Zhu Wang [EMAIL PROTECTED] writes:
Now I think maybe two problems: one is that maybe I do not have Lapack and Blas
installed
I think this definitely needs to be solved.
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Re: [R] how to initialize random seed properly ?
For reproducibility, you probably want to specify the starting seeds.
I'd worry about using systime. (for selecting the seeds, you might
consider random draws from a uniform).
best,
-tony
[EMAIL PROTECTED] writes:
I want to start R processes on multiple processors from single shell
script
and I want all of them to have different random seeds.
One way of doing this is
sleep 2 # (with 'sleep 1' I am often getting the same number)
...
set.seed(unclass(Sys.time()))
Is there a simpler way without a need to sleep between invoking
different R processes ?
Ryszard
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Re: [R] clustalw
Might be a compilation problem, or change of system libraries.
[EMAIL PROTECTED] [EMAIL PROTECTED] writes:
Hi,
I'm using the function clustalw in packages dna, but every time i have a
segmentation fault!
In your opinion What is the problem?Memory?
Please help me
Daniela
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Re: [R] clustalw
It's on Jim Lindsey's WWW site. It's a nice package. We've got an
extension that is somewhat incomplete that incorporates BLAST results
(from NCBI, though could config for local use) in a package called
BioSeq1 on Bioconductor's dev site -- I don't think that the CVS
viewer is available, but I could provide a tarball for builds (might
need a bit of hacking in its current state) if there is interest.
Email me privately if so.
best,
-tony
Wolski [EMAIL PROTECTED] writes:
Hi Daniela!
From where you got this package?
I even havent found it at cran.
It is not a bioconductor package either.
and
search.help(clustalW)
In any case it is better to contact the package provider directly.
Sincerely Eryk
*** REPLY SEPARATOR ***
On 6/8/2004 at 6:38 PM [EMAIL PROTECTED] wrote:
Hi,
I'm using the function clustalw in packages dna, but every time i have a
segmentation fault!
In your opinion What is the problem?Memory?
Please help me
Daniela
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Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic
Ihnestrasse 63-73 14195 Berlin 'v'
tel: 0049-30-83875219 / \
mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski
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Re: [R] Distributed computing with R
No -- the point is that they are mostly orthogonal solutions, not
mutually exclusive. Mostly implies that sometimes, 1 + 1 = 0.5
(i.e. negative interactions can happen if you do not think through
what each is doing for scheduling/job transfer/migration).
For example, you can use SGE, OpenMOSIX, and SNOW-on-PVM (or other
message passing library) all together.
SGE and OpenMOSIX might not be too happy, since they are trying to do
the same thing at different levels, but it would work (perhaps
inefficiently).
best,
-tony
Paul Gilbert [EMAIL PROTECTED] writes:
Tony
Thanks, this categorization has cleared up a few things I have found
confusing. But should I read this to mean that SNOW would not run on
a system or kernel level parallel setup?
Thanks,
Paul Gilbert
A.J. Rossini wrote:
Also see SNOW (which simplifies parallel programming, sits on top of
rpvm, Rmpi, or a socket-based system).
Depends on whether you want parallelism on the:
1. User-level -- the libraries such as PVM, LAM-MPI, etc will help,
and there are various packages which provide an API
to those.
2. System-level -- then Condor, Sun Grid Engine / Maui scheduler, and
similar queueing/batching/allocation daemons will
help (computational grid software is usually a
generalization of this which adds authentication
and resource allocation).
3. Kernel-level -- then OpenMOSIX, BPROC, etc will help.
They are mostly orthogonal. Mostly... :-).
best,
-tony
Armin Roehrl [EMAIL PROTECTED] writes:
If you do some programming, you might want to look at MPI.
R-extensions for MPI exist (RMPI).
It all depends a lot on what kind of usage you envisage of your cluster.
Open-PBS is also a good batch system. Maybe you also want to
look at Mosix, which is a modified linux system.
Depending on what your ultimate computing ressources are,
maybe also look at IBM's Globus toolkit.
Parallel programming is fun. The world is inherently parallel!
Ciao,
-Armin.
Armin Roehrl, http://www.approximity.com
We manage risk
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Re: [R] Distributed computing with R
Also see SNOW (which simplifies parallel programming, sits on top of
rpvm, Rmpi, or a socket-based system).
Depends on whether you want parallelism on the:
1. User-level -- the libraries such as PVM, LAM-MPI, etc will help,
and there are various packages which provide an API
to those.
2. System-level -- then Condor, Sun Grid Engine / Maui scheduler, and
similar queueing/batching/allocation daemons will
help (computational grid software is usually a
generalization of this which adds authentication
and resource allocation).
3. Kernel-level -- then OpenMOSIX, BPROC, etc will help.
They are mostly orthogonal. Mostly... :-).
best,
-tony
Armin Roehrl [EMAIL PROTECTED] writes:
If you do some programming, you might want to look at MPI.
R-extensions for MPI exist (RMPI).
It all depends a lot on what kind of usage you envisage of your cluster.
Open-PBS is also a good batch system. Maybe you also want to
look at Mosix, which is a modified linux system.
Depending on what your ultimate computing ressources are,
maybe also look at IBM's Globus toolkit.
Parallel programming is fun. The world is inherently parallel!
Ciao,
-Armin.
Armin Roehrl, http://www.approximity.com
We manage risk
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Re: [R] X/Emacs and R in Linux
Dan Bolser [EMAIL PROTECTED] writes:
Yikes! whatever happened to a good old 'INSTALL' file?
There is a nice README file which you should read...
People should not assume that just because you use linux you automatically
know what you are doing!
Apparently :-).
First it took me ages to find the install instructions, they were hidden
on page nine of a pdf file called ess.pdf. Then it took me ages to
understand them. Their are a lot of comments in the file 'ess-site.el' and
I don't think I understood any of them.
In the end I ignored this file and I just added the (load
'path-to-ess-site.el-file') to my .emacs file.
compile bit code? not me!
Exactly. No reason to. And you know that if you read the
documentation.
Then it took me a long time to get going with emacs and ess, I had to
guess the R-mode command, as it is somehow assumed that you dont need it.
Now I am getting there, but easy it wasnt.
Sorry for all the complaints,
And you sent them to the wrong list, as well.
best,
-tony
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