Re: [R] repeat { readline() }
Ctrl-Break works: see the rw-FAQ and README.rterm. (You'll need a return
to see a new prompt.)
It is related to your reading directly from the console, so Ctrl-C is
getting sent to the wrong place, I believe. (There's a comment from Guido
somewhere in the sources about this, and this seems corroborated by the
fact that Ctrl-C will interrupt under Rterm --ess.)
On Sun, 8 Jan 2006, Henrik Bengtsson wrote:
Hi.
Using Rterm v2.2.1 on WinXP, is there a way to interrupt a call like
repeat { readline() }
without killing the Command window? Ctrl+C is not interrupting the loop:
R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.2.1 Patched (2006-01-01 r36947)
snip/snip
repeat { readline() }
^C
^C
^C
^C
On Unix it works. The problem seems to get the interrupt signal to
occur outside the readline() call so that repeat is interrupted. Doing
repeat { readline(); Sys.sleep(3) }
and it is likely that can generate an interrupt signal outside readline().
It seem like readline()/readLines(n=1) or an underlying method catches
the interrupt signal quietly and just waits for a symbol to come
through. Try readline() by itself and press Ctrl+C. Maybe this is a
property of the Windows Command terminal, I don't know, but is it a
wanted feature and are R core aware of it? Note that, in Rgui it is
possible to interrupting such a loop by pressing ESC.
Cheers
Henrik
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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
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Re: [R] repeat { readline() }
On a related note, does anyone know how to exit:
repeat { try( readline() ) }
The try block captures Ctrl-C.
Hadley
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Re: [R] Wikis etc.
On Sat, 7 Jan 2006 13:51:24 -0500 Jonathan Baron [EMAIL PROTECTED] wrote: On 01/07/06 12:25, Dirk Eddelbuettel wrote: So my $0.02 would be to a) go for it, if possible but b) make it visible, and closely tied to R Core / CRAN / R News / Which poses the chicken/egg problem of people running out of spare time to setup, admin, monitor, hand-hold the wiki, its database, watch out for spammers, etc. Volunteers to do this, and maybe help Jon Baron on a first run using TWiki? Great. I agree. But there are now at least 3 proposals floating around. Mine was to base the wiki on (I think) the individual help pages, each file in the help or html subdirectory of each package would be a wiki page. Since there are about 17000 of these at last count - oh, my, could that really be true? - this must be automated. It should be fairly easy, but I just haven't done it yet. What this would amount to is an extended help system. Then there is the decision about what happens with updates. I'm beginning to think that there is just no other way to handle this than to INCLUDE the latest version of each help file in the wicki page, have the comments come AFTER it, and just don't worry about it if the comments become out of date. Eventually, someone will edit them if it is important. Here I strongly disagree. Nothing is worse than searching for help and stumble upon wrong hintsight. It is better to find nothing, than to _think_ to have found an answer only to find it not working. I was just bitten by outdated docu after updating qemu. Did cost some time and frustration. Think of the beginner left with useless, or worse, wrong advise. Detlef But I'm not at all sure this is the best way to go. Given that all the functions in each package are related, it might be better to have one wiki page per package. In this case, there is less difference between my proposal and the other existing wikis. It is possible that too many wikis is bad. On the other hand, it is possible that too few is bad. May be true. Have a nice sunday, Detlef Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison I love this. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ 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 -- Keinen Gedanken zweimal denken, außer er ist schön. Unbekannte Quelle __ 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-pkgs] sudoku
Hey, you spoiled my course! :-) I planned using this as an excersise. Alternative ideas anyone ... Detlef On Fri, 6 Jan 2006 11:43:44 -0500 Brahm, David [EMAIL PROTECTED] wrote: Any doubts about R's big-league status should be put to rest, now that we have a Sudoku Puzzle Solver. Take that, SAS! See package sudoku on CRAN. The package could really use a puzzle generator -- contributors are welcome! -- David Brahm ([EMAIL PROTECTED]) [[alternative HTML version deleted]] ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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 -- Keinen Gedanken zweimal denken, außer er ist schön. Unbekannte Quelle __ 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] repeat { readline() }
On Sun, 8 Jan 2006, Prof Brian Ripley wrote:
Ctrl-Break works: see the rw-FAQ and README.rterm. (You'll need a return
to see a new prompt.)
It is related to your reading directly from the console, so Ctrl-C is
getting sent to the wrong place, I believe. (There's a comment from Guido
somewhere in the sources about this, and this seems corroborated by the
fact that Ctrl-C will interrupt under Rterm --ess.)
Although the comment is there (in psignal.c), on closer examination the
cause is a change Guido made to getline.c, so Ctrl-C is treated as a
character during keyboard input. I doubt if that was intentional (0 is
not the default state) and I have changed it for R-devel.\
On Sun, 8 Jan 2006, Henrik Bengtsson wrote:
Hi.
Using Rterm v2.2.1 on WinXP, is there a way to interrupt a call like
repeat { readline() }
without killing the Command window? Ctrl+C is not interrupting the loop:
R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.2.1 Patched (2006-01-01 r36947)
snip/snip
repeat { readline() }
^C
^C
^C
^C
On Unix it works. The problem seems to get the interrupt signal to
occur outside the readline() call so that repeat is interrupted. Doing
repeat { readline(); Sys.sleep(3) }
and it is likely that can generate an interrupt signal outside readline().
It seem like readline()/readLines(n=1) or an underlying method catches
the interrupt signal quietly and just waits for a symbol to come
through. Try readline() by itself and press Ctrl+C. Maybe this is a
property of the Windows Command terminal, I don't know, but is it a
wanted feature and are R core aware of it? Note that, in Rgui it is
possible to interrupting such a loop by pressing ESC.
Cheers
Henrik
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
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
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
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
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Re: [R] Wikis etc.
Kris over at Wiki That! has a post today about what makes for a good wiki: http://www.wikithat.com/wiki_that/2006/01/wiki_of_the_wee_1.html Most wikis I’ve looked at are in danger of facing the same fate as most websites and CMS - death by boredom. They are focused on content that is used as reference for some off-line activity OR as the end-result of an off-line activity. Collaboration and participation is more than just sharing information and making it accessible. It’s all about the PROCESS of planning and executing events, projects, tasks, and deliverables. Content is boring - action is engaging. Make your wiki activity- centric, not just data-centric (content). If the wiki is a place where people just go to look things up -- we're toast. It needs to be made into an active learning environment, a place where experts and beginners alike come to interact. Some to share their knowledge, and others to learn from the masters. It's the same dynamic that makes the mailing list so active, and yet also what exposes its weakness (i.e. it doesn't scale well). Kevin Kevin J. Gamble. Ph.D. Associate Director eXtension Initiative Box 7647 NCSU Raleigh, NC 27694-7641 v: 919.515.8447 c: 919.605.5815 AIM: k1v1n Web: intranet.extension.org __ 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] Filters in waveslim
Dear R Users, For running wavelet functions using dwt( ), modwt( ), and mra( ), a wavelet filter algorithm is applied. For all these functions, default is la8 and other possibility is haar. In related documents, another possibilities like as symlet and coiflet ... are not cited. Besides la8 and haar, which wavelet filters can be used? Thank you for any help, Amir Safari - [[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] packages and tex files
Erin Hodgess wrote: Dear R People: I am trying to build a package (yet again!) I have both PCTex and WinEdt. I want the *.tex files to use WinEdt. Erin, please check the R Installation and Administration manual on how to set up a working environment to build and install packages. I don't know PCTex, it is not mentioned in the manual cited above, hence it might not work without some hiccups. You do not need to care about .tex files, they are produced and afterwards compiled into the appropriate format automatically from .Rd files by the R tools. I have looked into the produced tex files only in very rare circumstances where some debugging of Rd files was required. Or do you want to edit the Rd files in WinEdt? Then, I recommend to set up WinEdt appropriately to handle them in the same manner as LaTeX files. How should I set that, please? Just in the path? You LaTeX binaries must be in the path (but probably they already are ...). Also, where would I get Rd.sty, please? The supported LaTeX distributions are told to look into the right place by the R CMD tools. And this is: path-to-R/share/texmf/Rd.sty Uwe Ligges Thanks, R Version 2.2.1 Windows Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [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-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] exporting methods/classes
Erin Hodgess wrote:
Dear R People:
I'm still struggling with sending methods and classes as part of
creating a new package.
Where does the .onLoad function go? Within R itself or in a file
in one of the new package directories?
Simply save the .onLoad function in some .R file (e.g. zzz.R) in the
package's ./R directory.
Here are my latest efforts:
Here's the last part of the woof1-Ex.Rout
library('woof1')
Error in loadNamespace(package, c(which.lib.loc, lib.loc),
keep.source = keep.source) :
in 'woof1' classes for export not defined: dog
Error: package/namespace load failed for 'woof1'
Execution halted
So this looks like you have defined S4 classes for export in your
Namespace but you have no call that starts with
setClass(dog, ..
in the R code in your package, hence the class dog is undefined.
Here's the NAMESPACE
importFrom(graphics,plot)
exportClasses(dog)
exportMethods(plot,show)
You don't export any other functions?
Uwe Ligges
thanks yet again,
Sincerely,
Erin
mailto: [EMAIL PROTECTED]
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Re: [R] Wikis etc.
Hello all, Sorry for not taking part of this discussion earlier, and for not answering Detlef Steuer, Martin Maechler, and others that asked more direct questions to me. I am away from my office and my computer until the 16th of January. Just quick and partial answers: 1) I did not know about Hamburg RWiki. But I would be happy to merge both in one or the other way, as Detlef suggests it. 2) I choose DokuWiki as the best engine after a careful comparison of various Wiki engines. It is the best one, as far as I know, for the purpose of writting software documentation and similar pages. There is an extensive and clearly presented comparison of many Wikki engines at: http://www.wikimatrix.org/. 3) I started to change DokuWiki (addition of various plugins, addition of R code syntax coloring with GESHI, etc...). So, it goes well beyond all current Wiki engines regarding its suitability to present R stuff. 4) The reasons I did this is because I think the Wiki format could be of a wider use. I plan to change a little bit the DokuWiki syntax, so that it works with plain .R code files (Wiki part is simply embedded in commented lines, and the rest is recognized and formatted as R code by the Wiki engine). That way, the same Wiki document can either rendered by the Wiki engine for a nice presentation, or sourced in R indifferently. 5) My last idea is to add a Rpad engine to the Wiki, so that one could play with R code presented in the Wiki pages and see the effects of changes directly in the Wiki. 6) Regarding the content of the Wiki, it should be nice to propose to the authors of various existing document to put them in a Wiki form. Something like Statistics with R (http://zoonek2.free.fr/UNIX/48_R/all.html) is written in a way that stimulates additions to pages in perpetual construction, if it was presented in a Wiki form. It is licensed as Creative Commons Attribution-NonCommercial-ShareAlike 2.5 license, that is, exactly the same one as DokuWiki that I choose for R Wiki. Of course, I plan to ask its author to do so before putting its hundreds of very interesting pages on the Wiki... I think it is vital to have already something in the Wiki, in order to attract enough readers, and then enough contributors! 7) Regarding spamming and vandalism, DokuWiki allows to manage rights and users, even individually for pages. I think it would be fine to lock pages that reach a certain maturity (read-only / editable by selected users only) , with link to a discussion page which remaining freely accessible at the bottom of locked pages. 8) I would be happy to contribute this work to the R foundation in one way or the other to integrate it in http://www.r-project.org or http://cran.r-project.org. But if it is fine keeping it in http://www.sciviews.org as well, it is also fine for me. I suggest that all interested people drop a little email to my mailbox. I'll recontact you when I will be back to my office to work on a more elaborate solution altogether when I am back at my office. Best, Philippe Grosjean __ 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] lmer error message
Also, please try setting options(verbose = TRUE) immediately before your call to lmer. This will provide verbose output on the progress of the iterations and will probably give an indication of where the problem lies. On 1/7/06, Spencer Graves [EMAIL PROTECTED] wrote: I am not familiar with this particular error message, but I will offer a few suggestions that might help you isolate it. 1. PLEASE do read the posting guide! www.R-project.org/posting-guide.html. The limited information supplied with your question does NOT include data requested of all posts. The command sessionInfo() can proved some of the standard basics that many potential respondants want to know before they consider replying. 2. Have you tried traceback()? This may or may not help you, but it's quick and worth a try. 3. Can you provide this list with a very simple, self contained example that produces the error message you mention? 4. I suggest you list lmer by typing the function name and a commmand prompt. In this case, lmer consists solely of a call to standardGeneric. The documentation for standardGeneric led me to the documentation for GenericFunctions, which led me to showMethods. 'showMethods(lmer)' indicated only one method, namely for 'formula = formula'. Then 'dumpMethod(lmer, file=lmer.R, signature=formula)' produced a listing of that function for me in the working directory. If you have trouble finding the working directory, try 'getwd()'. I would then modify the function it lmer.R to create a new function lmer.formula. Then I would try debug(lmer.formula). Then I would replace lmer by lmer.formula in the command that generated the error and execute that modified formula. This will open a browser and allow you to walk through the function line by line, examining (and changing) anything you want in the environment of that function. Doing this will, I believe, lead you to exactly the line in the lmer code that generated the error message you don't understand. With only a modest amount of luck, you should be able to find in this way what you can do to avoid that error. Anecdotal evidence suggests that people who use the techniques described in suggestions 1-3 tend to get quicker, more useful replies from this list. Moreover, in virtually every case that I've tried suggestion 4, I've been able to figure out how to overcome that particular difficulty. In addition, I've often learned useful things about R that I didn't know befor. hope this helps. spencer graves Abderrahim Oulhaj wrote: Dear All, I have the following error message when I fitted lmer to a binary data with the AGQ option: Error in family$mu.eta(eta) : NAs are not allowed in subscripted assignments In addition: Warning message: IRLS iterations for PQL did not converge Any help? Thanks in advance, Abderrahim [[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 __ 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
Re: [R] Suggestion for big files [was: Re: A comment about R:]
[Brian Ripley] [François Pinard] [Brian Ripley] One problem [...] is that R's I/O is not line-oriented but stream-oriented. So selecting lines is not particularly easy in R. I understand that you mean random access to lines, instead of random selection of lines. That was not my point. [...] Skipping lines you do not need will take longer than you might guess (based on some limited experience). Thanks for telling (and also for the expression reservoir sampling). OK, then. All summarized, if I ever need this for bigger datasets, selection might better be done outside of R. -- François Pinard http://pinard.progiciels-bpi.ca __ 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] lmer error message
Hi, Doug: Thanks. My copy of the 'lmer' documentation does not list the 'verbose' argument. Is this something you plan to discontinue or modify, or was it recently added to the script but not to the documentation I have? Also, I just tried it modifying one of the examples in the documentation: fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy, + verbose=TRUE) trace: lmer(Reaction ~ Days + (Days | Subject), sleepstudy, verbose = TRUE) Maybe this example converges so quickly it senses no need for greater verbosity. Thanks, Spencer Graves # R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base other attached packages: lme4 latticeMatrix 0.98-1 0.12-11 0.99-4 Douglas Bates wrote: Also, please try setting options(verbose = TRUE) immediately before your call to lmer. This will provide verbose output on the progress of the iterations and will probably give an indication of where the problem lies. On 1/7/06, Spencer Graves [EMAIL PROTECTED] wrote: I am not familiar with this particular error message, but I will offer a few suggestions that might help you isolate it. 1. PLEASE do read the posting guide! www.R-project.org/posting-guide.html. The limited information supplied with your question does NOT include data requested of all posts. The command sessionInfo() can proved some of the standard basics that many potential respondants want to know before they consider replying. 2. Have you tried traceback()? This may or may not help you, but it's quick and worth a try. 3. Can you provide this list with a very simple, self contained example that produces the error message you mention? 4. I suggest you list lmer by typing the function name and a commmand prompt. In this case, lmer consists solely of a call to standardGeneric. The documentation for standardGeneric led me to the documentation for GenericFunctions, which led me to showMethods. 'showMethods(lmer)' indicated only one method, namely for 'formula = formula'. Then 'dumpMethod(lmer, file=lmer.R, signature=formula)' produced a listing of that function for me in the working directory. If you have trouble finding the working directory, try 'getwd()'. I would then modify the function it lmer.R to create a new function lmer.formula. Then I would try debug(lmer.formula). Then I would replace lmer by lmer.formula in the command that generated the error and execute that modified formula. This will open a browser and allow you to walk through the function line by line, examining (and changing) anything you want in the environment of that function. Doing this will, I believe, lead you to exactly the line in the lmer code that generated the error message you don't understand. With only a modest amount of luck, you should be able to find in this way what you can do to avoid that error. Anecdotal evidence suggests that people who use the techniques described in suggestions 1-3 tend to get quicker, more useful replies from this list. Moreover, in virtually every case that I've tried suggestion 4, I've been able to figure out how to overcome that particular difficulty. In addition, I've often learned useful things about R that I didn't know befor. hope this helps. spencer graves Abderrahim Oulhaj wrote: Dear All, I have the following error message when I fitted lmer to a binary data with the AGQ option: Error in family$mu.eta(eta) : NAs are not allowed in subscripted assignments In addition: Warning message: IRLS iterations for PQL did not converge Any help? Thanks in advance, Abderrahim [[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 __ 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
Re: [R] lmer error message
Spencer: It is an option, not an argument, and sets the default for the lmerControl arguments msVerbose and EMverbose (see ?lmer) options(verbose=TRUE) fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy) EM iterations 0 1768.412 ( 3.75000 106.875 0.0:3.210.1740.663) 1 1749.892 ( 2.67539 62.5305 -5.17591:2.360.1760.479) ... 0 1743.63: 0.918936 0.0531527 -0.304877 ... On Sun, 8 Jan 2006, Spencer Graves wrote: Hi, Doug: Thanks. My copy of the 'lmer' documentation does not list the 'verbose' argument. Is this something you plan to discontinue or modify, or was it recently added to the script but not to the documentation I have? Also, I just tried it modifying one of the examples in the documentation: fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy, + verbose=TRUE) trace: lmer(Reaction ~ Days + (Days | Subject), sleepstudy, verbose = TRUE) Maybe this example converges so quickly it senses no need for greater verbosity. Thanks, Spencer Graves # R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base other attached packages: lme4 latticeMatrix 0.98-1 0.12-11 0.99-4 Douglas Bates wrote: Also, please try setting options(verbose = TRUE) immediately before your call to lmer. This will provide verbose output on the progress of the iterations and will probably give an indication of where the problem lies. On 1/7/06, Spencer Graves [EMAIL PROTECTED] wrote: I am not familiar with this particular error message, but I will offer a few suggestions that might help you isolate it. 1. PLEASE do read the posting guide! www.R-project.org/posting-guide.html. The limited information supplied with your question does NOT include data requested of all posts. The command sessionInfo() can proved some of the standard basics that many potential respondants want to know before they consider replying. 2. Have you tried traceback()? This may or may not help you, but it's quick and worth a try. 3. Can you provide this list with a very simple, self contained example that produces the error message you mention? 4. I suggest you list lmer by typing the function name and a commmand prompt. In this case, lmer consists solely of a call to standardGeneric. The documentation for standardGeneric led me to the documentation for GenericFunctions, which led me to showMethods. 'showMethods(lmer)' indicated only one method, namely for 'formula = formula'. Then 'dumpMethod(lmer, file=lmer.R, signature=formula)' produced a listing of that function for me in the working directory. If you have trouble finding the working directory, try 'getwd()'. I would then modify the function it lmer.R to create a new function lmer.formula. Then I would try debug(lmer.formula). Then I would replace lmer by lmer.formula in the command that generated the error and execute that modified formula. This will open a browser and allow you to walk through the function line by line, examining (and changing) anything you want in the environment of that function. Doing this will, I believe, lead you to exactly the line in the lmer code that generated the error message you don't understand. With only a modest amount of luck, you should be able to find in this way what you can do to avoid that error. Anecdotal evidence suggests that people who use the techniques described in suggestions 1-3 tend to get quicker, more useful replies from this list. Moreover, in virtually every case that I've tried suggestion 4, I've been able to figure out how to overcome that particular difficulty. In addition, I've often learned useful things about R that I didn't know befor. hope this helps. spencer graves Abderrahim Oulhaj wrote: Dear All, I have the following error message when I fitted lmer to a binary data with the AGQ option: Error in family$mu.eta(eta) : NAs are not allowed in subscripted assignments In addition: Warning message: IRLS iterations for PQL did not converge Any help? Thanks in advance, Abderrahim [[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 __ 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!
[R] wicked wikis for R
Message: 41 Date: Sun, 08 Jan 2006 13:52:33 +1100 From: paul sorenson [EMAIL PROTECTED] Subject: Re: [R] Wikis etc. To: Frank E Harrell Jr [EMAIL PROTECTED],r-help r-help@stat.math.ethz.ch Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Frank E Harrell Jr wrote: paul sorenson wrote: I am a fan of wiki's and I reckon it would really help with making R more accessible. On one extreme you have this email list and on the other extreme you have RNews and the PDF's on CRAN. A wiki might hit the spot between them and reduce the traffic on the email list. Thanks Paul. But as long as the email list is active I fear a wiki won't be. That would be sad if that were true. They are different beasts, as would be an IRC channel. I say complementary, not mutually exclusive. A wiki takes time to reach critical mass (eg my home brew wiki http://brewiki.org/ or wikipedia) and you couldn't just pull the plug on this list without a serious impact on the uptake of R I would have thought. Contributions to the wiki from mugs like me with less R/statistics experience would hopefully make R more accessible to newbies - pointing out the traps for new players. One way to bootstrap it is to simply add a wiki menu entry into the r-project.org menu. This is what the guys over at http://wiki.wxpython.org/ have done. Over time, some of the other items there might morph in to wiki pages as appropriate. I have no doubt that if the R-Wiki was supported in the same thoughtful, thorough and patient way in which questions on R-Help are answered, it would be one of the lowest entropy wiki's around. I think that's a great idea there. In fact, wikis and this mailing list can potentially complement each other in very efficient ways. In contrast to traditional wikis (eg. wikipedia), for R we may have to figure out some kind of novel ways of automated/manual transfer of information between wikis and mailing lists going back and forth. Specific responses or groups of responses to questions from the mailing list find a way to the wikis in the form of editable topics, and wikis get updated as people start filling in. Also, a link from the mailing list or from the main R page to the Wikis could be very useful. As the mailing list grows, so does the wiki, except the information flow from the mailing list is more controlled and fine-tuned as to what goes in there and what stays in the mailing list. Among others, here's one long-term benefit for the newbies. Instead of people getting admonished/thrashed with harsh expressions/advices like go see the mailing list publishing etiquettes, or you should search the archives and help files, and read all manuals, and ask others first before posting here... (which can turn away many a newcomer from posting or using the mailing list or using R for that matter), wiki could make life a little easy for newbies/less experienced who could then receive more polite one liners like, please check the wikipages..., or solution #xyz in the wikipages for the solution. However, for an R-wiki to be a repository of robust R guidance, quality control is extremely important. While it is somewhat easier to warn and correct each other for wrong information in an email list, that level of vigilance may not always be achievable in a wiki, particularly if it is open to be editable by everyone, which, btw, is also its touted strength. That said, with the volume of posts in this mailing list increasing, and with numerous repeats of similar problems posted and replied over and over again, wikis may just provide an easy compromise. /Arin Basu [[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
[R] wicked wikis for R
Message: 41 Date: Sun, 08 Jan 2006 13:52:33 +1100 From: paul sorenson [EMAIL PROTECTED] Subject: Re: [R] Wikis etc. To: Frank E Harrell Jr [EMAIL PROTECTED],r-help r-help@stat.math.ethz.ch Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Frank E Harrell Jr wrote: paul sorenson wrote: I am a fan of wiki's and I reckon it would really help with making R more accessible. On one extreme you have this email list and on the other extreme you have RNews and the PDF's on CRAN. A wiki might hit the spot between them and reduce the traffic on the email list. Thanks Paul. But as long as the email list is active I fear a wiki won't be. That would be sad if that were true. They are different beasts, as would be an IRC channel. I say complementary, not mutually exclusive. A wiki takes time to reach critical mass (eg my home brew wiki http://brewiki.org/ or wikipedia) and you couldn't just pull the plug on this list without a serious impact on the uptake of R I would have thought. Contributions to the wiki from mugs like me with less R/statistics experience would hopefully make R more accessible to newbies - pointing out the traps for new players. One way to bootstrap it is to simply add a wiki menu entry into the r-project.org menu. This is what the guys over at http://wiki.wxpython.org/ have done. Over time, some of the other items there might morph in to wiki pages as appropriate. I have no doubt that if the R-Wiki was supported in the same thoughtful, thorough and patient way in which questions on R-Help are answered, it would be one of the lowest entropy wiki's around. I think that's a great idea there. In fact, wikis and this mailing list can potentially complement each other in very efficient ways. In contrast to traditional wikis (eg. wikipedia), for R we may have to figure out some kind of novel ways of automated/manual transfer of information between wikis and mailing lists going back and forth. Specific responses or groups of responses to questions from the mailing list find a way to the wikis in the form of editable topics, and wikis get updated as people start filling in. Also, a link from the mailing list or from the main R page to the Wikis could be very useful. As the mailing list grows, so does the wiki, except the information flow from the mailing list is more controlled and fine-tuned as to what goes in there and what stays in the mailing list. Among others, here's one long-term benefit for the newbies. Instead of people getting admonished/thrashed with harsh expressions/advices like go see the mailing list publishing etiquettes, or you should search the archives and help files, and read all manuals, and ask others first before posting here... (which can turn away many a newcomer from posting or using the mailing list or using R for that matter), wiki could make life a little easy for newbies/less experienced who could then receive more polite one liners like, please check the wikipages..., or solution #xyz in the wikipages for the solution. However, for an R-wiki to be a repository of robust R guidance, quality control is extremely important. While it is somewhat easier to warn and correct each other for wrong information in an email list, that level of vigilance may not always be achievable in a wiki, particularly if it is open to be editable by everyone, which, btw, is also its touted strength. That said, with the volume of posts in this mailing list increasing, and with numerous repeats of similar problems posted and replied over and over again, wikis may just provide an easy compromise. /Arin Basu [[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] Suggestion for big files [was: Re: A comment about R:]
[Martin Maechler] FrPi Suppose the file (or tape) holds N records (N is not known FrPi in advance), from which we want a sample of M records at FrPi most. [...] If the algorithm is carefully designed, when FrPi the last (N'th) record of the file will have been processed FrPi this way, we may then have M records randomly selected from FrPi N records, in such a a way that each of the N records had an FrPi equal probability to end up in the selection of M records. I FrPi may seek out for details if needed. [...] I'm also intrigued about the details of the algorithm you outline above. I went into my old SPSS books and related references to find it for you, to no avail (yet I confess I did not try very hard). I vaguely remember it was related to Spearman's correlation computation: I did find notes about the severe memory limitation of this computation, but nothing about the implemented workaround. I did find other sampling devices, but not the very one I remember having read about, many years ago. On the other hand, Googling tells that this topic has been much studied, and that Vitter's algorithm Z seems to be popular nowadays (even if not the simplest) because it is more efficient than others. Google found a copy of the paper: http://www.cs.duke.edu/~jsv/Papers/Vit85.Reservoir.pdf Here is an implementation for Postgres: http://svr5.postgresql.org/pgsql-patches/2004-05/msg00319.php yet I do not find it very readable -- but this is only an opinion: I'm rather demanding in the area of legibility, while many or most people are more courageous than me! :-). -- François Pinard http://pinard.progiciels-bpi.ca __ 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-help Digest, Vol 35, Issue 7
Uwe Ligges пишет:
Evgeniy Kachalin wrote:
Hello, dear participants!
Could you tip me, is there any simple and nice way to build
scatter-plot for three different types of data (, and o and * - signs,
for example) with legend.
Now i can guess only that way:
plot(x~y,data=subset(mydata,factor1=='1'), pch='.',col='blue')
points(x~y,data=subset(mydata,factor1=='2'), pch='*',col='green')
points( etc
What is the simple and nice way?
Thank you very much for your kindness and help.
Example:
with(iris,
plot(Sepal.Length, Sepal.Width, pch = as.integer(Species)))
with(iris,
legend(7, 4.4, legend = unique(as.character(Species)),
pch = unique(as.integer(Species
Uwe, sorry for my stupid question. You mean that when pch=factor , plot
can recycle the factor and use it for subscripts or marks.
Then pch=as.integer(Species) results in c(1,2,3) for 3 factor levels.
And I need symbols 15,16,17 and colors red, blue, green.
So then I do:
iris$Species-spec.symb
iris$Species-spec.col
levels(spec.symb)-c(15,16,17)
levels(spec.col)-c('red','green','blue')
That's the only way?
More of that!!! 'Plot' does not like factors in 'pch'. So it must be so:
plot(x~y,data, pch=as.integer(as.character(spec.symb))).
That's totally crazy...
--
Evgeniy
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[R] Wikis etc.
Philippe's idea to start a wiki that grows out of the content on http://zoonek2.free.fr/UNIX/48_R/all.html is really great. Here's why. My hypothesis is that the basic reason that people ask questions on R-help rather than first looking elsewhere is that looking elsewhere doesn't get them the info they need. People think in terms of the tasks they have to do. The documentation for R, which can be very good, is organized in terms of the structure of R, its functions. This mismatch -- people think of tasks, the documentation thinks in functions -- causes people to turn to the mailing list. What we need is documentation that can be browsed in terms of tasks, like http://zoonek2.free.fr/UNIX/48_R/all.html. If that can be edited by the community, all the better. This is especially good for newbies (like myself) who try a tutorial, find that it lacks in some aspect, and can give immediate feedback, e.g., via a Wiki. As far as keeping current with the latest versions of R, I think we'll have to arrive at some sort of convention that says: the code in this example works with R version X, package version Y. Then, if that code is found to fail in some future version, it's easy enough to make a second exampe. (As a bonus, these examples could be an automated test suite for R.) Philippe, if you find you'd like assistance, I'd like to help. __ 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] Finding R mailing list archives {was Wikis etc.}
I really wonder if adding yet another URL to the footer of every message will be the solution; as others have correctly remarked, the problem is that for many newbies it is more convenient to ask rather than to first read something that contains more than three words. ;-) hahaha. the balance between (i) harsh to the newbie and (ii) boring to the experts. balance is hard. :) __ 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] maptools, write.polylistShape
On Sat, 7 Jan 2006, Patrick Giraudoux wrote:
Dear Roger,
I am trying to use the write.polylistShape() function of maptools for
the first time and realize that it handles list of polygons of class
'polylist'. However, it seems that no as.polylist() function exist in
the package. The question behind that is: in your opinion, which would
be the best way to convert a list of matrix of polygon nodes
coordinates into an object of class polylist?
Certainly through sp classes - construct a list of Polygons objects each
with one (or more) Polygon objects, raise to SpatialPolygons, then back
out through writePolyShape(). Assuming each list member matrix is the
perimeter of a single polygon, and each Polygons object only has one
Polygon:
n - length(list_of_matrices)
list_of_polygons - vector(mode=list, length=n)
for (i in 1:n) {
Pl - Polygon(list_of_matrices[[i]])
list_of_polygons[[i]] - Polygons(list(Pl), ID=as.character(i))
}
# could be done with lapply too
SPs - SpatialPolygons(list_of_polygons)
rownames(mydata) - as.character(1:n)
SPDF - SpatialPolygonsDataFrame(SPs, mydata)
writePolyShape(SPDF, outfile)
(untried - but close enough).
Best wishes,
Roger
All the best,
Patrick
--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: [EMAIL PROTECTED]
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[R] How to unload a package or undo library(package)
Hello! I would like to unload a package form a current R session. I tried datach(package:packagename), however it does not work. The reason I want to unload it is that I want to correct some files in the package and reinstall it without closing an R session. Best, Ales Ziberna PS: I am using R 2.1.1 on Windows XP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to unload a package or undo library(package)
Here are some things to try: detach() - detach most recent attached package detach(2) - detach package which is in position 2 on search list. Same as detach() detach(package:mypackage) - mypackage from search list search() - display search list On 1/8/06, Aleš Žiberna [EMAIL PROTECTED] wrote: Hello! I would like to unload a package form a current R session. I tried datach(package:packagename), however it does not work. The reason I want to unload it is that I want to correct some files in the package and reinstall it without closing an R session. Best, Ales Ziberna PS: I am using R 2.1.1 on Windows XP __ 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
Re: [R] Suggestion for big files [was: Re: A comment about R:]
Thanks as well for these hints. Googling around as your suggested (yet keeping my eyes in the MySQL direction, because this is what we use), getting MySQL itself to do the selection is a bit discouraging, as according to comments I've read, MySQL does not seem to scale well with the database size according to the comments I've read, especially when records have to be decorated with random numbers and later sorted. With SQL there is always a way to do what you want quickly, but you need to think carefully about what operations are most common in your database. For example, the problem is much easier if you can assume that the rows are numbered sequentially from 1 to n. This could be enfored using a trigger whenever a record is added/deleted. This would slow insertions/deletions but speed selects. Just for fun: here, sample(1, 10) in R is slowish already :-). This is another example where greater knowledge of problem can yield speed increases. Here (where the number of selections is much smaller than the total number of objects) you are better off generating 10 numbers with runif(10, 0, 100) and then checking that they are unique Another possibility is to generate a large table of randomly distributed ids and then use that (with randomly generated limits) to select the appropriate number of records. I'm not sure I understand your idea (what mixes me in the randomly generated limits part). If the large table is much larger than the size of the wanted sample, we might not be gaining much. Think about using a table of random numbers. They are pregenerated for you, you just choose a starting and ending index. It will be slow to generate the table the first time, but then it will be fast. It will also take up quite a bit of space, but space is cheap (and time is not!) Hadley __ 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] lmer p-vales are sometimes too small
I have just uploaded version 0.99-6 of the Matrix package to the incoming area at CRAN. It should appear on the archives in the next day or two. In this version all degrees of freedom, test statistics and p-values have been removed from the summary, show and anova methods. I agree with John Maindonald that it is better not to give any p-values than to give misleading, sometimes seriously misleading, p-values. All the code for lmer is, of course, open source. At present it resides in the Matrix package but it may return to the lme4 package following the release of R-2.3.0. The sources for the Matrix package are available at https://svn.r-project.org/R-packages/trunk/Matrix An experimental version of lmer based on a supernodal sparse Cholesky factorization is at https://svn.r-project.org/R-packages/branches/Matrix-mer2 That is the current development branch. Once I get issues with the PQL and Laplace methods for GLMMs resolved this branch will be merged back into the trunk. If you are only interested in linear mixed models it is better to work with this branch. In both branches there is an R function called getFixDF that currently is a stub returning incorrect answers (as indicated in the comments). At present I don't know to get correct answers for the range of models that can be fit by lmer. I welcome submissions of patches. On 1/6/06, Olof Leimar [EMAIL PROTECTED] wrote: This concerns whether p-values from lmer can be trusted. From simulations, it seems that lmer can produce very small, and probably spurious, p-values. I realize that lmer is not yet a finished product. Is it likely that the problem will be fixed in a future release of the lme4 package? Using simulated data for a quite standard mixed-model anova (a balanced two-way design; see code for the function SimMixed pasted below), I compared the output of lmer, for three slightly different models, with the output of aov. For an example where there is no fixed treatment effect (null hypothesis is true), with 4 blocks, 2 treatments, and 40 observations per treatment-block combination, I find that lmer gives more statistical significances than it should, whereas aov does not have this problem. An example of output I generated by calling SimMixed(1000) is the following: Proportion significances at the 0.05 level aov: 0.05 lmer.1: 0.148 lmer.2: 0.148 lmer.3: 0.151 Proportion significances at the 0.01 level aov: 0.006 lmer.1: 0.076 lmer.2: 0.076 lmer.3: 0.077 Proportion significances at the 0.001 level aov: 0.001 lmer.1: 0.047 lmer.2: 0.047 lmer.3: 0.047 which is based on 1000 simulations (and takes about 5 min on my PowerMac G5). The different models fitted are: fm.aov - aov(y ~ Treat + Error(Block/Treat), data = dat) fm.lmer.1 - lmer(y ~ Treat + (Treat|Block), data = dat) fm.lmer.2 - lmer(y ~ Treat + (Treat-1|Block), data = dat) fm.lmer.3 - lmer(y ~ Treat + (1|Block) + (Treat-1|Block), data = dat) It seems that, depending on the level of the test, lmer gives between a factor of 3 to a factor of around 50 times too many significances. The first two lmer models seem to give identical results, whereas the third (which I think perhaps is the one that best represents the data generated by the simulation) differs slightly. In running the simulations, warnings like this are occasionally generated: Warning message: optim or nlminb returned message false convergence (8) in: LMEoptimize-(`*tmp*`, value = list(maxIter = 200, tolerance = 1.49011611938477e-08, They seem to derive from the third of the lmer models. Perhaps there is some numerical issue in the lmer function? From running SimMixed() several times, I have noticed that large p-values (say, larger than 0.5) agree very well between lmer and aov, but there seems to be a systematic discrepancy for smaller p-values, where lmer gives smaller values than aov. The F-values agree between all analyzes (except for fm.lmer.3 when there is a warning), so there is a systematic difference between lmer and aov in how a p-value is obtained from the F-value, which becomes severe for small p-values. My output from sessionInfo() R version 2.2.1, 2005-12-20, powerpc-apple-darwin7.9.0 attached base packages: [1] methods stats graphics grDevices utils datasets base other attached packages: lme4 latticeMatrix 0.98-1 0.12-11 0.99-3 Pasted code for the SimMixed function (some lines might wrap): # This function generates n.sims random data sets for a design with 4 # blocks, 2 treatments applied to each block, and 40 replicate # observations for each block-treatment combination. There is no true # fixed treatment effect, so a statistical significance of a test for # a fixed treatment effect ought to occur with a probability equal to # the nominal level of the test. Four tests are applied to each # simulated data set: the classical aov and three versions of lmer, #
Re: [R] Question about graphics in R
Martin Erwig wrote:
Considering the R function/plot shown below, I wonder whether
it is possible to do the following changes:
(1) Change the color of each point to be picked from
list of colors according to its z-value. (The range
should be from blue (z=0) to red (z=1).) The grid
should then be omitted. [I have seen terrain.colors, but
don't know how to use it for this purpose.]
(2) Add two lines to the surface for, say z=0.8 and
z=0.3. [Can contour or contourLines be used?]
---
x - seq(0, 1, length = 50)
y - x
f - function(x,y) { sin ((1-x)*y) }
z - outer(x,y,f)
persp(x, y, z,
theta = 30, phi = 30,
shade = 0.3, col = red
)
---
Finally, I would also produce a flattened 2D map
of the same function, i.e. a map in which each point
(x,y) is mapped to a color in a range according to
f(x,y). Also two lines for f(x,y)=c1 and f(x,y)=c2
should be added.
Is this possible?
Hi Martin,
The function color.scale will linearly transform numeric values into
colors between arbitrary color endpoints specified as red, green and blue:
Your example would be
redrange=c(0,1),greenrange=c(0,0),bluerange=c(1,0).
For the 2D plot, have a look at color2D.matplot. Both are in the plotrix
package.
You might also want to look at colorRampPalette in the grDevices package.
Jim
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Re: [R] repeat { readline() }
Prof Brian Ripley wrote:
On Sun, 8 Jan 2006, Prof Brian Ripley wrote:
Ctrl-Break works: see the rw-FAQ and README.rterm. (You'll need a return
to see a new prompt.)
It is related to your reading directly from the console, so Ctrl-C is
getting sent to the wrong place, I believe. (There's a comment from
Guido
somewhere in the sources about this, and this seems corroborated by the
fact that Ctrl-C will interrupt under Rterm --ess.)
Although the comment is there (in psignal.c), on closer examination the
cause is a change Guido made to getline.c, so Ctrl-C is treated as a
character during keyboard input. I doubt if that was intentional (0 is
not the default state) and I have changed it for R-devel.\
Thank you very much this.
Henrik
On Sun, 8 Jan 2006, Henrik Bengtsson wrote:
Hi.
Using Rterm v2.2.1 on WinXP, is there a way to interrupt a call like
repeat { readline() }
without killing the Command window? Ctrl+C is not interrupting the
loop:
R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.2.1 Patched (2006-01-01 r36947)
snip/snip
repeat { readline() }
^C
^C
^C
^C
On Unix it works. The problem seems to get the interrupt signal to
occur outside the readline() call so that repeat is interrupted.
Doing
repeat { readline(); Sys.sleep(3) }
and it is likely that can generate an interrupt signal outside
readline().
It seem like readline()/readLines(n=1) or an underlying method catches
the interrupt signal quietly and just waits for a symbol to come
through. Try readline() by itself and press Ctrl+C. Maybe this is a
property of the Windows Command terminal, I don't know, but is it a
wanted feature and are R core aware of it? Note that, in Rgui it is
possible to interrupting such a loop by pressing ESC.
Cheers
Henrik
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Re: [R] Suggestion for big files [was: Re: A comment about R:]
[hadley wickham] [...] according to comments I've read, MySQL does not seem to scale well with the database size according to the comments I've read, especially when records have to be decorated with random numbers and later sorted. With SQL there is always a way to do what you want quickly, but you need to think carefully about what operations are most common in your database. For example, the problem is much easier if you can assume that the rows are numbered sequentially from 1 to n. This could be enfored using a trigger whenever a record is added/deleted. This would slow insertions/deletions but speed selects. Sure (for a caricature example) that if database records are already decorated with random numbers, and an index is built over the decoration, random sampling may indeed be done quicker :-). The fact is that (at least our) databases are not especially designed for random sampling, and people in charge would resist redesigning them merely because there would be a few needs for random sampling. What would be ideal is being able to build random samples out of any big database or file, with equal ease. The fact is that it's doable. (Brian Ripley points out that R textual I/O has too much overhead for being usable, so one should rather say, sadly: It's doable outside R.) Just for fun: here, sample(1, 10) in R is slowish already :-). This is another example where greater knowledge of problem can yield speed increases. Here (where the number of selections is much smaller than the total number of objects) you are better off generating 10 numbers with runif(10, 0, 100) and then checking that they are unique Of course, my remark about sample() is related to the previous discussion. If sample(N, M) was more on the O(M) side than being on the O(N) side (both memory-wise and cpu-wise), it could be used for preselecting which rows of a big database to include in a random sample, so building on your idea of using a set of IDs. As the sample of M records will have to be processed in-memory by R anyway, computing a vector of M indices does not (or should not) increase complexity. However, sample(N, M) is likely less usable for randomly sampling a database, if it is O(N) to start with. About your suggestion of using runif and later checking uniqueness, sample() could well be implemented this way, when the arguments are proper. The greater knowledge of the problem could be built in right into the routine meant to solve it. sample(N, M) could even know how to take advantage of some simplified case of a reservoir sampling technique :-). [...] a large table of randomly distributed ids [...] (with randomly generated limits) to select the appropriate number of records. [...] a table of random numbers [...] pregenerated for you, you just choose a starting and ending index. It will be slow to generate the table the first time, but then it will be fast. It will also take up quite a bit of space, but space is cheap (and time is not!) Thanks for the explanation. In the case under consideration here (random sampling of a big file or database), I would be tempted to guess that the time required for generating pseudo-random numbers is negligible when compared to the overall input/output time, so it might be that pregenerating randomized IDs is not worth the trouble. Also given that whenever the database size changes, the list of pregenerated IDs is not valid anymore. -- François Pinard http://pinard.progiciels-bpi.ca __ 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] Wikis for R
On Fri, 6 Jan 2006, Detlef Steuer wrote: ... Back to operating wikis:The wiki spamming is a serious problem, especially because I HATE to login to read or edit anything. So the choice is: take the wiki as seriously as work and have a look every other day to remove the spam (or better: form a group of volunteers). That hurts or at least is no fun. Or put restrictions on it. That hurts even more. Perhaps I do not understand Philippe`s loggable. What does a logfile with IPs help? The spammers are strangers selling viagra; I don`t want to find them :-) Sometimes you can mark the spammer's IP's as spammers and then ban editing by them. For my own UseMod wiki, I avoid spam by rejecting edits that change more than 3 URLS. But this is getting off of the R help topic. To sum it up:There is a very simple way to proceed:Philippe uses his Docuwiki install as official, _general_ Rwiki and I close down mine. The beginners will find their niche in there, if there is a real demand. I wouldn´t mind to give up my wiki, because I have to admit it failed to achieve what I would have liked. I like wikis too, and contributed a few pages to your wiki. The low use-rate and high wiki spamming content makes it not a place I frequent. So, Philippe, if you like, you can take over. I would replace my wiki with a notice where to find yours and the community gets a second chance :-) http://fawn.unibw-hamburg.de/cgi-bin/Rwiki.pl does have some useful content. Maybe it would be good to wade through it and figure out how to patch the standard R documentation to include those contributions. An advantage of a wiki is the low barrier to adding correctable documentation. The email list also provides low-barrier-to-entry documentation, and its success demonstrates the clear need for additional documentation. Considering that, maybe there would be a benefit in rolling references to good email threads into the documentation in some sort of an automatic method. Perhaps if an email question leads to a clarification or good example of a feature, someone could post a message to the thread that tags it for inclusion by reference to relevant documentation in the next release cycle. If this wishful thinking would come to pass, then the standard documentation could point people towards using the mail archive in a more directly useful manner, and we'd retain the peer-reviewed answer quality of the email list. Dave -- Dr. David Forrest [EMAIL PROTECTED](804)684-7900w [EMAIL PROTECTED] (804)642-0662h http://maplepark.com/~drf5n/ __ 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] Clustering and Rand Index - VS-KM
Dear WizaRds, I have been trying to compute the adjusted Rand index as by Hubert/ Arabie, and could not correctly approach how to define a partition object as in my last request yesterday. With package fpc I try to work around the problem, using my original data: mat - matrix( c(6,7,8,2,3,4,12,14,14, 14,15,13,3,1,2,3,4,2, 15,3,10,5,11,7,13,6,1, 15,4,10,6,12,8,12,7,1), ncol=9, byrow=T ) rownames(mat) - paste(v, 1:4, sep= ) ## and the given partitions: p1=c(1,1,1,2,2,2,3,3,3) p2=c(1,1,1,3,2,2,3,3,2) p3=c(1,2,1,3,1,3,1,3,2) p4=c(1,2,1,3,1,3,1,3,2) ## Now cluster.stats(d=dist(mat), clustering=p1, alt.clustering=p2) ## just gives Error in as.dist(dmat[clustering == i, clustering == i]) : (subscript) logical subscript too long I think I don't understand the use of 'd' here. How can I calculate the corrected Rand matrix: ( .000 .407 -.071 -.071) ( .407 .000 -.071 -.071) (-.071 -.071 .000 1.000) (-.071 -.071 1.000 .000) Does the clue package help me here? Does anyone know if there is a VS-KM algorithm (Variable Selection Heuristic for K-Means Clustering) implemented in R? Unfortunately, I did not find any serach entries. Thank you for your help and support Mark __ 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 comment about R:
[Uwe Ligges] François Pinard wrote: [David Forrest] [...] A few end-to-end tutorials on some interesting analyses would be helpful. I'm in the process of learning R. While tutorials are undoubtedly very useful, and understanding that working and studying methods vary between individuals, what I (for one) would like to have is a fairly complete reference manual to the library [...] organised by topics. Have a look at help.start() -- Search Engine Keywords -- Section Keywords by Topic. Yes, thanks. This is quite in the spirit, or direction, of what I was proposing. Is that resource exhaustive? (I'm asking out of laziness, as it might take me several months to really check.) One serious drawback (for me) is that it requires an heavy weight browser to be used, with Javascript enabled. I do not find this very practical. Another point is that the presentation, while useful, is a rather dry. In another message, I suggested the Emacs Lisp Reference Manual as a good example of a fluid presentation of a voluminous library. There might be some workable compromise between the current situation with R, even through the Keywords by Topic, and that fluidity. (Wikis also have the drawback of requiring heavy machinery, and the editor they force us into if usually unbearable.) I may be back with this subject, but only in a good while. I'm slowly building a kind of documentation plan I want (yet in French), as I learn R, and guess I may complete my base learning in one or two years from now (hoping I'll stay courageous enough). If I then get something usable or shareable enough, I'll offer it -- because I like returning a little something for the nice tools given to me! :-) In any case, thanks for listening! -- François Pinard http://pinard.progiciels-bpi.ca __ 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] Ordering boxplot factors; thank you!
Profs. Ripley and Schwartz, Thank you both very much for the suggestions! These are exactly what I was looking for. I'll re-read the boxplot help yet again; every time I read it something essential worms its way into my consciousness, but it enters more freely when I have a hint where to look. The sad truth is that I was heading for a ~10-line hacker solution. You've saved me from my usual code-writing ignomy. Happy new year, -Joseph Prof Brian Ripley wrote: On Thu, 5 Jan 2006, Marc Schwartz wrote: On Thu, 2006-01-05 at 20:27 -0600, Joseph LeBouton wrote: Hi all, what a great help list! I hope someone can help me with this puzzle... I'm trying to find a simple way to do: boxplot(obs~factor) so that the factors are ordered left-to-right along the x-axis by median, not alphabetically by factor name. The thing to realize is that they are not alphabetic, but ordered by factor levels. So the key is to set the levels. (The help page for boxplot does say that, as I was relieved to find.) Complicated ways abound, but I'm hoping for a magical one-liner that'll do the trick. Any suggestions would be treasured. Thanks, -jlb Using the first example in ?boxplot, which is: boxplot(count ~ spray, data = InsectSprays, col = lightgray) Get the medians for 'count by spray' using tapply() and then sort the results in increasing order, by median: med - sort(with(InsectSprays, tapply(count, spray, median))) med CEDAFB 1.5 3.0 5.0 14.0 15.0 16.5 Now do the boxplot, setting the factor levels in order by median: boxplot(count ~ factor(spray, levels = names(med)), data = InsectSprays, col = lightgray) So...technically two lines of code. This was answered yesterday in terms of bwplot. See ?reorder.factor for the same example done using reorder.factor. That will give you the single line asked for, and be self-explanatory. -- Joseph P. LeBouton Forest Ecology PhD Candidate Department of Forestry Michigan State University East Lansing, Michigan 48824 Office phone: 517-355-7744 email: [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] Clustering and Rand Index - VS-KM
You can comput the adjusted Rand with function classAgreement form package e1071: classAgreement(table(p1,p2))$crand You can also use cluster.stats(d=dist(t(mat)), clustering=p1, alt.clustering=p2) However in your code below, the orientation of mat is wrong (that's why there is a t() around the mat in my code above). The variables should be represented by rows and the cases by columns. Best, Ales Ziberna -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Hempelmann Sent: Monday, January 09, 2006 12:43 AM To: r-help@stat.math.ethz.ch Subject: [R] Clustering and Rand Index - VS-KM Dear WizaRds, I have been trying to compute the adjusted Rand index as by Hubert/ Arabie, and could not correctly approach how to define a partition object as in my last request yesterday. With package fpc I try to work around the problem, using my original data: mat - matrix( c(6,7,8,2,3,4,12,14,14, 14,15,13,3,1,2,3,4,2, 15,3,10,5,11,7,13,6,1, 15,4,10,6,12,8,12,7,1), ncol=9, byrow=T ) rownames(mat) - paste(v, 1:4, sep= ) ## and the given partitions: p1=c(1,1,1,2,2,2,3,3,3) p2=c(1,1,1,3,2,2,3,3,2) p3=c(1,2,1,3,1,3,1,3,2) p4=c(1,2,1,3,1,3,1,3,2) ## Now cluster.stats(d=dist(mat), clustering=p1, alt.clustering=p2) ## just gives Error in as.dist(dmat[clustering == i, clustering == i]) : (subscript) logical subscript too long I think I don't understand the use of 'd' here. How can I calculate the corrected Rand matrix: ( .000 .407 -.071 -.071) ( .407 .000 -.071 -.071) (-.071 -.071 .000 1.000) (-.071 -.071 1.000 .000) Does the clue package help me here? Does anyone know if there is a VS-KM algorithm (Variable Selection Heuristic for K-Means Clustering) implemented in R? Unfortunately, I did not find any serach entries. Thank you for your help and support Mark __ 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
[R] (sans objet)
Dear R People: in the function loess, how can one add the weight of the points which is contained in the variable nbtotal Data : Nbtotal P_alim H_eau xyplot(P_alim ~ H_eau, auto.key = list(points = T, lines = F),data = data, type = c(p, smooth), span=.2, scales = free, layout = c(1, 1), main=, xlab=Hauteur d'eau (en m), ylab=taux d'alimentation) the graph xyplot is not modified if the weights term is added xyplot(P_alim ~ H_eau, auto.key = list(points = T, lines = F),data = data, type = c(p, smooth), span=.2,weights=Nb_total, scales = free, layout = c(1, 1), main=, xlab=Hauteur d'eau (en m), ylab=taux d'alimentation) Thanks in advance, Alain ponsero __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to unload a package or undo library(package)
If I do detach(package:blockmodeling) My package blockmodeling does not appear in (.packages()) [1] methods stats graphics grDevices utils datasets [7] base However, if I want to install a newer version from a local zip file, I get: utils:::menuInstallLocal() package 'blockmodeling' successfully unpacked and MD5 sums checked Error: cannot remove prior installation of package 'blockmodeling' Is there any way around that? Best, Ales Ziberna -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gabor Grothendieck Sent: Sunday, January 08, 2006 10:42 PM To: Aleš Žiberna Cc: r-help@stat.math.ethz.ch Subject: Re: [R] How to unload a package or undo library(package) Here are some things to try: detach() - detach most recent attached package detach(2) - detach package which is in position 2 on search list. Same as detach() detach(package:mypackage) - mypackage from search list search() - display search list On 1/8/06, Aleš Žiberna [EMAIL PROTECTED] wrote: Hello! I would like to unload a package form a current R session. I tried datach(package:packagename), however it does not work. The reason I want to unload it is that I want to correct some files in the package and reinstall it without closing an R session. Best, Ales Ziberna PS: I am using R 2.1.1 on Windows XP __ 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 __ 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-help Digest, Vol 35, Issue 7
Hi!
Just use your factors for indexing c(15,16,17) and
c(red,green,blue). So, with the iris data:
with(iris, plot(Sepal.Length, Sepal.Width,
pch=c(15,16,17)[as.integer(Species)],
col=c(red,green,blue)[as.integer(Species)] ))
Best regards,
Kyosti Kurikka
Evgeniy Kachalin wrote:
Hello, dear participants!
Could you tip me, is there any simple and nice way to build
scatter-plot for three different types of data (, and o and * - signs,
for example) with legend.
Now i can guess only that way:
plot(x~y,data=subset(mydata,factor1=='1'), pch='.',col='blue')
points(x~y,data=subset(mydata,factor1=='2'), pch='*',col='green')
points( etc
What is the simple and nice way?
Thank you very much for your kindness and help.
Example:
with(iris,
plot(Sepal.Length, Sepal.Width, pch = as.integer(Species)))
with(iris,
legend(7, 4.4, legend = unique(as.character(Species)),
pch = unique(as.integer(Species
Uwe, sorry for my stupid question. You mean that when pch=factor , plot
can recycle the factor and use it for subscripts or marks.
Then pch=as.integer(Species) results in c(1,2,3) for 3 factor levels.
And I need symbols 15,16,17 and colors red, blue, green.
So then I do:
iris$Species-spec.symb
iris$Species-spec.col
levels(spec.symb)-c(15,16,17)
levels(spec.col)-c('red','green','blue')
That's the only way?
More of that!!! 'Plot' does not like factors in 'pch'. So it must be so:
plot(x~y,data, pch=as.integer(as.character(spec.symb))).
That's totally crazy...
--
Evgeniy
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[R] paste tab and print
Dear all,
info = paste('a', 'b', sep='\t')
print(info , quote=F)
doesn't produce the same result with R201 and R220
(under Windows2000)
R 2.0.1 : [1] a b
R 2.2.0 : [1] a\tb
I did read the CHANGESR220 file and tried also the search
engine but couldn't find an answer.
I certainly missed the point, and apologize about that.
So if somebody could tell me how to insert a tab inside
strings under R.2.2.0., it would be very kind.
Thanks
Vincent
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Re: [R] R-help Digest, Vol 35, Issue 7
Evgeniy Kachalin wrote:
Uwe Ligges пишет:
Evgeniy Kachalin wrote:
Hello, dear participants!
Could you tip me, is there any simple and nice way to build
scatter-plot for three different types of data (, and o and * -
signs, for example) with legend.
Now i can guess only that way:
plot(x~y,data=subset(mydata,factor1=='1'), pch='.',col='blue')
points(x~y,data=subset(mydata,factor1=='2'), pch='*',col='green')
points( etc
What is the simple and nice way?
Thank you very much for your kindness and help.
Example:
with(iris,
plot(Sepal.Length, Sepal.Width, pch = as.integer(Species)))
with(iris,
legend(7, 4.4, legend = unique(as.character(Species)),
pch = unique(as.integer(Species
Uwe, sorry for my stupid question. You mean that when pch=factor , plot
can recycle the factor and use it for subscripts or marks.
Yes, it can recycle, but in the example above it does not recycle but
takes the whole Species vector.
Then pch=as.integer(Species) results in c(1,2,3) for 3 factor levels.
And I need symbols 15,16,17 and colors red, blue, green.
What about adding 14 as in as.integer(Species)+14, or 1 for the colors,
respectively?
So then I do:
iris$Species-spec.symb
iris$Species-spec.col
levels(spec.symb)-c(15,16,17)
levels(spec.col)-c('red','green','blue')
That's the only way?
This is one qay of many.
More of that!!! 'Plot' does not like factors in 'pch'. So it must be so:
plot(x~y,data, pch=as.integer(as.character(spec.symb))).
That's totally crazy...
You can set up your own pch variable of course, if you don't like it
this fast and easy way.
Uwe Ligges
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Re: [R] Missing value representation in Excel before extraction to R with RODBC
Hi I believe it has something to do with the column identification decision. When R decides what is in a column it uses only some values from the beginning of a file. I do not use RODBC as read.delim(clipboard, ...) is usually more convenient but probably there is a way how to tell RODBC what is in the column instead of let R decide from the top of the file. But I may be completely mistaken. HTH Petr On 6 Jan 2006 at 20:47, Fredrik Lundgren wrote: From: Fredrik Lundgren [EMAIL PROTECTED] To: R-help r-help@stat.math.ethz.ch Date sent: Fri, 6 Jan 2006 20:47:29 +0100 Subject:[R] Missing value representation in Excel before extraction to R with RODBC Dear list, How should missing values be expressed in Excel before extraction to R via RODBC. I'm bewildered. Sometimes the representation with NA in Excel appears to work and shows up in R as NA but sometimes the use of NA in Excel changes the whole vector to NA's. Blank or nothing or NA as representation for missing values in Excel with dateformat gives NA's of the whole vector in R but with general format in Excel gives blanks for missing values in R. How should I represent missing values in Excel? Best wishes and thanks for any help Fredrik Lundgren __ 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 Petr Pikal [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
