[R] geodesic distance (solution)
Hi,
has anyone ever seen implemented in R the following geodesic
distance between positive definite pxp matrices A and B?
d(A,B) = \sum_{i=1}^p (\log \lambda_i)^2
were \lambda is the solution of det(A -\lambda B) = 0
thanks
stefano
as I received few private email on the claimed solution, I'm posting
it to r-help.
when matrix B is invertible (which is always my case), one approach
is to notice that
solving
det(A -\lambda * B) = 0
is equivalent to solve
det(B^-1*A -\lambda *I) = 0
which is a standard eigen value problem for the matrix B^-1 * A, hence
eigen(solve(B) %*% A)$values
is the answer.
I'm pretty sure that the problem can also be solved using some svd
decomposition when B is not invertible.
hope it helps
stefano
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[R] geodesic distance
Hi,
has anyone ever seen implemented in R the following geodesic
distance between positive definite pxp matrices A and B?
d(A,B) = \sum_{i=1}^p (\log \lambda_i)^2
were \lambda is the solution of det(A -\lambda B) = 0
thanks
stefano
__
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] geodesic distance (solved)
I found the answer to my problem. stefano __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-SIG-Mac] Hist for different levels of a factor
The list of your interest is R-help not R-sig-mac stefano Il giorno 26/gen/06, alle ore 01:20, Sylvain Charlat ha scritto: Hi, Is there any simple way to get histogram for different levels of factor? Say you have the following data set: Island Sp.diam Moorea 1.21 Moorea 1.27 Moorea 1.28 Moorea 1.22 Moorea 1.28 Rurutu 1.5 Rurutu 1.67 Rurutu 1.75 Rurutu 1.55 Rurutu 1.7 Rurutu 1.55 Rurutu 1.59 Rurutu 1.66 Rurutu 1.7 Is there anything better than: hist(Sp.diam[factor(Island)==Moorea],main=Island=Moorea) followed by hist(Sp.diam[factor(Island)==Rurutu],main=Island=Rurutu) Sorry for this very stupid and basic question... Thanks for any help, Sylvain. --- Sylvain Charlat [EMAIL PROTECTED] / [EMAIL PROTECTED] http://www.ucl.ac.uk/~ucbtghu/Sylvain.htm - Department of Biology, University College London 4 Stephenson Way, London, NW1 2HE, UK - Fieldwork address: Gump Station, University of California Berkeley BP 244 Maharepa, 98728 Moorea, French Polynesia - Phone (Moorea): (+689) 56 43 97 or 26 90 18 or 56 52 87 - Fax (Moorea): (+689) 56 32 72 - Phone / Fax (London): (+44)20 76795072 / +(44) 20 76795052 --- __ _ Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez sur http://fr.messenger.yahoo.com ___ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac __ 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] Forum of Mac questions (Was: loading packages - mac user)
On 19/ott/05, at 13:36, Martin Maechler wrote: BDR == Prof Brian Ripley [EMAIL PROTECTED] on Wed, 19 Oct 2005 08:58:20 +0100 (BST) writes: BDR On Wed, 19 Oct 2005, Jari Oksanen wrote: On Tue, 2005-10-18 at 13:13 -0700, Thomas Lumley wrote: Both for this and for working out why Tcl/Tk isn't installed you might be better off trying R-sig-mac rather than r-help This is a very common piece of advice. However, this is not what you would imagine if you read the description of R-SIG-mac on the R home page: BDR It is not actually on the R home page or even on BDR www.r-project.org. I think you mean BDR https://stat.ethz.ch/mailman/listinfo/r-sig-mac BDR This arises because the purpose of the list has changed BDR from BDRR Special Interest Group on Macintosh Development BDR and Porting, both for MacOS 8.6 - 9.x and MacOS X BDR I think a wording like R-sig-debian namely BDRR Special Interest Group for MacOS X ports of R Brian's definition seems appropriate to me nowadays and the (extended) disclaimer should include both development issues specific to OS X (ports, etc) and user feedback on R.app GUI (we don't want R.app bugs go into the R-bugs list), but NOT general R- help topics which should go to R-help indeed. I think we should keep the devel part in R-sig-Mac. I'm including Simon Urbanek and waiting for some reaction before taking actions on R-sig-mac. stefano BDR would be better. yes, thank you both IFF this is really the intention. Stefano Iacus is the maintainer (and initiator) of the list and should say (and maybe ask on the R-SIG-Mac list) what he (and the subscribers) really wants. R-SIG-Mac R Special Interest Group on Mac Development This is very similar to the description of R-devel: This list is intended for questions and discussion about code development in R. And that description is even more intimidating when you read further: Questions likely to prompt discussion unintelligible to non-programmers or topics that are too technical for R-help's audience should go to R-devel Would it make sense to change the description of R-SIG-mac so that it would welcome question on R usage in Mac, instead of being a Mac Devolepment forum that sounds like being unintelligible to non-programmers? BDR Which seems quite reasonable to me. The topics which BDR provoke this response usually are questions BDR unintelligible except to Mac sysadmins/programmers and BDR definitely `too technical for R-help's audience'. I agree. We shouldn't let R users on the Mac think that all their questions should go to R-SIG-Mac. Regular R questions should continue to come to R-help (or R-devel) just as per the posting guide. Martin Maechler BDR -- Brian D. Ripley, [EMAIL PROTECTED] Professor of BDR Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ BDR University of Oxford, Tel: +44 1865 272861 (self) 1 BDR South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, BDR UK Fax: +44 1865 272595 !DSPAM:43562fae226121420620285! __ 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-SIG-Mac] r version 2.1.0 and graphics in mac os 10.3.9
Hi Luis, please remove /usr/local/lib/libxml* files and in particular /usr/local/lib/libxml2.2.dylib from your system sudo rm /usr/local/lib/libxml2.2.dylib stefano On 04/lug/05, at 20:42, Luis Borda de Agua wrote: I use mac os 10.3.9 and I've installed in my computer R 2.1.0 (I believe this is the latest R version). Although it works alright when I open R by clicking in the R icon, I cannot use the graphics facility when I open R from a X-terminal window (or x-11 window). In fact, when I try to open R I get the message that I pasted below. Is this a R bug? Is R assuming that I should have the latest Mac OS Tiger installed? Or is it a problem related to my computer only? I did not have this problem when I used a previous version of R (I don't know which one was). Thank you in advance for your help. Luis BA. ___ % R R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.0 Patched (2005-05-12), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/Resources/library/grDevices/libs/ grDevices.so': dlcompat: dyld: /Library/Frameworks/R.framework/Resources/bin/ exec/R version mismatch for library: /usr/local/lib/libxml2.2.dylib (compatibility version of user: 9.0.0 greater than library's version: 8.0.0) Loading required package: grDevices Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/Resources/library/grDevices/libs/ grDevices.so': dlcompat: dyld: /Library/Frameworks/R.framework/Resources/bin/ exec/R version mismatch for library: /usr/local/lib/libxml2.2.dylib (compatibility version of user: 9.0.0 greater than library's version: 8.0.0) In addition: Warning message: package grDevices in options(defaultPackages) was not found Error: package 'grDevices' could not be loaded Luis Borda de Agua 2502 Department of Plant Biology University of Georgia Athens GA 30602 USA Phone: (706) 583-0943 Fax: (706) 542-1805 ___ R-SIG-Mac mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-sig-mac __ 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] RAqua 1.8.1 binaries available on CRAN
New binaries for RAqua 1.8.1 are now available on CRAN (main site) and will be propagated soon over the network. Stefano __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] gregmisc
In Carbon R 1.7.1 recommnded packages are already installed. VR itself is a bundle of package and not a package itself. MASS, rpart, spatial and nnet are already present in Carbon R. BTW, From 1.8.0 MacOS X users can take advange of the new (forthcoming) RAqua (http://www.economia.unimi.it/R/ for a preview) stefano On Venerdì, ago 8, 2003, at 04:10 Europe/Rome, Marc Schwartz wrote: On Thu, 2003-08-07 at 18:42, atsuya fujito wrote: Thank you, Marc; I installed car, R commander and Bioconductor. I am using R 1.7.1, on MAC OSX 10.2.6 [Long listing of packages snipped] Atsuya, Thanks for the listing. If that is the complete list, then you are missing the VR bundle of packages, which includes MASS and is typically part of the 'recommended' package bundle, at least under Windows and Linux/Unix. I did a search of the Mac FAQ (**which appears to be for 1.6.0**), the R Admin manual and the r-help archive, since I do not have hands on experience with Macs. I may have to defer to other Mac OSX users for detailed guidance here. I also just checked Jan de Leeuw's web site at UCLA (http://gifi.stat.ucla.edu/pub/index.php) based upon a review of the README at http://cran.r-project.org/bin/macosx/ReadMe.txt. The indication is that the Mac port for V1.7.0 includes the base and recommended packages, however V1.7.1 is the base package set only, if my read is correct. If that is indeed the case, the solution to your problem may be as simple as using: install.packages(VR) being sure that you have appropriate R/W access permissions to the library directory tree on your system when you use that R command. If that solves the problem, then you should be ok and can load 'gregmisc' after VR is installed. I am copying both Jan de Leeuw and Stefano Iacus on this communication to be sure that I am offering appropriate advice here. Given the various time zones involved here, hopefully someone can expediently confirm the resolution to your problem. I hope this helps. Regards, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Carbon R 1.7.1 on CRAN
I have just uploaded Carbon R 1.7.1 on CRAN. It will be available to you with the usual timing of mirroring. Contributed packages and the BioConductore bunble will follow shortly. stefano iacus --- Stefano M. Iacus Department of Economics University of Milan Via Mercalli, 23 I-20123 Milan - Italy Ph.: +39 02 50321 461 Fax: +39 02 50321 505 Please don't send me Word or PowerPoint attachments if not absolutely necessary. See: http://www.gnu.org/philosophy/no-word-attachments.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
