On Mon, 2007-03-12 at 16:02 -0700, Sender wrote: > Thanks for the suggestion Christian. I'm trying to avoid expanding the dist > object to a matrix, since i'm usually working with microarray data which > produces a distance matrix of size 5000 x 5000. > > If i can keep it in its condensed form i think it will speed things up. > > Is my thinking correct?
That will all depend on what you want to do with it... A dist object of that size is c. 100 MB in memory, and c. 200 MB in size as the full dissimilarity matrix - values from object.size(). Of course, you'll need a reasonable amount of free memory over and above this to do anything useful with the matrix as copies may be required during analysis/processing etc. Of course, a dist object is just a vector of observed distances with various attributes, so one can always use "[" for vectors, but I imagine that anything other than trivial operations will become fiddly, complicated and time consuming - if you have the memory, give the as.matrix option a try and see how it works for your specific problems. G > > > On 3/12/07, Christian Hennig <[EMAIL PROTECTED]> wrote: > > > > On Mon, 12 Mar 2007, Sender wrote: > > > > > Hello: > > > > > > Does anyone know if there exists a package that handles methods for [ > > for > > > dist objects? > > > > > > I would like to access a dist object using matrix notation > > > > > > e.g. > > > > > > dMat = dist(x) > > > dMat[i,j] > > > > Try > > dMat <- as.matrix(dist(x)) > > > > Christian > > > > > > > > *** --- *** > > Christian Hennig > > University College London, Department of Statistical Science > > Gower St., London WC1E 6BT, phone +44 207 679 1698 > > [EMAIL PROTECTED], www.homepages.ucl.ac.uk/~ucakche > > > > [[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 > and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC [f] +44 (0)20 7679 0565 UCL Department of Geography Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street London, UK [w] http://www.ucl.ac.uk/~ucfagls/ WC1E 6BT [w] http://www.freshwaters.org.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 and provide commented, minimal, self-contained, reproducible code.
