Hi,
Gavin Simpson wrote: > What do you want to do with the dissimilarities? Clustering. Gavin Simpson wrote: > If clustering, try the clara() function I can't because the variables are mixed (numeric and categorical) and (I suppose..) I should use "gower" distance in advance, shouldn't I? Thanks Giuseppe -----Messaggio originale----- Da: Gavin Simpson [mailto:gavin.simp...@ucl.ac.uk] Inviato: 26 August 2010 17:47 A: abanero Cc: r-help@r-project.org Oggetto: Re: [R] daisy(): space allocation issue On Thu, 2010-08-26 at 07:35 -0700, abanero wrote: > Hi, > > I'm trying to apply the function daisy() to a data.frame 10000x10 but I have > not enough space (error message: cannot allocate vector of length > 1476173280). > > I didn't imagine I was not able to work with a matrix of just 10000 > observations... I have setted in Rgui --max-mem-size=2G (I'm not able to set > more space..) You are trying make a 10,000 x 10,000 matrix of dissimilarities. > How can I solve this issue? Separating observations depending on some rules? Get/use a machine with more RAM? I doubt separating observations into chunks and doing the dissimilarity computations on those chunks then recombining will work as the end result will still be the 10k x 10k matrix. (If that is what you meant.) What do you want to do with the dissimilarities? If clustering, try the clara() function in the same package (cluster) as daisy. But then you'd need to work out whether clustering such a large number of observations is a useful activity... If something else, perhaps let us know what you want to do with the dissimilarities or what you are trying to achieve as there may be other things that you can do instead. > thanks HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help@r-project.org 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.
