Thanks for taking the time! In the meanwhile I checked PDL::Transform and arrived at the same conclusion…
I know Maggies's module -- PDL::Stats::Kmeans is the step in my chain (clustering on the reduced matrix). However PCA is not the same a PCoA… If don't think that exists under PDL or more generally for perl. I have a little hope with R, since Rserve can quite speed up things (http://www.rforge.net/Rserve/), and someone just started a pelr lint (http://search.cpan.org/~djunkim/Statistics-RserveClient-0.01/lib/Statistics/RserveClient.pm). We'll see… Le 31 janv. 2013 à 22:27, Derek Lamb <[email protected]> a écrit : > OK, with this information I can tell you that PDL::Transform is probably not > what you want--that does coordinate transforms (I was interpreting your > question as in, "can I scale things (images, coordinates, etc) in multiple > dimensions"). Thank you for the MDS wikipedia link. > > PCA might be a better search term. Look at Maggie's PDL::Stats module, which > contains PDL::Stats::GLM. That includes some PCA routines. > > I don't know that GSL does PCA explicitly, but it should handle the > eigenvalue or SVD portions of PCA just fine. There are some PDL::GSL:: > modules but I don't think they include the eigen calculations. > > PDL::Slatec has the 'eigsys' function which may also be helpful. > > PDL::MatrixOps has the eigens. These last two I found by doing > > $pdldoc -a eigen > > from the command line after PDL was installed. > > There is a general R/Splus <--> Perl package here: > http://www.omegahat.org/RSPerl/ but it has not been updated in many years, > and I have never used it. > > best, > Derek > > > On Jan 31, 2013, at 1:52 PM, Jean Véronis wrote: > >> Thanks Derek, I am going to check PDL::Transform right away. >> >> My need is to reduce dimensionality on large distance matrices. For this is >> use multidimensional scaling >> (http://en.wikipedia.org/wiki/Multidimensional_scaling) by calling R from >> perl (cmdscale function : >> http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cmdscale.html). >> >> It's perfectly fine, expect in terms of performance, since at the moment I >> didn't find any better way than use Statistics:R, which basically passes >> data through stdin/stdout. When it comes to huge matrices, it is extremely >> inefficient. Hence my question. >> >> I tried to google "pdl multidimensional scaling", "gsl multidimensional >> scaling", "perl multidimensional scaling", and all possible variants >> involving "pcinipal coordinates analysis", "PCoA", with no success. >> >> Many thanks, again. >> --j >> >> Le 31 janv. 2013 à 21:41, Derek Lamb <[email protected]> a écrit : >> >>> Hi Jean, >>> >>> The best hint I can provide based on the extremely limited information you >>> have given is PDL::Transform. >>> >>> You might get a better response if you describe what you are trying to do >>> in more than one sentence, what you have tried, whether you are new to PDL >>> or Perl or are already using one or both, and what documentation you have >>> looked at. >>> >>> best, >>> Derek >>> >>> On Jan 31, 2013, at 1:24 PM, Jean Véronis wrote: >>> >>>> Hi all, >>>> >>>> I am looking for a multidimensional scaling package. >>>> Any hint would be appreciated. >>>> >>>> Many thanks >>>> --j >>> >> >
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