Basically the random forest algorithm can generate a proximity matrix of the data, and it's up to you how you would want to proceed from there. You can feed that into clustering algorithms that accept a similarity matrix, or turn it into a distance matrix for clustering algorithms that need a distance matrix (e.g., hclust()). You may or may not want to do ordination as the UCLA folks suggest.
I think this is one of the great things about working in R: you have the freedom to choose how you want to proceed from some intermediate result, and not locked in to something some one decide to hardwire into the software. Andy From: Gavin Simpson > > On Wed, 2007-08-15 at 09:44 -0700, David Katz wrote: > > Several searches turned up nothing. Perhaps I will try to > implement it if > > nobody else has. Thanks. > > You can do this with Andy Liaw's randomForest package can do this and > the first hit on a Google search (on term "RFclustering") was this: > > http://www.genetics.ucla.edu/labs/horvath/RFclustering/RFclust > ering.htm > > which shows how one might go about this with some helper functions. > > G > > -- > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > 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 > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > ______________________________________________ > [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. > > > ------------------------------------------------------------------------------ Notice: This e-mail message, together with any attachments,...{{dropped}} ______________________________________________ [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.
