On Wed, 2009-10-14 at 16:57 +0200, Kim Vanselow wrote: > Dear r-helpers! > How can I integrate other distances (in the form of a dist object) > into function metaMDS? The problem: metaMDS needs the original > data.frame for the calculation and only the default distances of > function vegdist are allowed. > Any suggestions are greatly appreciated! > Thank you, > Kim
Read the help page for metaMDS more closely? ;-) the first argument of metaMDS is 'comm'; this is documented as: comm: Community data. Alternatively, dissimilarities either as a 'dist' structure or as a symmetric square matrix. In the latter case all other stages are skipped except random starts and centring and pc rotation of axes. notice the bit about dissimilarities - which can either by square symmetric matrices or objects of class 'dist'. When you supply your own distances, not all the transformations and other options in metaMDS are turned on, so you may want to check the effects of transformations etc yourself, which you would apply before computing the dissimilarity matrix. 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.