On Sat, 2006-10-21 at 13:19 +0200, Leonard Sandin wrote: > Hi > I have just (finally) started to poke around in R and wanted to analyse > a stream fish dataset with 28 sites and 18 species. When trying to > follow the Vegan manual to run nmds from distance measures calculated by > the vegdist function it turns out that I have two sites (streams) with > the exactly the same four species (I have used pres-abs data in this > case). When I try to run isoMDS I get an error message saying that: > Error in isoMDS(vare.dis) : zero or negative distance between objects 14 > and 15 > i.e. the two sites with the same fish species. I can run the decorana > function with "sensible" results so the dataset seems to be ok. > My next step would be to compare the results of the fish ordination with > some other datasets from the same sites (i.e. through procrustes > rotation) - so I wouldn´t like to remove one of the "twin" sites. > Any suggestion on how to circumvent this or am I simply using the wrong > method? > > Best wishes, Leonard >
Hi Leonard, I assume you are running isoMDS (package MASS) directly? If so, take a look at metaMDS function in vegan which has an argument zerodist which if you set it to "add" adds a small distance so you don't get this error. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC & ENSIS, 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/cv/ London, UK. WC1E 6BT. [w] http://www.ucl.ac.uk/~ucfagls/ %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ [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.
