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/
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
__
R-help@stat.math.ethz.ch 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.
