R help - Oct 2006 - Problems running IsoMDS using vegdist with pres-abs data and two sites with zero distance

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

-- 
Dr. Leonard Sandin
Department of Environmental Assessment / Milj?analys
Swedish University of Agricultural Sciences / SLU
P.O. Box 7050
SE-750 07 Uppsala
Sweden
Work phone +46-(0)18-673813
fax        +46-(0)18-673156
http://www.ma.slu.se
--

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

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