[R-sig-eco] Ordination with vegan's metaMDS

[tyler]

Michele Tobias <mmtobias at ucdavis.edu>
writes:

> I have plant cover data for a number of sample plots and would like to
> do an ordination plot with the vegan package's metaMDS. The problem is
> that some of my plots have matching data (for example, two plots have
> 5% cover by one species and nothing else). Because of this, the
> dissimilarity measure between these is zero and the ordination doesn't
> work. It gives me this message: "Error in metaMDSdist(comm, distance =
> distance, autotransform = autotransform, : Zero dissimilarities are
> not allowed". Does anyone have any suggestions on how to work with
> this? Thank you for your help!
>

You can add the option zerodist = "add", which will add a small value to
all zero distances. See the help page for metaMDS.

Cheers,

Tyler

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