[R] p-value for Nonmetric Multidimentional Scaling?

Gavin Simpson gavin.simpson at ucl.ac.uk
Sat Jul 5 11:28:12 CEST 2008

On Fri, 2008-07-04 at 21:14 -0700, Michael Denslow wrote:
> Dear R-helpers,
> I am running metaMDS in the vegan package, which uses isoMDS in MASS,
> to perform Nonmetric Multidimentional Scaling (NMDS).
> I have seen some authors report a p-value for the NMDS ordination
> based on randomization of the dataset. As I understand it this is
> meant to compare the stress in your dataset to multiple runs of
> randomized data.
> I do not see a way to perform such a test in vegan or MASS.
> So my questions are:
> Is this necessary? and Does R have a function to do this?

No, but the following discussion on the r-forge repository for vegan
presents some ways that an analysis of this type could be done using


But read Jari's comments carefully. If your data are species, then
consider whether permuting row, columns or both is appropriate when they
don't preserve the row or column totals. So a question to ask yourself
is, is permuting rows, columns or both going to derive the appropriate
Null hypothesis for the test you have in mind?

Please feel free to follow this up in the forum post I refer to.

All the best,


> Thanks in advance for your help,
> Michael
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