[R] p-value for Nonmetric Multidimentional Scaling?

[Bill.Venables at csiro.au]

You need to ask yourself a number of questions, e.g.

What is the hypothesis you wish to test?
What is the test statistic you wish to use to test it?
How can I get some information on where my value of that statistic sits
with respect to its null hypothesis distribution?

p-values do not exist independently of hypothesis tests.


(It would also be a coutresy to the list to give your name and
affiliation, as the posting guide suggests.) 


Bill Venables
CSIRO Laboratories
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AUSTRALIA
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mailto:Bill.Venables at csiro.au
http://www.cmis.csiro.au/bill.venables/ 

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Michael Denslow
Sent: Saturday, 5 July 2008 2:14 PM
To: r-help at r-project.org
Subject: [R] p-value for Nonmetric Multidimentional Scaling?

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?

Thanks in advance for your help,
Michael

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