[R-sig-eco] envfit and adonis restricted permutations

[Jari Oksanen]

On 29/06/11 09:07 AM, "Gavin Simpson" <gavin.simpson at ucl.ac.uk> wrote:

> On Tue, 2011-06-28 at 16:27 -0700, Steve Leonard wrote:
>> Thanks Gavin, that is really helpful.
>> 
>> I'm still a bit uncertain re your parting words:
>> 
>> "These results, at first blush, would suggests to me that easting
>> and northing effects are in the parts of the dissimilarity matrix not
>> represented well by the 3-d nMDS solution."
>> 
>> If this was the case, wouldn't easting and northing have low r2 values in
>> envfit results?
> 
> The restricted permutation test is telling you that there is nothing
> special about the r2 values for those covariates in the envfit case.
> 
> That was speculation; as I said, the two techniques are testing very
> different things so it is difficult to make definitive statements.
> Remember in nMDS all you are doing is getting a low dimensional mapping
> that best fits the *rank* ordering of the dissimilarities between you
> samples. adonis is able to work with the actual dissimilarities. In
> terms of the rank ordering mapping, easting and northing do not appear
> to be important, yet they are able to "explain" significant amounts of
> the "variance" in the actual dissimilarities.
> 
Yep, and you should also note that when you use 'strata', the significance
of easting and northing are evaluated *within* strata, whereas R2 of envfit
is evaluated over all data disregarding strata (the value of R2 does not
change when you use 'strata'). If easting and northing differ between
strata, but are fairly constant within strata, you can get high R2, but no
significant results. You know your data best (and you have access to your
data), so check yourself.

Cheers, Jari Oksanen