[R-sig-eco] envfit permutation significance

[jsgro]

Thanks very much Gavin. I guess to distill your comments you would agree
with my last thought...the envfit vector placement has meaning, it just
can't be predicted from the RDA with great confidence.

On Mon, Nov 10, 2014 at 11:50 PM, Gavin Simpson-2 [via r-sig-ecology] <
ml-node+s471788n7579207h25 at n2.nabble.com> wrote:

> Well, just because the vector(s) in question don't hit some a priori
> specified statistical significance doesn't mean the vector doesn't exist;
> we can still plot it.
>
> As for interpretation, the length of the vector is not unusual when
> considered against a null distribution of r values generated by
> permutation. This doesn't mean the vector is random, just that it is no
> more "important" than a vector in ordination space where there was no
> relationship between the axis scores and the variable for which the vector
> is being tested.
>
> You need to ask yourself whether the permutation test is valid - are you
> allowed to permute the things you permuted? - and whether you have
> sufficient power to detect an "effect", which usually boils down to having
> enough unique permutations to get a "significant" p value.
>
> If you want to restrict the plot to only those vectors that are
> "significant", then look at the `p.max` argument in `?plot.envfit
>
> HTH
>
> Gavin
>
> On 10 November 2014 22:08, jsgro <[hidden email]
> <http://user/SendEmail.jtp?type=node&node=7579207&i=0>> wrote:
>
> > I have fitted a vector (a variable) using envfit to an RDA of sites,
> > species,
> > and environmental variables. The envfit permutation (999 permutations)
> was
> > not significant, but envfit placed the vector on the RDA plot. How
> exactly
> > do I interpret this plot? Is the placement of the vector meaningless
> (just
> > random) because the permutation result was not significant? or does the
> > vector placement have meaning, but it just cannot be predicted from the
> RDA
> > with confidence?
> >
> >
> >
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>
> --
> Gavin Simpson, PhD
>
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