[R-sig-eco] residual with protest in vegan

[tyler]

Christopher Chizinski <chizi001 at umn.edu> writes:

> I am using protest (in vegan) to assess the concordance between NMDS scores, as shown below:
>
> fishbug.fit <- protest(scores.bug, scores.fish,permutations = 9999)
>
> I would like to get the average residuals from protest.  When I use residuals(),
>
> resids.fit<-residuals(fishbug.fit)
>
> which residuals is this returning to me?  Are these the average residuals from the 9999 permutations or are these the
> residuals from the most recent permutation?
>

The residuals are from the unpermuted procrustes test. Compare:

residuals(protest(scores.bug, scores.fish))
residuals(procrustes(scores.bug, scores.fish, symmetric = TRUE))

Cheers,

Tyler

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