[R-sig-eco] Mantel() with strata

[Gavin Simpson]

On Thu, 2013-05-16 at 08:39 +0000, SILVIA CALVO ARANDA wrote:
> Hi all
> Im computing mantel test between species
> dissimilarity and geographic distance between all pairwise island comparisons
> in three archipelagos (each with 9, 7 and 3 islands) within the same
> biogeographical region. Im using mantel() of vegan package, and I was
> wondering if I should use the strata argument to control for the archipelago
> effect. Does anyone know if using archipelago as random effect with only 3
> levels is enough to obtain reliable estimates of variance? I dont think so.
> Instead, if in the same scatter plot of species dissimilarity vs geographic
> distance I mark differently the points corresponding to within-archipelago and
> between-archipelago comparisons, how can I test (through permutations) the
> statistical significance of both correlations?
> Any input on this issue will be ok for me!
> Thank you in advance 		 	   		  

`strata` controls the way the permutation test is performed. It is
essentially a block term whereby permutations are derived by random
permutation of samples *within* each block (i.e. samples are *not*
shuffled between blocks). This preserves the clustering of the data
whilst perturbing the exact link between the geographic and
compositional distances. `strata` is therefore usually a factor
variable.

This isn't really a random effect; where one probably wouldn't use a
variable with only three levels as a random effect there is no reason
not to use it for `strata` in the permutation test if the null
distribution you are testing needs to retain the archipelago-based
clustering of samples.

HTH

G

-- 
Gavin Simpson, PhD                          [t] +1 306 337 8863
Adjunct Professor, Department of Biology    [f] +1 306 337 2410
Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca
523 Research and Innovation Centre          [tw] @ucfagls
University of Regina
Regina, SK S4S 0A2, Canada