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Mantel() with strata
2 messages · SILVIA CALVO ARANDA, Gavin Simpson
8 days later
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