On Thu, 2013-05-16 at 08:39 +, 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.simp...@uregina.ca
523 Research and Innovation Centre [tw] @ucfagls
University of Regina
Regina, SK S4S 0A2, Canada
___
R-sig-ecology mailing list
R-sig-ecology@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
