Thanks for the words of caution on simper.

Am I completely off base in thinking that betadiver function (analgous to
Levene's test) could be used to examine variation between levels within
main effects?

Cheers


On Mon, Mar 24, 2014 at 5:08 PM, Brandon Gerig <bgerig@nd.edu> wrote:

> I am assessing the level of similarity between PCB congener profiles in
> spawning salmon and resident stream in stream reaches with and without
> salmon to determine if salmon are a significant vector for PCBs in
> tributary foodwebs of the Great Lakes.
>
> My data set is arranged in a matrix where the columns represent the
> congener of interest and the rows represent either a salmon (migratory) or
> resident fish (non migratory) from different sites.  You can think of this
> in a manner analogous to columns representing species composition and rows
> representing site.
>
> Currently, I am using the function Adonis to test for dissimilarity
> between fish species, stream reaches (with and without salmon) and lake
> basin (Superior, Huron, Michigan).
> The model statement is:
>
> m1<adonis(congener~FISH*REACH*BASIN,data=pcbcov,method="bray",permutations=999)
>
> The output indicates significant main effects of FISH, REACH, and BASIN
> and significant interactions between FISH and BASIN, and BASIN and REACH.
>
> Is it best to then interpret this output via an NMDS ordination plot or
> use something like the betadiver function to examine variances between main
> effect levels or both?
>
> Also,  can anyone recommend a procedure to identify the congeners that
> contribute most to the dissimilarity between fish, reaches, and basins?. I
> was thinking the SIMPER procedure but am not yet sold.
>
> Any advice is appreciated!
> --
> Brandon Gerig
> PhD Student
> Department of Biological Sciences
> University of Notre Dame
>



-- 
Brandon Gerig
PhD Student
Department of Biological Sciences
University of Notre Dame

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