For SIMPER you can read this thread:
https://www.researchgate.net/post/What_do_you_think_about_Similarity_Percentage_analysis_SIMPER_to_measure_species_indicator_value

Moreover read the function help(simper) carefully, because: "The results of
'simper' can be very difficult to interpret. The method very badly
confounds the mean between group differences and within group variation,
and seems to single out variable species instead of distinctive species
(Warton et al. 2012). Even if you make groups that are copies of each
other, the method will single out species with high contribution, but these
are not contributions to non-existing between-group differences but to
within-group variation in species abundance."

Warton, D.I., Wright, T.W., Wang, Y. 2012. Distance-based multivariate
analyses confound location and dispersion effects. *Methods in Ecology and
Evolution*, 3, 89-101.

hope that helped,
Gian


On 24 March 2014 22:08, 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
>
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>
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