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 <[email protected]> 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 [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
