[R-sig-eco] Vegan-Adonis-NMDS-SIMPER

[Liz Pryde]

Further to the Warton paper, he and colleagues developed an R package that I've used in place of SIMPER called ' mvabund'. This runs multivariate GLMs and gives effects sizes and adjusted significance values of species that can be used to determine those having the greatest effect.

I haven't looked at it recently but when I used the package they had it working for count and binary data. It's very simple to use and there are excellent references for both the methods and theory. David even uploaded possibly the most entertaining stats video about it on you tube which explains reasons for the approach very clearly.

Good luck,
Liz

Liz Pryde


> On 25 Mar 2014, at 9:19 pm, Gian Maria Niccolò Benucci <gian.benucci at gmail.com> wrote:
> 
> 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 at 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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