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

[Gavin Simpson]

Note that `betadisper()` only considers statistically dispersions
about the group centroids. It might show the centroids and return
their values, but it doesn't consider differences in those centroids.
As far is `betadisper()` is concerned, the group centroids could all
be made exactly equal and it wouldn't change the results as it is only
the spread about the centroid that is used.

HTH

G

On 27 March 2014 06:47, Brandon Gerig <bgerig at nd.edu> wrote:
> Hi Steve,
>
> Yes, this is precisely what I am interested in doing. It seems like
> betadisper might be a good way to visualize differences/similarities in the
> dispersion and examine differences among centroids for the levels within a
> factor. Am I correct in thinking that if I conduct additional PERMANOVA
> tests on a reduced data set, I could be evaluating differences between the
> levels of a main effect?
>
> Could anyone provide a citation for a paper that uses a similar procedure?
>
>
> On Wed, Mar 26, 2014 at 3:21 PM, Steve Brewer <jbrewer at olemiss.edu> wrote:
>
>> Brandon,
>>
>> Are you asking if you can use betadisper as a substitute for post-anova
>> pairwise comparisons among levels? After using betadisper to obtain
>> dispersions, I believe you can plot the centroids for each level. In
>> addition to telling you if the dispersions differ among levels, you could
>> see how the centroids differ from one another. Is this what you want to
>> know? If so, realize that it won't give you pairwise significance tests
>> for differences between levels. For that, you might want to do additional
>> permanovas on reduced datasets containing only the two levels you want to
>> compare. You could then adjust the p-values for multiple tests after the
>> fact.
>>
>> Hope this helps,
>>
>> Steve
>>
>>
>> J. Stephen Brewer
>> Professor
>> Department of Biology
>> PO Box 1848
>>  University of Mississippi
>> University, Mississippi 38677-1848
>>  Brewer web page - http://home.olemiss.edu/~jbrewer/
>> FAX - 662-915-5144
>> Phone - 662-915-1077
>>
>>
>>
>>
>> On 3/26/14 10:57 AM, "Brandon Gerig" <bgerig at nd.edu> wrote:
>>
>> >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 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",permutation
>> >>s=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]]
>> >
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>>
>>
>>
>
>
> --
> Brandon Gerig
> PhD Student
> Department of Biological Sciences
> University of Notre Dame
>
>         [[alternative HTML version deleted]]
>
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-- 
Gavin Simpson, PhD