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

[Johannes Björk]

Hi,

For that I believe you can run TukeyHSD.betadisper... to getting significant values between levels. see ?TukeyHSD.betadisper

Cheers,
On Mar 27, 2014, at 1:47 PM, Brandon Gerig 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
>>> 
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>>> 
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>> 
>> 
>> 
> 
> 
> -- 
> Brandon Gerig
> PhD Student
> Department of Biological Sciences
> University of Notre Dame
> 
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> 
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