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

[Gavin Simpson]

No, that will just consider the dispersions *about the centroids* not
location shifts of the centroids. The latter is what `adonis()` does,
but we don't have pairwise comparisons (with/without permutation test)
there or the Tukey post-hoc tests. I suppose we *could* automate the
process that Steve suggests, just as I automated it for
`betadisper()`, and I think this has been raised before, but it hasn't
risen to the top of anyone's TODO list yet to actually see it
implemented. Patches welcome :-) !

G

On 27 March 2014 06:55, Johannes Björk <bjork.johannes at gmail.com> wrote:
> 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
>>>>
>>>>      [[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