Thanks for the responses!
Even if I reduced the size of my dataset and ran a separate Adonis model
just on an individual factor, betadisper should not be used to infer
pairwise differences between levels because betadisper is not measuring
differences between centroids but differences in dispersion variance within
a level.

Would it be justifiable to then to run the Adonis model and use an NMDS
plot to interpret differences and interactions among factors?

I wish I were a gifted enough programmer to add a patch, but being a
neophyte with multivariate statistics I think it best I not contribute :)




On Thu, Mar 27, 2014 at 11:51 AM, Gavin Simpson <ucfagls@gmail.com> wrote:

> 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@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@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@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@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]]
> >>>>
> >>>> _______________________________________________
> >>>> R-sig-ecology mailing list
> >>>> R-sig-ecology@r-project.org
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >>>
> >>>
> >>>
> >>
> >>
> >> --
> >> Brandon Gerig
> >> PhD Student
> >> Department of Biological Sciences
> >> University of Notre Dame
> >>
> >>       [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> R-sig-ecology mailing list
> >> R-sig-ecology@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >
> > _______________________________________________
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> > R-sig-ecology@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
>
>
> --
> Gavin Simpson, PhD
>



-- 
Brandon Gerig
PhD Student
Department of Biological Sciences
University of Notre Dame

	[[alternative HTML version deleted]]

