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

Thu Mar 27 19:28:02 CET 2014

Gavin and Brandon,

Yes, I am aware that betadisper() does not actually give you a test of
differences between centroids, but the fact that it does calculate
centroids is quite valuable for interpretation, in my opinion, especially
when using non-euclidean distance matrices (e.g., Bray-Curtis) and also if
you would prefer NOT to do additional pairwise tests between levels, but
still would like to have some idea as to which pairwise differences
between levels might be most responsible for the effect. When using
bray-curtis distances, you can't get centroids by calculating averages of
abundances among the observations of interest. If you just want to use a
NMDS ordination with levels symbol-coded to make them distinct, that's
fine. Sometimes folks calculate the average axis score per group or level
of group and plot that. That's fine, too. The nice thing about obtaining
centroids calculated using betadisper() is that they are based on a
principal coordinates analysis that uses ALL the axes, not just the first
two or three axes in the ordination. It is likely that if the first two or
three axes of the NMDS explain most of the important variation, the
average scores per level for those three axes will probably tell the same
information as the centroids will.

Even though it wasn't intended for this purpose, Sharon Graham and I,
together, figured out that you could use the centroids calculated by
betadisper() to analyze split-plot and repeated-measures designs using
adonis. So, its value extends beyond what it was intended for.

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 3/27/14 10:47 AM, "Gavin Simpson" <ucfagls at gmail.com> wrote:

>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",permutat
>>>>>ion
>>> >>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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>>> >R-sig-ecology at 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]]
>>
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>
>
>
>-- 
>Gavin Simpson, PhD