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

[Steve Brewer]

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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