[R-sig-eco] different result for permutest (vegan, R) and permdisp (PERMANOVA/Primer)

[Cade, Brian]

Ellen:  Not sure why these differences would occur but note that with two
groups of 3 observations each there are only 6!/(3!3!) = 20 possible
permutations.  Not sure where your 720 came from.  Also, I would not expect
a permutation test for homogeneity of dispersions to be very useful with
such small sample sizes.

Brian

Brian S. Cade, PhD

U. S. Geological Survey
Fort Collins Science Center
2150 Centre Ave., Bldg. C
Fort Collins, CO  80526-8818

email:  cadeb at usgs.gov <brian_cade at usgs.gov>
tel:  970 226-9326


On Wed, Nov 23, 2016 at 5:40 AM, Ellen Pape <ellen.pape at gmail.com> wrote:

> Dear all,
>
> As I want to switch for my multivariate data analyses from PRIMER/PERMANOVA
> to R, I am comparing all tests I am doing in the former with those
> performed in the latter program, to see whether results agree.
>
> I performed a test for the homogeneity of multivariate dispersions in both
> programs (R: betadisper + permutest, Primer: PERMDISP, both using
> centroids), and I have very different results, i.e. very different P
> values. The P value of the permutest (in R) is 0.0013; the one of PERMDISP
> is 0.30. I am really puzzled by this difference, as:
>
> - I have used the same pre-treatment for the data, i.e. standardize (divide
> all entries by row totals, with 1 sample per row) and square-root transform
> -I have used Bray-Curtis dissmilarities in both cases; however in
> Primer/Permanova you calculate a resemblance matrix and thereon you perform
> the PERMDISP. In R you calculate Bray-Curtis distances, which you then
> submit to betadisper and then you can test significance of differences
> using permutations with permutest (if you don't want to use ANOVA)
>
> I have looked at the Bray-Curtis resemblance values in Primer/Permanova and
> I have converted them to distances (Tools-> Dissim), but I get different
> values for Bray-Curtis distances (though they all seem to be higher for
> Primer)! I have pasted the values in Excel so you can have a look for
> yourself. I think this might be the reason for these underlying
> differences?
>
>
> One thing I also saw was,  in the case of my dataset, where I have two
> groups of 3 observations each, permutest had to perform a complete
> enumeration of permutations (=720-1=719), but that the PERMDISP in
> Primer/PERMANOVA still gave as output that it did 9999 permutations, which
> then seems inpossible to me!
>
> Thank you for any advise!
>
> Bets regards
> Ellen
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