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

[Ellen Pape]

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