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 _______________________________________________ R-sig-ecology mailing list [hidden email] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology |
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: [hidden email] <[hidden email]> tel: 970 226-9326 On Wed, Nov 23, 2016 at 5:40 AM, Ellen Pape <[hidden email]> 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 > _______________________________________________ > R-sig-ecology mailing list > [hidden email] > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [hidden email] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology |
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