On Fri, 2011-11-25 at 11:41 +0200, Jari Oksanen wrote: <snip /> > Howdy Folks, > > It seems that empty groups (count is zero) are the source of the > problem. You can drop them using factor() command for your interaction > -- this drops empty levels: > > mod <- betadisper(betad, factor(groupA)) > > works for me.
droplevels() would be what the cool kids would use, just to be hip ;-) It's new to recent versions of R (>= 2.13.0 IIRC). For factors it is just a roundabout way of doing `factor(myfac)`: > droplevels.factor function (x, ...) factor(x) <environment: namespace:base> but there is a data.frame method which drops empty levels for all factors in a data frame, and package authors can write other methods which might become useful in various places in the future. So good to know that `droplevels()` exists. > However, like Gav said, this may not be a meaningful test (but still > calls for a fix in vegan). I'll take a look at adding a test/fix to vegan. G > If I remember correctly, Marti Anderson had > interactions in her software, but that was dropped from current > versions. > > Cheers, jari oksanen > > > > For the dune dataset, the above error occured. But for my data, the > > > interaction works. I wonder if i continue to use the new factor generated > > > from the factor-interaction for the betadisper, will it affects the > > > results? If this is wrong, what would be the recommended function to use? > > > > I would need to check more carefully, but this may not be what Marti > > Anderson's software would fit as an interaction model. I may be > > misremembering, but IIRC PERMDISP can handle two-way ANOVA type models > > within her framework and betadisper is not set-up for that. What you > > have done is look at whether certain combinations of your two factors of > > interest are more variable/dispersed than others. Which seems a > > reasonable hypothesis to me. > > > > G > > > > > Sincerely Yours, > > > J > > > > > > On Nov 17 2011, Kay Cecil Cichini wrote: > > > > > > >..to be save I would consider to exclude an effect due to different > > > >multivariate spread. See chapter 5.2, Homogeneity of groups and beta > > > >diversity, in the vegan tutorial at > > > >http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf. > > > > > > > >best, > > > >kay > > > > > > > > > > > >Zitat von Gavin Simpson <[email protected]>: > > > > > > > >> On Wed, 2011-11-16 at 03:43 +0100, Gian Maria Niccolò Benucci wrote: > > > >>> Hi all, > > > >>> > > > >>> I had 84 samples collected in 7 different sites. In each sample were > > > >>> individuated the different fungal species and recorded. I would test > > > >>> if > > > >>> exist a real difference between the sites and if exist a sort of site > > > >>> effect that structure the fungal communities... Then, I did adonis > > > >>> test > > > >>> > > > >>> > adonis(community.sq ~ location, data=env.table, permutations=999) > > > >>> > > > >>> Call: adonis(formula = community.sq ~ location, data = env.table, > > > >>> permutations = 999) > > > >>> > > > >>> Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) > > > >>> location 6 12.593 2.09886 6.8867 0.34922 0.001 *** > > > >>> Residuals 77 23.467 0.30477 0.65078 > > > >>> Total 83 36.060 1.00000 > > > >>> --- > > > >>> Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 > > > >>> > > > >>> > > > >>> > > > >>> The significance is R2=0.349 at P=0.001 Can I assure that exist a > > > >>> strong site effect in structuring the communities in each site? > > > >> > > > >> Depends. The test is one of no effect of `location`. You have found > > > >> evidence against this hypothesis and thus could reject this hypothesis, > > > >> instead accepting the alternative hypothesis that there is an effect of > > > >> `location`. As to the strength of this effect? ~35% of the sums of > > > >> squares can be explained by `location`. Substantially more of the > > > >> variance remains unexplained. As I know nothing about your subject > > > >> area, > > > >> I am unable to comment further on the strength of the relationship. > > > >> > > > >> Seeing as many ecologists whose work I read would say an effect is > > > >> significant if the p-value was >= 0.05. Not that I subscribe to this > > > >> way > > > >> or working, but by that criterion, you have identified a significant > > > >> `location` effect. > > > >> > > > >> HTH > > > >> > > > >> G > > > >> > > > >>> > > > >>> Thanks for helping, > > > >>> > > > >>> G. > > > >>> > > > >>> [[alternative HTML version deleted]] > > > >>> > > > >>> _______________________________________________ > > > >>> R-sig-ecology mailing list > > > >>> [email protected] > > > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > >> > > > >> -- > > > >> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > > >> Dr. Gavin Simpson [t] +44 (0)20 7679 0522 > > > >> ECRC, UCL Geography, [f] +44 (0)20 7679 0565 > > > >> Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk > > > >> Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ > > > >> UK. WC1E 6BT. [w] http://www.freshwaters.org.uk > > > >> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > > >> > > > >> _______________________________________________ > > > >> R-sig-ecology mailing list > > > >> [email protected] > > > >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > >> > > > >> > > > > > > > >_______________________________________________ > > > >R-sig-ecology mailing list > > > >[email protected] > > > >https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > > > > > > > > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. 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