On Wed, 2013-04-24 at 13:13 -0700, Rémi Lesmerises wrote: > Thank you! > > A last question: Is it still the same explanation if I remove the > condition "first=TRUE" (and then testing for all axis) and permutest > gives the same result?
No; again `permutest(...., first = FALSE)` and `envfit()` are testing different models/fits but how they are different is not the same as with your previous question. `permutest(...., first = FALSE)` is testing whether the variance explained by the k environmental variable (k = 4 I believe in your case) is sufficiently large as to be unusual when compared to the variance explained under a null model (achieved by permuting residuals, propagating those residuals plus fitted values to give new data and refitting the model on those new data). `envfit()` is doing what it always did; assessing whether the correlation between the vector and the 2-d configuration is unusually large. In the `permutest(...., first = FALSE)` case, you have a model with 4df. In the `envfit()` case you have 4 models each with 1 degree of freedom. The two methods also differ in terms of the role played by the environmental data. In the `permutest` case, the environmental data are the predictors. In the `envfit` case the env data are the responses and the axis scores in the 2 dimensions chosen are the predictors. HTH G > Rémi Lesmerises, biol. M.Sc., > Candidat Ph.D. en Biologie > Université du Québec à Rimouski > remilesmeri...@yahoo.ca > > > > On Wed, 2013-04-24 at 10:38 -0700, Rémi Lesmerises wrote: > > Dear all, > > > > I did a RDA and when I looked to the signification of the test with > > permutest, the output was non-significant. But when I used the envfit > > function, some of the vectors are significant. All the test's > > conditions are respected. What it means? Is it an error in the script? > > The two functions are testing two fundamentally different things. > `permutest` (as you invoked it --- `first = TRUE`) is testing the first > axis of the RDA. That axis is a linear combination of the constraints. > > The `envfit` procedure is testing the individual correlations between > the 2-d configuration of samples in the RDA space and the direction of > maximal variance of the environmental data. Each variable is considered > separately. > > I can easily imagine a case, where the variance explained on the first > axis is not significant but variance over 2 axes is significant, as one > where the vectors do not point solely along the first RDA axis but also > point along the 2nd axis. By looking only at their contributions to the > first axis and summing them you don't explain a whole lot, but when you > look at the directions in 2D space each variable explains a significant > amount of variance. > > HTH > > G > > > Commands and output: > > > > > permutest(rda.ind, perm=999, first=TRUE) > > > > Permutation test for rda > > > > Call: rda(formula = x ~ ARH_frs + CON_frs + PRP_frs + RUI_frs + > > VAM_frs, data = z) > > Permutation test for first constrained eigenvalue > > Pseudo-F: 4.093568 (with 1, 10 Degrees of Freedom) > > Significance: 0.413 > > Based on 999 permutations under reduced model. > > > > > fit <- envfit(rda.ind, z, perm = 999, display = "lc") > > > fit > > > > ***VECTORS > > > > RDA1 RDA2 r2 Pr(>r) > > VAM_frs 0.145281 -0.989390 0.2388 0.147 > > > > ARH_frs -0.876494 -0.481413 0.6127 0.002 ** > > CON_frs 0.904278 0.426944 0.4846 0.013 * > > PRP_frs -0.997634 0.068755 0.9433 0.001 *** > > RUI_frs -0.648512 -0.761204 0.6243 0.004 ** > > --- > > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > P values based on 999 permutations. > > > > > > Rémi Lesmerises, biol. M.Sc., > > Candidat Ph.D. en Biologie > > Université du Québec à Rimouski > > remilesmeri...@yahoo.ca > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
