On Wed, 2010-06-30 at 18:02 -0300, afso...@unisinos.br wrote: > Hi all, > > I am using the vegan package to run a prcincipal components analysis > on forest structural variables (tree density, basal area, average > height, regeneration density) in R. > > However, I could not find out how to extract factor loadings > (correlations of each variable with each pca axis), as is straightforwar > in princomp. > > Do anyone know how to do that?
It is easier than I thought when I answered your Q on ECOLOG-L the other day ;-) If ord is your fitted PCA ordination done using rda() from vegan, then we just need to extract the *unscaled* species scores to get the same things as is given by loadings() on a princomp ordination or the $rotation from a prcomp ordination require(vegan) foo <- princomp(USArrests, cor = TRUE) FOO <- prcomp(USArrests, scale = TRUE) bar <- rda(USArrests, scale = TRUE) loadings(foo) with(FOO, rotation) scores(bar, choices = 1:4, display = "species", scaling = 0) > Moreover, do anyone knows a function r package that produces > rotated-pca and biplots? Most packages I found did only one of these > tasks (princomp, psych, vegan). I'm not sure what you mean here; biplot() is a convenience wrapper method for rda() ordinations that produces a biplot of the PCA ordination. The plot methods for rda() objects allow you to create a biplot by hand if you want or just plot one set of scores. The biplot() method just tries to simplify this process. As is typical in ecology though, we want to scale sites or species to best represent relationships between sites or between species, so you need to choose the scaling most appropriate for your data/question. Scaling = 3 is usually a good compromise. More about scalings in vegan and prcomp/princomp can be found in the design decisions vignette: http://cran.r-project.org/web/packages/vegan/vignettes/decision-vegan.pdf Can you explain what you mean by "rotated-pca"? PCA is just a rotation of the data and that is what vegan does and plots. This may just be an issue of terminology, so if you can explain or point me to a reference that describes what you want, I'll look into it some more. HTH G > > Thanks a lot, > > Alexandre > > > > Dr. Alexandre F. Souza > Programa de Pós-Graduação em Biologia: Diversidade e Manejo da Vida > Silvestre > Universidade do Vale do Rio dos Sinos (UNISINOS) > Av. UNISINOS 950 - C.P. 275, São Leopoldo 93022-000, RS - Brasil > Telefone: (051)3590-8477 ramal 1263 > Skype: alexfadigas > afso...@unisinos.br > http://www.unisinos.br/laboratorios/lecopop > > ______________________________________________ > 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.
