On Sun, 2009-07-19 at 15:34 +0000, Alexandre F. Souza wrote: > Hello All, > > Do anyone has ever performed a constrained NMDS with community data? I > have read in McCune and Graces' Analysis of Ecological Communities that > the theory of such analysis already exists (i.e., associating vectors of > environmental variables to a NMDS ordination) but has seldon been used > by ecologists. It would be a better alternative to CCA, which has > stingent premises that ecological data does not match properly most of > times. > > I suppose that this could be implemented in R, but I could not find it > in Vegan or other packages.
If I understand the above, see ?vectorfit ?envfit and ?ordisurf in vegan, to relate an a priori developed nMDS configuration to associated covariates. If you really meant a constrained nMDS, I'm not sure how one would go about doing it. There are no axes to constrain, and the purpose of the constraints in RDA/CCA is to express on the first n axes the variance you can explain with the covariates available; this isn't an issue with nMDS as you are expressly interested in a low dimensional representation of the original dissimilarities. More flexible versions of RDA/CCA include constrained analysis of principal coordinates (capscale() in vegan) and you can use the kind of transformation envisaged by Legendre and Gallagher 2001 Oecologia with RDA. Alternatively, for a more statistically-based solution, take a look at the work of Thomas Yee and vector GLMs and GAMs, particularly the quadratic reduced rank VGLMs or constrained additive ordination. This is available in the VGAM package for R. HTH G > > Thanks in advance, > > 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 > [email protected] > http://www.unisinos.br/laboratorios/lecopop > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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 %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
