Distance matrix analyses
Thank you for your kind response, I am sorry about the lack of details behind my original question, I will explain now why is important to me to test for the among group combinations. Specifically, I have sampled apple orchards and two neighboring seminatural habitats (forest and grasslands). I am interested in evaluating how the community composition change across these different habitats. In particular, I expect that a significant interaction between the nestedness of two habitats will be an indicative of high spillover between these habitats. For instance, I have a distance matrix of the ?relativized nestedness? of Podani and Schmera (2011) and I would like to test the contribution of forest and grassland habitats to the local diversity of apple orchards. Therefore, I would like to compute the variances in nestedness across these different habitats. For example, the ?adonis? function in vegan does this work, but my problem is that I cannot test for the variance among habitats (following the original example it would be the *ba*, *ca*, and *cb* combinations). If I specify in ?adonis? to do the grouping as *a*, *b* and *c*, it will do the test on the *aa*, *bb* and *cc* of the matrix. Is it a way to specify the groupings so that it will subset the distance matrix to test for *ba*, *ca* and *cb* combinations? Thank you, Diego 2014-09-18 17:29 GMT+02:00 Sarah Goslee <sarah.goslee at gmail.com>:
Test them for what? If you can formulate your hypotheses more clearly, you might try the model matrix approach outlined in Legendre, P. and M.-J. Fortin. 1989. Spatial pattern and ecological analysis. Vegetatio, 80: 107-138. and subsequent references. But there might be better ways, depending on what you are trying to achieve. Sarah On Thu, Sep 18, 2014 at 11:17 AM, Diego Javier Inclan Luna <diegojavier.inclanluna at studenti.unipd.it> wrote:
Hi, I would like to test dissimilarities among different groups in a dist matrix. For instance, if I have a dist matrix with three factors a, b, c, functions like adonis and betadisper in vegan will test the aa, bb and cc combinations. However, I am interested in testing the ba, ca, and cb combinations. How I could test for these combinations? *a a a b b b c c c* *a* aa *a* aa aa *a* aa aa aa *b* ba ba ba bb *b* ba ba ba bb bb *b* ba ba ba bb bb bb *c* ca ca ca cb cb cb cc *c* ca ca ca cb cb cb cc cc *c* ca ca ca cb cb cb cc cc cc Thanks! --
-- Sarah Goslee http://www.functionaldiversity.org
---- Diego J. Inclan PhD Student DAFNAE-Entomology, University of Padova Viale dell'Universit? 16, 35020, Legnaro (PD) - Italy webpage: http://www.biodiversity-lorenzomarini.eu/Diego.html [[alternative HTML version deleted]]