Pierre-- That's actually an easy question. Look at the vegan package https://cran.r-project.org/web/packages/vegan/index.html. It has functions for various dissimilarity & distance metrics (and can use distance matrices from other packages such as ecodist), MDS and allied processes, anosim and restricted mantel tests, and many many other approaches.
More broadly, the cran task view for environmetrics is a great place to start for finding packages directed at ecological questions and analyses. https://cran.r-project.org/web/views/Environmetrics.html Tom On Fri, Mar 22, 2019 at 3:43 AM Pierre THIRIET <pierre.d.thir...@gmail.com> wrote: > Dear useRs, > > I want to perform 2nd stage nMDS, as described in Clarke, K.R., et al > (2006). Exploring interactions by second-stage community analyses. > Journal of Experimental Marine Biology and Ecology 338, 179-192. See > Abstract below > > Do you know a package in R for that ? Or would you have home-made > scripts, at least a function for computing the distance matrix of > pair-wise correlations among dissimilarity matrices ? > > Thank you, > > Pierre > > > Abstract of Clarke et al 2006 : > > Many biological data sets, from field observations and manipulative > experiments, involve crossed factor designs, analysed in a univariate > context by higher-way analyses of variance which partition out ‘main’ > and ‘interaction’ effects. Indeed, tests for significance of > interactions among factors, such as differing Before–After responses at > Control and Impact sites, are the basis of the widely used BACI strategy > for detecting impacts in the environment. There are difficulties, > however, in generalising simple univariate definitions of interaction, > from classic linear models, to the robust, non-parametric multivariate > methods that are commonly required in handling assemblage data. The size > of an interaction term, and even its existence at all, depends crucially > on the measurement scale, so it is fundamentally a parametric construct. > Despite this, certain forms of interaction can be examined using > non-parametric methods, namely those evidenced by changing assemblage > patterns over many time periods, for replicate sites from different > experimental conditions (types of ‘Beyond BACI’ design) – or changing > multivariate structure over space, at many observed times. *Second-stage > MDS, which can be thought of as an MDS plot of the pairwise similarities > between MDS plots (e.g. of assemblage time trajectories), can be used to > illustrate such interactions, and they can be formally tested by > second-stage ANOSIM permutation tests. Similarities between > (first-stage) multivariate patterns are assessed by rank-based matrix > correlations, preserving the fully non-parametric approach common in > marine community studies. *The method is exemplified using time-series > data on corals from Thailand, macrobenthos from Tees Bay, UK, and > macroalgae from a complex recolonisation experiment carried out in the > Ligurian Sea, Italy. The latter data set is also used to demonstrate how > the analysis copes straightforwardly with certain repeated-measures > designs. > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
