Partitioning beta diversity into turnover and nestedness components


betapart allows computing pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities, separating the turnover and nestedness-resultant components of taxonomic (incidence and abundance based), functional and phylogenetic beta diversity.


The partitioning of incidence-based dissimilarity can be performed for two different families of indices: Sorensen and Jaccard. The pairwise function beta.pair yields 3 distance matrices accounting for the spatial turnover and the nestedness components of beta-diversity. The third distance matrix accounts for the sum of both componentes, i.e. totaal dissimilarity (a monotonic transoformation of beta diversity. The multiple site function beta.multi yields the spatial turnover and the nestedness components of overall dissimilarity, and the sum of both components, total dissimilarity. The basic calculations for all these multiple-site measures and pairwise dissimilarity matrices can be computed using the function betapart.core, which returns an object of class betapart. This is useful for large datasets as the consuming calculations are done only once, and its result can then be used for computing many indices. The multiple-site values can be randomly sampled a specified number of times for a specified number of sites using the function beta.sample. The aforementioned indices used for assessing spatial patterns can also be used for measuring temporal changes in community composition with the function beta.temp. Likewise, an analogous framework has been implemented for separating the two components of abundance-based dissimilarity (balanced changes in abundance vs. abundance gradients) using commands beta.pair.abund, beta.multi.abund, betapart.core.abund, and beta.sample.abund. The framework has been extended for functional beta diversity with commands functional.betapart.core, functional.beta.pair and functional.beta.multi, and for phylogenetic beta diversity with commands phylo.betapart.core, phylo.beta.pair and phylo.beta.multi.


Andrés Baselga, David Orme, Sébastien Villeger, Julien De Bortoli and Fabien Leprieur


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