zetadiv: an R package for computing compositional change across multiple sites, assemblages or cases

Spatial variation in compositional diversity, or species turnover, is necessary for capturing the components of heterogeneity that constitute biodiversity. However, no incidence-based metric of pairwise species turnover can calculate all components of diversity partitioning. Zeta (ζ) diversity, the mean number of species shared by any given number of sites or assemblages, captures all diversity components produced by assemblage partitioning. zetadiv is an R package for analysing and measuring compositional change for occurrence data using zeta diversity. Four types of analyses are performed on bird composition data in Australia: (i) decline in zeta diversity; (ii) distance decay; (iii) multi-site generalised dissimilarity modelling; and (iv) hierarchical scaling. Some analyses, such as the zeta decline, are specific to zeta diversity, whereas others, such as distance decay, are commonly applied to beta diversity, and have been adapted using zeta diversity to differentiate the contribution of common and rare species to compositional change. Highlights An R package to analyse compositional change using zeta diversity is presented. Zeta diversity is the mean number of species shared by any number of assemblages Zeta diversity captures all diversity components produced by assemblage partitioning Analyses relate zeta diversity to space, environment and spatial scale Analyses differentiate the contribution of rare and common species to biodiversity