BAT – Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity

Summary Novel algorithms have been recently developed to estimate alpha and partition beta diversity in all their dimensions (taxon, phylogenetic and functional diversity – TD , PD and FD ), whether communities are completely sampled or not. The R package BAT – Biodiversity Assessment Tools – performs a number of analyses based on either species identities ( TD ) or trees depicting species relationships ( PD and FD ). Functions include building randomized accumulation curves for alpha and beta diversity, alpha diversity estimation from incomplete samples and the partitioning of beta diversity in its replacement and richness difference components. All functions allow the rarefaction of communities. Estimation methods include curve‐fitting and nonparametric algorithms. Beta diversity indices include the Jaccard and Sørensen families of measures and deal with both incidence and abundance data. Two auxiliary functions that allow judging the efficiency of the algorithms are also included. Several examples are shown using the data included in the package, which demonstrate the usefulness of the different methods. The BAT package constitutes an open platform for further development of new biodiversity assessment tools.