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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. [ABSTRACT FROM AUTHOR]

Summary: Complete sampling of all dimensions of biodiversity is a formidable task, even for small areas. Undersampling is the norm, and the underquantification of diversity is a common outcome. Estimators of taxon diversity (TD) are widely used to correct for undersampling. Yet, no similar strategy has been developed for phylogenetic (PD) or functional (FD) diversity. We propose three ways of estimating PD and FD, building on estimators originally developed for TD: (i) correcting PD and FD values based on the completeness of TD; (ii) fitting asymptotic functions to accumulation curves of PD and FD; and (iii) adapting nonparametric estimators to PD and FD data. Using trees as a common framework for the estimation of PD and FD, we tested the approach with European mammal and Azores Islands arthropod data. We demonstrated that different methods were able to considerably reduce the undersampling bias and often correctly estimated true diversity using a fraction of the samples necessary to reach complete sampling. Besides the utility of knowing the true diversity of an assemblage from incomplete samples, the use of estimators may present further advantages. For instance, comparisons between sites or time periods are possible only if either sampling is complete or sampling effort is equivalent and sufficient to allow sensible comparisons. Also, as PD and FD asymptote faster than TD, comparisons between these different dimensions may require unbiased values. The framework now proposed combines taxon, phylogenetic and functional diversity into a single framework, offering a tool for future developments involving these different facets of biological diversity. [ABSTRACT FROM AUTHOR]