hilldiv3: a unified Hill-number framework for neutral, phylogenetic and functional diversity analysis in R

Abstract

1. Hill numbers provide a coherent family of diversity measures that can incorporate phylogenetic relatedness and functional trait dissimilarity, but applying them consistently across neutral, phylogenetic and functional diversity, and across measurement, partitioning and (dis)similarity, still requires combining several packages with incompatible conventions. 2. We present hilldiv3, an R package that provides per-sample diversity, nested multiplicative partitioning across scales for all three diversity types, bounded (dis)similarities and pairwise matrices, diversity profiles, evenness and redundancy, and the allocation of Hill power sums and dissimilarities to taxa or taxonomic sets. 3. hilldiv3 directly supported all twelve benchmarked combinations of operation and diversity type, and built pairwise (dis)similarity matrices 15-820 times faster than hilldiv2 and hillR, with up to two orders of magnitude less memory. We showcased the package by analysing Microflora Danica data (360 samples, 5,518 genomes, eight habitats), demonstrating that neutral, phylogenetic and functional diversity turned over at very different rates between habitats, and a near-constant Actinomycetota share concealed opposing shifts of two orders. 4. By deriving every metric from the same Hill-number formulation, hilldiv3 makes neutral, phylogenetic and functional results directly comparable, and lowers the barrier to rigorous diversity analysis of community-ecology and high-throughput sequencing data.