Abstract
Hill numbers provide a powerful framework for measuring, estimating, comparing and partitioning the diversity of biological systems as characterised using high throughput DNA sequencing approaches. However, the implementation of Hill numbers in this context remains limited. In order to facilitate the implementation of Hill numbers into such analyses, whether focussing on diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses, we present a new R package. Hilldiv provides a set of functions to assist analysis of diversity based on Hill numbers, using OTU tables and associated phylogenetic trees as inputs. Multiple functionalities of the library are introduced, including (phylo)diversity measurement, (phylo)diversity profile plotting, (phylo)diversity comparison between samples and groups, (phylo)diversity partitioning and (dis)similarity measurement. All of these are grounded in abundance-based and incidence-based Hill numbers. We provide a supplement that demonstrates the main functions of the package using an OTU table representing the diet of eight bat species. The package can be directly installed from github (https://github.com/anttonalberdi/hilldiv).
