hilldiv: an R package for the integral analysis of diversity based on Hill numbers

Abstract

O_LIHill 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. C_LIO_LIIn 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. C_LIO_LIMultiple 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. C_LIO_LIWe provide a supplement that demonstrates the packages main functions using an OTU table representing the diet of eight bat species. The package can be directly installed from github (https://github.com/anttonalberdi/hilldiv). C_LI