PT  - JOURNAL ARTICLE
AU  - Antton Alberdi
AU  - M Thomas P Gilbert
TI  - hilldiv: an R package for the integral analysis of diversity based on Hill numbers
AID  - 10.1101/545665
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 545665
4099  - http://biorxiv.org/content/early/2019/02/10/545665.short
4100  - http://biorxiv.org/content/early/2019/02/10/545665.full
AB  - 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 package’s 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).