hilldiv3: Integral Analysis of Diversity Based on Hill Numbers

Measures and compares the diversity of biological communities (e.g. tables of operational taxonomic units (OTUs), amplicon sequence variants (ASVs) or metagenome-assembled genomes (MAGs)) based on Hill numbers, in a unified framework for neutral, phylogenetic and functional diversity measurement, diversity partitioning, (dis)similarity measurement, diversity profiles, evenness and redundancy. The statistical framework encompasses richness, Shannon and Simpson diversity, Faith's phylogenetic diversity (PD), Rao's quadratic entropy and Sorensen- and UniFrac-type dissimilarities, all grounded in a single Hill-number framework. Methods are described in Jost (2007) doi:10.1890/06-1736.1 , Chao et al. (2010) doi:10.1098/rstb.2010.0272 , Chiu et al. (2014) doi:10.1890/12-0960.1 and reviewed in Alberdi & Gilbert (2019) doi:10.1111/1755-0998.13014 . Optional import adapters interoperate with the Bioconductor packages 'phyloseq', 'SummarizedExperiment' and 'TreeSummarizedExperiment', which are available from https://bioconductor.org.

See also

Useful links:

• https://github.com/alberdilab/hilldiv3

• https://alberdilab.github.io/hilldiv3/

• Report bugs at https://github.com/alberdilab/hilldiv3/issues

Author

Maintainer: Antton Alberdi antton.alberdi@sund.ku.dk (ORCID)