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, redundancy and attribution of Hill power-sum weight and beta dissimilarity to taxa and sets. 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)