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 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>.

Version: 3.1.1
Depends: R (≥ 4.1.0)
Imports: ape, cli, grDevices, graphics, methods, rlang, stats, utils
Suggests: cluster, furrr, future, ggplot2, knitr, patchwork, phyloseq, progressr, rmarkdown, SummarizedExperiment, testthat (≥ 3.0.0), tibble, TreeSummarizedExperiment, vegan
Published: 2026-10-16
DOI: 10.32614/CRAN.package.hilldiv3
Author: Antton Alberdi ORCID iD [aut, cre]
Maintainer: Antton Alberdi <antton.alberdi at sund.ku.dk>
BugReports: https://github.com/alberdilab/hilldiv3/issues
License: GPL-3
URL: https://github.com/alberdilab/hilldiv3, https://alberdilab.github.io/hilldiv3/
NeedsCompilation: no
Language: en-GB
Materials: README, NEWS
CRAN checks: hilldiv3 results

Documentation:

Reference manual: hilldiv3.html , hilldiv3.pdf
Vignettes: Getting started with hilldiv3 (source, R code)

Downloads:

Package source: hilldiv3_3.1.1.tar.gz
Windows binaries: r-devel: hilldiv3_3.0.0.zip, r-release: hilldiv3_3.0.0.zip, r-oldrel: hilldiv3_3.1.1.zip
macOS binaries: r-release (arm64): hilldiv3_3.1.1.tgz, r-oldrel (arm64): hilldiv3_3.1.1.tgz, r-release (x86_64): hilldiv3_3.1.1.tgz, r-oldrel (x86_64): hilldiv3_3.1.1.tgz
Old sources: hilldiv3 archive

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