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 [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_3.1.1.zip, r-release: hilldiv3_3.1.1.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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