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>.

Version:	3.0.0
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:	2026-10-06
DOI:	10.32614/CRAN.package.hilldiv3 (may not be active yet)
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_3.0.0.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): hilldiv3_3.0.0.tgz, r-oldrel (arm64): hilldiv3_3.0.0.tgz, r-release (x86_64): hilldiv3_3.0.0.tgz, r-oldrel (x86_64): hilldiv3_3.0.0.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=hilldiv3 to link to this page.