Package: hilldiv3
Title: Integral Analysis of Diversity Based on Hill Numbers
Version: 3.1.0.9000
Authors@R: 
    person("Antton", "Alberdi", , "antton.alberdi@sund.ku.dk", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-2875-6446"))
Description: 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>.
License: GPL-3
Language: en-GB
URL: https://github.com/alberdilab/hilldiv3,
        https://alberdilab.github.io/hilldiv3/
BugReports: https://github.com/alberdilab/hilldiv3/issues
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
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Repository: https://alberdilab.r-universe.dev
Date/Publication: 2026-10-08 08:28:12 UTC
RemoteUrl: https://github.com/alberdilab/hilldiv3
RemoteRef: HEAD
RemoteSha: 263360c04c265e3a60aadbcd8c41acaaf6f631ec
NeedsCompilation: no
Packaged: 2026-10-08 09:19:57 UTC; root
Author: Antton Alberdi [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2875-6446>)
Maintainer: Antton Alberdi <antton.alberdi@sund.ku.dk>