Package: hilldiv3
Title: Integral Analysis of Diversity Based on Hill Numbers
Version: 3.0.0
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 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>.
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
RoxygenNote: 7.3.3
NeedsCompilation: no
Packaged: 2026-09-26 03:27:49 UTC; anttonalberdi
Author: Antton Alberdi [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2875-6446>)
Maintainer: Antton Alberdi <antton.alberdi@sund.ku.dk>
Repository: CRAN
Date/Publication: 2026-10-06 16:40:02 UTC
Built: R 4.5.2; ; 2026-10-06 18:41:24 UTC; unix
