Changes in version 3.1.0.9000                      

  - Added hillcontrib() to rank taxa or named sets by their additive
    contributions to pairwise or collective Hill dissimilarity. It
    supports neutral, phylogenetic and functional diversity and all four
    dissimilarity metrics. Collective comparisons can be run for named
    groups of samples.
  - Functional partitioning now handles an all-zero distance matrix
    through the shared functional-similarity kernel.
  - Expanded the gut microbiome vignette with MAG power-sum shares and
    an illustrated example of MAG contributions to dissimilarity.

                        Changes in version 3.1.0                        

  - Added hillshare() to allocate neutral, phylogenetic and functional
    Hill power-sum weight to individual taxa or named sets. Its first
    allocation method is "qpower"; empty samples have undefined (NA)
    shares.
  - Functional Hill numbers now handle all-zero distance matrices and
    empty samples consistently: identical taxa have diversity 1, and
    empty samples have diversity 0.

                        Changes in version 3.0.1                        

  - Added contributing guidelines (CONTRIBUTING.md), a code of conduct,
    issue templates, citation metadata (CITATION.cff) and the full GPL-3
    licence text, and a Journal of Open Source Software paper (paper/).
  - Breaking: the out = "matrix" form of the per-sample functions
    (hilldiv(), hillprof(), hilleven()) now returns samples in rows and
    diversity orders (q0, q1, ...) in columns, instead of the previous
    orders-in-rows/samples-in-columns layout. This matches the usual
    observations-in-rows convention and joins cleanly with per-sample
    metadata. Code that indexed these matrices by ["q0", ] should switch
    to [, "q0"] (or transpose). The component/metric matrices from
    hillpart(), hilldiss() and hillred() are unchanged.
  - hilldiv() and friends now accept count tables whose first column
    holds taxa names: a leading non-numeric column is automatically
    promoted to row names (instead of failing with "Count data must be
    numeric"). Any other non-numeric column raises a clear error asking
    the user to fix the input.
  - Verbose output now reports the number of taxa and samples being
    analysed.

                 Changes in version 3.0.0 (2026-10-06)                  

First published on CRAN on 6 October 2026.

Complete redesign of the package built on a tested, isolated compute
engine.

Architecture

  - Math separated into an internal, unit-tested engine (hill_alpha(),
    hill_partition(), hill_beta_to_dissim()); the user-facing hill*
    functions are thin wrappers around it.
  - Single validation/alignment layer (prep_data()) that checks names
    with setequal() and reorders data to match the tree/distance matrix,
    fixing the silent-misalignment behaviour of hilldiv2.
  - New as_hill_input() adapter accepting matrices, data frames,
    tibbles, phyloseq and TreeSummarizedExperiment objects.
  - Fast ape-based post-order tree traversal replaces geiger::tips().

New features

  - hillprof() — diversity profiles across a sweep of q values.
  - hilleven() — evenness from Hill numbers.
  - Real match_data() helper (previously only referenced in the docs).
  - Tidy output by default. hilldiv(), hillpart(), hilldiss(),
    hillsim(), hilleven(), hillprof() and hillred() now return
    long-format data.frames with print(), plot() and (when ggplot2 is
    installed) autoplot() methods. Pass out = "matrix" for the legacy
    shape.
  - Explicit type argument — type = c("auto", "neutral", "phylogenetic",
    "functional") on every entry point; "auto" keeps input-based
    detection, an explicit value asserts and validates the diversity
    type.
  - hillpair() computes the type-specific structure once over all
    samples and reuses it per pair (no more full re-partition per pair),
    and reports a progressr bar when available.
  - Bundled, documented example data: gut_counts, gut_tree, gut_traits.
  - reference argument on hilldiv() — reference = c("pool", "sample")
    selects the reference tree depth for phylogenetic Hill numbers.
    "pool" (default) reads every sample at one common depth T =
    mean(T_j) so values are mutually comparable (hilldiv2's multi
    behaviour); "sample" reads each sample at its own depth T_j. The two
    coincide on ultrametric trees. The option is deliberately absent
    from hillpart(), where T is fixed at the Chiu et al. (2014) mean
    per-sample depth — the unique value for which gamma / alpha is a
    valid decomposition with beta in [1, N].

Bug fixes

  - Phylogenetic hilldiv() alpha corrected. The per-sample phylogenetic
    Hill number previously raised branch length L_i to the power q along
    with abundance ((L_i a_i / T)^q), which matched no standard quantity
    and disagreed with the partition engine. Branch length is now a
    linear weight ((L_i / T) a_i^q, Chao et al. 2010), so q = 0 recovers
    Faith's PD / T and the per-sample value matches hillpart() alpha at
    a single sample. This changes phylogenetic hilldiv() and hillprof()
    outputs relative to earlier 3.0.0 development snapshots.

Infrastructure

  - Added test-coverage (Codecov) and lint (lintr) GitHub Actions
    workflows.
  - Added golden-value tests cross-checking the engine against vegan and
    hand-computed constants, plus edge cases (single taxon, empty
    sample, q = 1).

Compatibility

  - The hilldiv(), hillpart(), hilldiss(), hillsim(), hillpair(),
    hillred(), tss() and traits2dist() names from hilldiv2 are
    preserved. The default return shape is now a tidy data.frame; use
    out = "matrix" for the hilldiv2-style matrix.