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.Complete redesign of the package built on a tested, isolated compute engine.
hill_alpha(), hill_partition(),
hill_beta_to_dissim()); the user-facing hill*
functions are thin wrappers around it.prep_data()) that
checks names with setequal() and reorders
data to match the tree/distance matrix, fixing the silent-misalignment
behaviour of hilldiv2.as_hill_input() adapter accepting matrices, data
frames, tibbles, phyloseq and
TreeSummarizedExperiment objects.ape-based post-order tree traversal replaces
geiger::tips().hillprof() — diversity profiles across a sweep of q
values.hilleven() — evenness from Hill numbers.match_data() helper (previously only referenced in
the docs).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.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.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].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.vegan and hand-computed constants, plus edge cases (single
taxon, empty sample, q = 1).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.