Package index • hilldiv3

Diversity measurement

Compute neutral, phylogenetic or functional Hill numbers and their derived diagnostics.

hilldiv(): Hill numbers computation
hillprof(): Diversity profile across a range of orders
plot(<hill_profile>): Plot a diversity profile
hilleven(): Hill-number evenness

Partitioning and (dis)similarity

Decompose diversity across samples and turn beta into bounded (dis)similarity metrics.

hillpart(): Hill numbers diversity partitioning
hilldiss(): Hill numbers-based dissimilarity
hillsim(): Hill numbers-based similarity
hillpair(): Pairwise Hill numbers-based dissimilarity

Redundancy

How much phylogenetic/functional structure is duplicated across taxa.

hillred(): Hill numbers redundancy
plot(<hill_redundancy>): Plot a redundancy fit

Data preparation

Normalise, build functional distances, and align inputs.

tss(): Total Sum Scaling normalisation
traits2dist(): Convert a trait table into a distance matrix
match_data(): Match and align a count table to a tree or distance matrix

Datasets

Bundled simulated gut-microbiome example data.

gut_counts: Simulated gut microbiome MAG count table
gut_tree: Phylogeny for the simulated gut MAGs
gut_traits: Functional traits for the simulated gut MAGs

Package

hilldiv3 hilldiv3-package: hilldiv3: Integral Analysis of Diversity Based on Hill Numbers