Package index • ecodive

Alpha Diversity

Calculate within-sample diversity using various indices.

alpha_div(): Alpha Diversity Wrapper Function

Richness metrics

Estimators focused on the number of species (richness).

ace(): Abundance-based Coverage Estimator (ACE)
chao1(): Chao1 Richness Estimator
margalef(): Margalef's Richness Index
menhinick(): Menhinick's Richness Index
observed(): Observed Features
squares(): Squares Richness Estimator

Diversity metrics

Indices accounting for both richness and evenness.

brillouin(): Brillouin Index
fisher(): Fisher's Alpha
inv_simpson(): Inverse Simpson Index
shannon(): Shannon Diversity Index
simpson(): Gini-Simpson Index

Dominance metrics

Indices focused on the abundance of the most dominant species.

berger(): Berger-Parker Index
mcintosh(): McIntosh Index

Phylogenetic metrics

Diversity based on phylogenetic branch lengths.

faith(): Faith's Phylogenetic Diversity (PD)

Beta Diversity

Calculate between-sample similarity or distance.

beta_div(): Beta Diversity Wrapper Function

Abundance metrics

Distance measures using quantitative abundance data.

aitchison(): Aitchison distance
bhattacharyya(): Bhattacharyya distance
bray(): Bray-Curtis dissimilarity
canberra(): Canberra distance
chebyshev(): Chebyshev distance
chord(): Chord distance
clark(): Clark's divergence distance
divergence(): Divergence
euclidean(): Euclidean distance
gower(): Gower distance
hellinger(): Hellinger distance
horn(): Horn-Morisita dissimilarity
jensen(): Jensen-Shannon distance
jsd(): Jensen-Shannon divergence (JSD)
lorentzian(): Lorentzian distance
manhattan(): Manhattan distance
matusita(): Matusita distance
minkowski(): Minkowski distance
morisita(): Morisita dissimilarity
motyka(): Motyka dissimilarity
psym_chisq(): Probabilistic Symmetric Chi-Squared distance
soergel(): Soergel distance
squared_chisq(): Squared Chi-Squared distance
squared_chord(): Squared Chord distance
squared_euclidean(): Squared Euclidean distance
topsoe(): Topsoe distance
wave_hedges(): Wave Hedges distance

Presence/Absence metrics

Distance measures using binary (presence/absence) data.

hamming(): Hamming distance
jaccard(): Jaccard distance
ochiai(): Otsuka-Ochiai dissimilarity
sorensen(): Dice-Sorensen dissimilarity

Phylogenetic metrics

Distance measures based on phylogenetic branch lengths (UniFrac family).

unweighted_unifrac(): Unweighted UniFrac
weighted_unifrac(): Weighted UniFrac
normalized_unifrac(): Normalized Weighted UniFrac
generalized_unifrac(): Generalized UniFrac (GUniFrac)
variance_adjusted_unifrac(): Variance-Adjusted Weighted UniFrac

Utilities & Helpers

Tools for programmatic access, data manipulation, and configuration.

list_metrics() match_metric(): Find and Browse Available Metrics
read_tree(): Read a newick formatted phylogenetic tree.
rarefy(): Rarefy Observation Counts
n_cpus(): Number of CPU Cores

Datasets

Example data provided with the package.

ex_counts: Example counts matrix
ex_tree: Example phylogenetic tree