Package index • ecodive

Phylogenetic Alpha Diversity

faith(): Faith's PD

Classic Alpha Diversity

chao1(): Chao1

shannon(): Shannon

simpson(): Simpson

inv_simpson(): Inverse Simpson

Phylogenetic Beta Diversity

unweighted_unifrac(): Unweighted UniFrac

weighted_unifrac(): Weighted UniFrac

weighted_normalized_unifrac(): Normalized UniFrac

generalized_unifrac(): Generalized UniFrac

variance_adjusted_unifrac(): Variance Adjusted UniFrac

Classic Beta Diversity

bray_curtis(): Bray-Curtis

canberra(): Canberra

euclidean(): Euclidean

gower(): Gower

jaccard(): Jaccard

kulczynski(): Kulczynski

manhattan(): Manhattan

Utility

read_tree(): Read a newick formatted phylogenetic tree.

rarefy(): Rarefy OTU counts.

n_cpus(): Number of CPU Cores

Datasets

ex_counts: Example counts matrix

ex_tree: Example phylogenetic tree