Package index • ecodive

Alpha Diversity

alpha_div(): Alpha diversity wrapper

Phylogenetic

faith(): Faith's PD

Classic

observed(): Observed Features

chao1(): Chao1

shannon(): Shannon

simpson(): Simpson

inv_simpson(): Inverse Simpson

Beta Diversity

beta_div(): Beta diversity wrapper

Phylogenetic

unweighted_unifrac(): Unweighted UniFrac

weighted_unifrac(): Weighted UniFrac

normalized_unifrac(): Normalized UniFrac

generalized_unifrac(): Generalized UniFrac

variance_adjusted_unifrac(): Variance Adjusted UniFrac

Classic

bray_curtis() sorenson(): 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

metrics as_alpha_metric() as_beta_metric(): API for browsing functions

Datasets

ex_counts: Example counts matrix

ex_tree: Example phylogenetic tree