Package index

Alpha Diversity

alpha_div()

Alpha Diversity Wrapper Function

ace() berger() brillouin() chao1() faith() fisher() inv_simpson() margalef() mcintosh() menhinick() observed() shannon() simpson() squares()

Alpha Diversity Metrics

Beta Diversity

beta_div()

Beta Diversity Wrapper Function

aitchison() bhattacharyya() bray() canberra() chebyshev() chord() clark() divergence() euclidean() gower() hellinger() horn() jensen() jsd() lorentzian() manhattan() matusita() minkowski() morisita() motyka() psym_chisq() soergel() squared_chisq() squared_chord() squared_euclidean() topsoe() wave_hedges() hamming() jaccard() ochiai() sorensen() unweighted_unifrac() weighted_unifrac() normalized_unifrac() generalized_unifrac() variance_adjusted_unifrac()

Beta Diversity Metrics

Programmatic Access

list_metrics() match_metric()

Find and Browse Available Metrics

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