alpha_diversities |
Diversity measures implemented |
berger_parker_d |
Berger-Parker dominance |
beta_diversities |
Diversity measures implemented |
binomial_deviance |
Binomial deviance and CY index of dissimilarity |
bray_curtis |
Bray-Curtis distance |
bray_curtis_balanced |
Balanced variation and abundance gradient components for abundance data |
bray_curtis_components |
Balanced variation and abundance gradient components for abundance data |
bray_curtis_gradient |
Balanced variation and abundance gradient components for abundance data |
brillouin_d |
Shannon diversity and related measures |
canberra |
Canberra and related distances |
chebyshev |
Chebyshev distance |
chord |
Euclidean and related distances |
clark_coefficient_of_divergence |
Canberra and related distances |
correlation_distance |
Correlation and cosine distance |
cosine_distance |
Correlation and cosine distance |
cy_dissimilarity |
Binomial deviance and CY index of dissimilarity |
diversity_measures |
Diversity measures implemented |
dominance |
Simpson's index and related measures |
euclidean |
Euclidean and related distances |
faith_pd |
Faith's phylogenetic diversity |
faith_tree |
Example data for Faith's phylogenetic diversity |
generalized_unifrac |
UniFrac distance |
geodesic_metric |
Euclidean and related distances |
hamming |
Hamming distance |
heip_e |
Shannon diversity and related measures |
hellinger |
Euclidean and related distances |
horn_morisita |
The Morisita index and Horn-Morisita index |
information_unifrac |
UniFrac distance |
invsimpson |
Simpson's index and related measures |
jaccard |
Beta diversity for presence/absence data |
jaccard_components |
Nestedness and turnover components for presence/absence data |
jaccard_nestedness |
Nestedness and turnover components for presence/absence data |
jaccard_turnover |
Nestedness and turnover components for presence/absence data |
kempton_taylor_q |
Kempton-Taylor Q index |
kulczynski_first |
Beta diversity for presence/absence data |
kulczynski_second |
Beta diversity for presence/absence data |
kullback_leibler_divergence |
Kullback-Leibler divergence |
leprieur_tree |
Example data for phylogenetic nestedness and turnover components |
lozupone_panel_a |
Example data for UniFrac distance |
lozupone_panel_b |
Example data for UniFrac distance |
lozupone_tree |
Example data for UniFrac distance |
manhattan |
Manhattan and related distances |
margalef |
Margalef's richness index |
match_to_tree |
Match vector of counts to phylogenetic tree |
mcintosh_d |
McIntosh dominance index D |
mcintosh_e |
McIntosh's evenness measure E |
mean_character_difference |
Manhattan and related distances |
menhinick |
Menhinick's richness index |
minkowski |
Minkowski distance |
modified_mean_character_difference |
Manhattan and related distances |
morisita |
The Morisita index and Horn-Morisita index |
phylogenetic_alpha_diversities |
Diversity measures implemented |
phylogenetic_beta_diversities |
Diversity measures implemented |
phylosor |
UniFrac distance |
phylosor_nestedness |
Nestedness and turnover components of unweighted UniFrac distance |
phylosor_turnover |
Nestedness and turnover components of unweighted UniFrac distance |
pielou_e |
Shannon diversity and related measures |
richness |
Richness or number of observed species |
rms_distance |
Euclidean and related distances |
rogers_tanimoto |
Beta diversity for presence/absence data |
russel_rao |
Beta diversity for presence/absence data |
ruzicka |
Ruzicka or weighted Jaccard distance |
ruzicka_balanced |
Balanced variation and abundance gradient components for abundance data |
ruzicka_gradient |
Balanced variation and abundance gradient components for abundance data |
shannon |
Shannon diversity and related measures |
simpson |
Simpson's index and related measures |
simpson_e |
Simpson's index and related measures |
sokal_michener |
Beta diversity for presence/absence data |
sokal_sneath |
Beta diversity for presence/absence data |
sorenson |
Beta diversity for presence/absence data |
sorenson_nestedness |
Nestedness and turnover components for presence/absence data |
sorenson_turnover |
Nestedness and turnover components for presence/absence data |
strong |
Strong's dominance index |
unifrac |
UniFrac distance |
unifrac_components |
Nestedness and turnover components of unweighted UniFrac distance |
unweighted_unifrac |
UniFrac distance |
unweighted_unifrac_nestedness |
Nestedness and turnover components of unweighted UniFrac distance |
unweighted_unifrac_turnover |
Nestedness and turnover components of unweighted UniFrac distance |
variance_adjusted_unifrac |
UniFrac distance |
weighted_kulczynski_second |
Weighted Kulczynski distance |
weighted_normalized_unifrac |
UniFrac distance |
weighted_unifrac |
UniFrac distance |
yule_dissimilarity |
Beta diversity for presence/absence data |