R: Alpha and Beta Diversity Measures

# Alpha and Beta Diversity Measures

## Documentation for package ‘abdiv’ version 0.2.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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