Alpha and Beta Diversity Measures

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Documentation for package ‘abdiv’ version 0.2.0

• DESCRIPTION file.
• Package NEWS.

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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