Alpha and Beta Diversity Measures
Berger-Parker dominance
Binomial deviance and CY index of dissimilarity
Bray-Curtis distance
Balanced variation and abundance gradient components for abundance dat...
Canberra and related distances
Chebyshev distance
Correlation and cosine distance
Diversity measures implemented
Euclidean and related distances
Faith's phylogenetic diversity
Hamming distance
Beta diversity for presence/absence data
Nestedness and turnover components for presence/absence data
Kempton-Taylor Q index
Kullback-Leibler divergence
Manhattan and related distances
Margalef's richness index
Match vector of counts to phylogenetic tree
McIntosh dominance index D
McIntosh's evenness measure E
Menhinick's richness index
Minkowski distance
The Morisita index and Horn-Morisita index
Richness or number of observed species
Ruzicka or weighted Jaccard distance
Shannon diversity and related measures
Simpson's index and related measures
Strong's dominance index
UniFrac distance
Nestedness and turnover components of unweighted UniFrac distance
Weighted Kulczynski distance
A collection of measures for measuring ecological diversity. Ecological diversity comes in two flavors: alpha diversity measures the diversity within a single site or sample, and beta diversity measures the diversity across two sites or samples. This package overlaps considerably with other R packages such as 'vegan', 'gUniFrac', 'betapart', and 'fossil'. We also include a wide range of functions that are implemented in software outside the R ecosystem, such as 'scipy', 'Mothur', and 'scikit-bio'. The implementations here are designed to be basic and clear to the reader.