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abdiv

Alpha and Beta Diversity Measures

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.

Functions (34)

berger_parker_d

Berger-Parker dominance

binomial_deviance

Binomial deviance and CY index of dissimilarity

bray_curtis

Bray-Curtis distance

bray_curtis_components

Balanced variation and abundance gradient components for abundance data

canberra

Canberra and related distances

chebyshev

Chebyshev distance

correlation_distance

Correlation and cosine distance

diversity_measures

Diversity measures implemented

euclidean

Euclidean and related distances

faith_pd

Faith's phylogenetic diversity

faith_tree

Example data for Faith's phylogenetic diversity

hamming

Hamming distance

jaccard

Beta diversity for presence/absence data

jaccard_components

Nestedness and turnover components for presence/absence data

kempton_taylor_q

Kempton-Taylor Q index

kullback_leibler_divergence

Kullback-Leibler divergence

leprieur_tree

Example data for phylogenetic nestedness and turnover components

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

menhinick

Menhinick's richness index

minkowski

Minkowski distance

morisita

The Morisita index and Horn-Morisita index

richness

Richness or number of observed species

ruzicka

Ruzicka or weighted Jaccard distance

shannon

Shannon diversity and related measures

simpson

Simpson's index and related measures

strong

Strong's dominance index

unifrac

UniFrac distance

unifrac_components

Nestedness and turnover components of unweighted UniFrac distance

weighted_kulczynski_second

Weighted Kulczynski distance

abdiv

Alpha and Beta Diversity Measures

v0.2.0
MIT + file LICENSE
Authors
Kyle Bittinger [aut, cre]
Initial release

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