divo: Tools for Analysis of Diversity and Similarity in Biological...

Description Author(s) References


The package divo implements various algorithms for empirical analysis of diversity and similarity (overlap) in biological or ecological systems. The implemented indices of diversity and overlap are based both on the information-theoretic and geometric considerations. The indices have the capacity to naturally up-weight or down-weight rare and abundant population species counts, by applying the Good-Turing sample coverage correction. The functional version of a diversity index, the so-called diversity profile, is also implemented along with the diversity and overlap indices inversions known as the effective numbers of species (ENS).
For examples and detailed information on specific functions, see their manual pages:

cvg Coverage
dp Diversity Profile
dp.ht Diversity Profile with the Horvitz-Thompson Correction
ens Effective Number of Species
ens.ht Effective Number of Species with the Horvitz-Thompson Correction
i.in Information Index (I-index) for 2-Way Table
i.inp Information Index (I-index) for 2-Way, 2 Column Table
ji Jaccard Index
li Sorensen Index
mh Morisita-Horn Index
pg Power-Geometric Index
pg.ht Power-Geometric Index with the Horvitz-Thompson Correction
rd Renyi's Divergence
srd Symmetrized Renyi's Divergence


Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak pietrzak.20@osu.edu


Rempala G.A., Seweryn M. (2013) Methods for diversity and overlap analysis in T-cell receptor populations. J Math Biol 67:1339-68

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