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:
|Diversity Profile with the Horvitz-Thompson Correction|
|Effective Number of Species|
|Effective Number of Species with the Horvitz-Thompson Correction|
|Information Index (I-index) for 2-Way Table|
|Information Index (I-index) for 2-Way, 2 Column Table|
|Power-Geometric Index with the Horvitz-Thompson Correction|
|Symmetrized Renyi's Divergence|
Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak [email protected]
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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