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

In divo: Tools for Analysis of Diversity and Similarity in Biological Systems

Description

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

Author(s)

Christoph Sadee, Maciej Pietrzak, Michal Seweryn, Cankun Wang, Grzegorz Rempala
Maintainer: Maciej Pietrzak [e-mail]

References

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

divo documentation built on Dec. 18, 2019, 1:51 a.m.