Diversity-Dependent Diversification

Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, , Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, . Also contains functions to simulate the diversity-dependent process.


Reference manual

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5.0 by Rampal S. Etienne, 2 months ago

Browse source code at https://github.com/cran/DDD

Authors: Rampal S. Etienne & Bart Haegeman

Documentation:   PDF Manual  

Task views: Phylogenetics, Especially Comparative Methods

GPL-3 license

Imports deSolve, ape, phytools, subplex, Matrix, expm, SparseM, Rcpp

Suggests testthat, testit

Linking to Rcpp, BH

Imported by DAISIE, DAMOCLES, PBD, SADISA, secsse.

Suggested by nLTT.

See at CRAN