DDD: Diversity-Dependent Diversification

Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <doi:10.1098/rspb.2011.1439>. Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence. See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <doi:10.1086/667574>. Finally, DDD contains a function to simulate the diversity-dependent process.

Version: 3.2
Depends: R (≥ 3.0.2), deSolve, ape, ade4
Imports: phytools, subplex, Matrix, expoRkit, SparseM
Published: 2016-02-09
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne at rug.nl>
License: GPL-3
NeedsCompilation: no
In views: Phylogenetics
CRAN checks: DDD results

Downloads:

Reference manual: DDD.pdf
Package source: DDD_3.2.tar.gz
Windows binaries: r-devel: DDD_3.2.zip, r-release: DDD_3.2.zip, r-oldrel: DDD_3.2.zip
OS X Snow Leopard binaries: r-release: DDD_3.2.tgz, r-oldrel: DDD_2.7.tgz
OS X Mavericks binaries: r-release: DDD_3.2.tgz
Old sources: DDD archive

Reverse dependencies:

Reverse imports: PBD