DDD: 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, <doi:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <doi:10.1086/667574> and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <doi:10.1111/2041-210X.12565>. Also contains functions to simulate the diversity-dependent process.

Version: 3.7
Depends: R (≥ 3.0.2), deSolve, ape, ade4
Imports: phytools, subplex, Matrix, expm, SparseM, pracma, testthat
Published: 2018-04-24
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne at rug.nl>
License: GPL-3
NeedsCompilation: yes
In views: Phylogenetics
CRAN checks: DDD results

Downloads:

Reference manual: DDD.pdf
Package source: DDD_3.7.tar.gz
Windows binaries: r-devel: DDD_3.7.zip, r-release: DDD_3.7.zip, r-oldrel: DDD_3.7.zip
OS X binaries: r-release: DDD_3.7.tgz, r-oldrel: DDD_3.6.tgz
Old sources: DDD archive

Reverse dependencies:

Reverse imports: DAISIE, PBD, SADISA
Reverse suggests: nLTT

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