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>, Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <doi:10.1111/2041-210X.12565> and Laudanno et al. 2021. Syst. Biol. 70: 389–407, <doi:10.1093/sysbio/syaa048>. Also contains functions to simulate the diversity-dependent process.

Version:	5.2.4
Depends:	R (≥ 3.5.0)
Imports:	deSolve, ape, phytools, subplex, DEoptim, Matrix, expm, SparseM, Rcpp (≥ 1.0.10)
LinkingTo:	Rcpp (≥ 1.0.10), RcppEigen, BH (≥ 1.81.0-1)
Suggests:	testthat (≥ 3.0.0), testit, igraph
Published:	2025-11-28
DOI:	10.32614/CRAN.package.DDD
Author:	Rampal S. Etienne [aut, cre], Bart Haegeman [aut], Hanno Hildenbrandt [ctb], Giovanni Laudanno [ctb]
Maintainer:	Rampal S. Etienne <r.s.etienne at rug.nl>
License:	GPL-3
URL:	https://rsetienne.github.io/DDD/
NeedsCompilation:	yes
In views:	Phylogenetics
CRAN checks:	DDD results

Documentation:

Reference manual:

DDD.html , DDD.pdf

Downloads:

Package source:	DDD_5.2.4.tar.gz
Windows binaries:	r-devel: DDD_5.2.4.zip, r-release: DDD_5.2.4.zip, r-oldrel: DDD_5.2.4.zip
macOS binaries:	r-release (arm64): DDD_5.2.4.tgz, r-oldrel (arm64): DDD_5.2.4.tgz, r-release (x86_64): DDD_5.2.4.tgz, r-oldrel (x86_64): DDD_5.2.4.tgz
Old sources:	DDD archive

Reverse dependencies:

Reverse imports:	DAISIE, DAMOCLES, nodeSub, PBD, SADISA, secsse, treestats
Reverse suggests:	nLTT

Linking:

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