Diversity-Dependent Diversification R package DDD version 5.2.5 CRAN Task View: Phylogenetics (https://CRAN.R-project.org/view=Phylogenetics) 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. Software Depends: R (>= 3.5.0) Imports: deSolve, ape, phytools, subplex, DEoptim, pso, 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 Rampal S. Etienne <r.s.etienne@rug.nl> Comprehensive R Archive Network (CRAN) Rampal S. Etienne [aut, cre] (ORCID: <https://orcid.org/0000-0003-2142-7612>), Bart Haegeman [aut] (ORCID: <https://orcid.org/0000-0003-2325-4727>), Hanno Hildenbrandt [ctb] (ORCID: <https://orcid.org/0000-0002-6784-1037>), Giovanni Laudanno [ctb] (ORCID: <https://orcid.org/0000-0002-2952-3345>) GPL-3 2026-05-04 application/tgz https://CRAN.R-project.org/package=DDD doi:10.32614/CRAN.package.DDD