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 |
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