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: 389â407, <doi:10.1093/sysbio/syaa048>. Also contains functions to simulate the diversity-dependent process.
Version: 5.2.2 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: 2023-07-10 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 NeedsCompilation: yes In views: Phylogenetics CRAN checks: DDD results Documentation: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=DDD to link to this page.
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