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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: 5.2.2
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 ORCID iD [aut, cre], Bart Haegeman ORCID iD [aut], Hanno Hildenbrandt ORCID iD [ctb], Giovanni Laudanno ORCID iD [ctb]
Maintainer: Rampal S. Etienne <r.s.etienne at rug.nl>
License: GPL-3
NeedsCompilation: yes
In views: Phylogenetics
CRAN checks: DDD results

Documentation:

Reference manual: DDD.pdf

Downloads:

Package source: DDD_5.2.2.tar.gz
Windows binaries: r-devel: DDD_5.2.2.zip, r-release: DDD_5.2.2.zip, r-oldrel: DDD_5.2.2.zip
macOS binaries: r-release (arm64): DDD_5.2.2.tgz, r-oldrel (arm64): DDD_5.2.2.tgz, r-release (x86_64): DDD_5.2.2.tgz, r-oldrel (x86_64): DDD_5.2.2.tgz
Old sources: DDD archive

Reverse dependencies:

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=DDD to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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