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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 |
Maintainer: | Rampal S. Etienne <r.s.etienne at rug.nl> |
License: | GPL-3 |
NeedsCompilation: | yes |
In views: | Phylogenetics |
CRAN checks: | DDD results |
Reference manual: | DDD.pdf |
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 imports: | DAISIE, DAMOCLES, nodeSub, PBD, SADISA, secsse |
Reverse suggests: | nLTT, treestats |
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These binaries (installable software) and packages are in development.
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