Package: DDD
Type: Package
Title: Diversity-Dependent Diversification
Version: 5.2.5
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
Authors@R: c(
    person(given = "Rampal S.",
           family = "Etienne",
           email = "r.s.etienne@rug.nl",
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-2142-7612")),
    person(given = "Bart",
           family = "Haegeman",
           email = "bart.haegeman@sete.cnrs.fr",
           role = c("aut"),
           comment = c(ORCID = "0000-0003-2325-4727")),
    person(given = "Hanno",
           family = "Hildenbrandt",
           email = "h.hildenbrandt@rug.nl",
           role = c("ctb"),
           comment = c(ORCID = "0000-0002-6784-1037")),
    person(given = "Giovanni",
           family = "Laudanno",
           email = "glaudanno@gmail.com",
           role = c("ctb"),
           comment = c(ORCID = "0000-0002-2952-3345"))
           )
License: GPL-3
Encoding: UTF-8
Description: 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.
RoxygenNote: 7.3.3
Config/testthat/edition: 3
URL: https://rsetienne.github.io/DDD/
Config/pak/sysreqs: libglpk-dev libxml2-dev
Repository: https://rsetienne.r-universe.dev
Date/Publication: 2026-05-04 13:47:55 UTC
RemoteUrl: https://github.com/rsetienne/ddd
RemoteRef: HEAD
RemoteSha: e52af505d79bc35f8e3c1d9447b6783252a18d20
NeedsCompilation: yes
Packaged: 2026-06-24 08:46:19 UTC; root
Author: 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>)
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>