Package: treeducken
Type: Package
Title: Nested Phylogenetic Tree Simulator
Version: 1.1.0.9999
Authors@R: c(person("Wade", "Dismukes", email="wade.dismukes@gmail.com",
                    role=c("aut","cre")),
           person(c("Tracy","A."), "Heath", role=c("aut")),
           person("Josh", "Justison", role=c("ctb")),
           person("Damien", "de Vienne", role=c("ctb")),
           person("Liam", "Revell", role=c("ctb")),
           person("Emmanuel", "Paradis", role=c("ctb")),
           person("Klaus", "Schliep", role=c("ctb")),
           person("Ben", "Bolker", role=c("ctb")),
           person(c("Luke","J."), "Harmon", role=c("ctb")),
           person(c("Joseph","W."), "Brown", role=c("ctb")))
Description: Simulates nested phylogenetic trees (gene trees in species
        tree, symbiont trees in host trees) using birth-death processes
        and transfers between lineages. Simulations of gene trees
        within species trees are performed using a three-tree model
        with species trees, locus trees, and gene trees. The
        cophylogenetic birth-death process is used to simulate sets of
        host and symbiont trees with extant associations between tips.
        For more information about the three-tree model see: Mallo et
        al. (2015) <doi:10.1093/sysbio/syv082>, Rasmussen and Kellis
        (2012) <doi:10.1101/gr.123901.111>.
License: GPL-3
SystemRequirements: C++11
Imports: Rcpp (>= 1.0.2), apTreeshape, graphics, methods
Depends: ape
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 7.1.1
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Config/pak/sysreqs: make
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2023-03-19 16:35:31 UTC
RemoteUrl: https://github.com/wadedismukes/treeducken
RemoteRef: HEAD
RemoteSha: 032b92e3b4294f960854a0b497f6f87330db63ee
NeedsCompilation: yes
Packaged: 2026-05-28 06:01:47 UTC; root
Author: Wade Dismukes [aut, cre],
  Tracy A. Heath [aut],
  Josh Justison [ctb],
  Damien de Vienne [ctb],
  Liam Revell [ctb],
  Emmanuel Paradis [ctb],
  Klaus Schliep [ctb],
  Ben Bolker [ctb],
  Luke J. Harmon [ctb],
  Joseph W. Brown [ctb]
Maintainer: Wade Dismukes <wade.dismukes@gmail.com>