Li VG (2026). rphylo: Phylogenetic analysis with dependent discrete models in R. R package version 0.1.0.

Pagel M, Meade A, Barker D (2004). “Bayesian estimation of ancestral character states on phylogenies.” Systematic Biology, 53(5), 673-684.

Pagel M (1994). “Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters.” Proceedings of the Royal Society of London. Series B: Biological Sciences, 255(1342), 37-45.

Pagel M, Meade A (2006). “Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo.” The American Naturalist, 167(6), 808-825.

Corresponding BibTeX entries:

  @Manual{,
    title = {{rphylo}: Phylogenetic analysis with dependent discrete
      models in R},
    author = {Vivain G. Li},
    year = {2026},
    note = {R package version 0.1.0},
  }

  @Article{,
    title = {Bayesian estimation of ancestral character states on
      phylogenies},
    author = {M. Pagel and A. Meade and D. Barker},
    journal = {Systematic Biology},
    volume = {53},
    number = {5},
    pages = {673-684},
    year = {2004},
  }

  @Article{,
    title = {Detecting correlated evolution on phylogenies: a general
      method for the comparative analysis of discrete characters},
    author = {M. Pagel},
    journal = {Proceedings of the Royal Society of London. Series B:
      Biological Sciences},
    volume = {255},
    number = {1342},
    pages = {37-45},
    year = {1994},
  }

  @Article{,
    title = {Bayesian analysis of correlated evolution of discrete
      characters by reversible-jump Markov chain Monte Carlo},
    author = {M. Pagel and A. Meade},
    journal = {The American Naturalist},
    volume = {167},
    number = {6},
    pages = {808-825},
    year = {2006},
  }