# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "rphylo" in publications use:'
type: software
license: GPL-3.0-only
title: 'rphylo: Phylogenetic Analysis with Dependent Discrete Models'
version: 0.1.1
abstract: 'Implementation of dependent discrete models (with reversible jump MCMC)
  derived from ''BayesTraits'' V5.0.3 <https://github.com/AndrewPMeade/BayesTraits-Release/tree/Release>.
  Original software copyright Andrew Meade and contributors, distributed under GPL-3.
  Modifications for this package by Vivian G. Li <liguo.vivian@gmail.com>. The following
  articles should be referenced when using this package: Pagel, M., A. Meade and D.
  Barker (2004) "Bayesian estimation of ancestral character states on phylogenies"
  <https://doi.org/10.1080/10635150490522232>; Pagel, M. (1994) "Detecting correlated
  evolution on phylogenies: a general method for the comparative analysis of discrete
  characters" <https://doi.org/10.1098/rspb.1994.0006>; Pagel, M. and A. Meade (2006)
  "Bayesian analysis of correlated evolution of discrete characters by reversible-jump
  Markov chain Monte Carlo" <https://doi.org/10.1086/503444>.'
authors:
- family-names: Li
  given-names: Vivian G.
  email: liguo.vivian@gmail.com
preferred-citation:
  type: manual
  title: 'rphylo: Phylogenetic analysis with dependent discrete models in R'
  authors:
  - family-names: Li
    given-names: Vivain G.
  year: '2026'
  notes: R package version 0.1.0
repository: https://cran.r-universe.dev
commit: 4fe9a951b652e24d1199c6724fc0b77d6fcd0629
date-released: '2026-06-23'
contact:
- family-names: Li
  given-names: Vivian G.
  email: liguo.vivian@gmail.com
references:
- type: article
  title: Bayesian estimation of ancestral character states on phylogenies
  authors:
  - family-names: Pagel
    given-names: M.
  - family-names: Meade
    given-names: A.
  - family-names: Barker
    given-names: D.
  journal: Systematic Biology
  volume: '53'
  issue: '5'
  year: '2004'
  start: 673-684
- type: article
  title: 'Detecting correlated evolution on phylogenies: a general method for the
    comparative analysis of discrete characters'
  authors:
  - family-names: Pagel
    given-names: M.
  journal: 'Proceedings of the Royal Society of London. Series B: Biological Sciences'
  volume: '255'
  issue: '1342'
  year: '1994'
  start: 37-45
- type: article
  title: Bayesian analysis of correlated evolution of discrete characters by reversible-jump
    Markov chain Monte Carlo
  authors:
  - family-names: Pagel
    given-names: M.
  - family-names: Meade
    given-names: A.
  journal: The American Naturalist
  volume: '167'
  issue: '6'
  year: '2006'
  start: 808-825