Constructing random cophylogenetic trees and analysing their statistics

cophylogeny | Creates a cophylogeny object |

get_branchNThroughTime | Branch (species) numbers through time. |

get_GDist | Calculating the distance matrix between host branches alive... |

get_hostShifts | Counting parasite host-jumps. |

get_infectionFrequencies | Distribution of parasite numbers on the tips of a... |

get_infectionFrequenciesSubtrees | Parasite infection frequency per host subtree. |

get_infectionStatistics | Basic statistics describing a cophylogeny. |

get_PEventsThroughTime | Numbers of different events in parasite evolution. |

get_PextinctionTime | Parasite lineage extinction time |

get_PHDistCorrelation | Correlation between pairwise distances of associated hosts... |

get_PHDistSubtreeCorrelation | Correlation between pairwise distances of associated hosts... |

plot.cophylogeny | Cophylogeny plot |

print.cophylogeny | Printing a cophylogeny |

prune_Cophylo | A function that prunes a cophylogeny and plots the resulting... |

rcophylo | Simulate cophylogenies |

rcophylo_HP | Cophylogeny simulation |

rcophylo_HresP | Cophylogeny simulation |

rcophylo_PonH | Cophylogeny simulation on an existing host tree. |

rphylo_H | Phylogenetic (host) tree simulation |

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