Calculate density dependent likelihood of a phylogenetic tree

ape2time | Convert tree from 'phylo' format (ape) to event time format. |

epi2tree | Convert an 'epi' object from 'sim.epi' to 'phylo' format... |

expoTree.optim | Perform optimization to find a maximum likelihood estimate. |

expoTree-package | Calculate density dependent likelihood of a phylogenetic tree |

infExpoTree | Likelihood calculation without density dependence. |

plotLTT | Plot lineages through time. |

runExpoTree | Density-dependent likelihood caluculation |

sim.epi | Simulates epidemic outbreaks and sampled transmission trees. |

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