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Calculates the density dependent likelihood of a phylogenetic tree. It takes branching and sampling times as an argument and integrates the likelihoood function over the whole tree.
● Data Source:
CranContrib
● Keywords: likelihood, phylogenetics
● Alias: runExpoTree
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Simulate an instance of an epidemic outbreak along with a sampled transmission tree.
● Data Source:
CranContrib
● Keywords: likelihood, phylogenetics
● Alias: sim.epi
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Converts an 'epi' object from a simulation of 'sim.epi' to 'phylo' format (ape).
● Data Source:
CranContrib
● Keywords: ape, phylo, phylogeny
● Alias: epi2tree
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Creates a (or adds to an existing) plot of the lineages-through-time of a list of phylogenetic trees.
● Data Source:
CranContrib
● Keywords: likelihood, phylogenetics
● Alias: plotLTT
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Calculates the likelihood of a phylogenetic tree without density dependence. It takes branching and sampling times as an argument and integrates the likelihoood function over the whole tree.
● Data Source:
CranContrib
● Keywords: likelihood, phylogenetics
● Alias: infExpoTree
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Extract branching and sampling times from a tree in the native ape format.
● Data Source:
CranContrib
● Keywords: ape, phylo, phylogeny
● Alias: ape2time
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Perform optimization to find a maximum likelihood estimate.
● Data Source:
CranContrib
● Keywords: likelihood, phylogenetics
● Alias: expoTree.optim
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Calculates the density dependent likelihood of a phylogenetic tree. It takes branching and sampling times as an argument and integrates the likelihoood function over the whole tree.
● Data Source:
CranContrib
● Keywords: phylodynamics
● Alias: expoTree, expoTree-package
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providing 
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