statistical inference and modeling of genealogies generated by epidemic and ecological processes


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Documentation for package ‘rcolgem’ version 0.0.5

Help Pages

binaryDatedTree Create binary dated tree. The binaryDatedTree class includes heights for each node and other helper variables
calculate.cluster.size.moments.from.model Calculate cluster size moments from model
calculate.cluster.size.moments.from.tree Calculate cluster size moments from tree
coalescent.log.likelihood Compute the likelihood of a gene genealogy conditonal on a demographic history.
phylo.source.attribution Compute infector probabilities between all pairs of sampled lineages.
simulate.binary.dated.tree Simulate a binary dated tree using a coalescent model and given a demographic history