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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