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| expoTree-package | 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 (ape). |
| expoTree | Calculate density dependent likelihood of a phylogenetic tree |
| expoTree.optim | Perform optimization to find a maximum likelihood estimate. |
| 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. |