Calculates the density dependent likelihood of a phylogenetic tree. It takes branching and sampling times as an argument and integrates the likelihood function over the whole tree.
|Author||Gabriel E Leventhal, partly adapted from MATLAB code by Awad H. Al-Mohy and using the routines DLNAC1 and DLARPC by Sheung Hun Cheng, and DLAPST from ScaLAPACK.|
|Date of publication||2013-09-03 14:12:55|
|Maintainer||Gabriel E Leventhal <email@example.com>|
|License||BSD_3_clause + file LICENCE|
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.