Likelihood of the BiSSeCo model given rates of variant mutation, selection, a dated tree, and effective population size over time
Usage
loglikelihood_bisseco(
parms,
mu,
gamma,
dtr,
Net,
augment_likelihood = TRUE,
res = 200,
...
)Arguments
- parms
a 3-vector containing parameters alpha (ratio substitution rate to variant relative to ancestral type), omega (relative fitness = 1+s) and yscale (population size adjustment)
- mu
Mean clock rate of evolution
- gamma
1 / generation time
- dtr
A phydynR::DatedTree
- Net
Effective population size through time. This is stored as a two column
- augment_likelihood
if TRUE (default), will combine the coalescent likelihood with a binomial likelihood of sampling variants or ancestral types under the assumption of random sampling and mutation-selection balance
- res
integer number of time points used for coalescent approximation matrix, such that the first column is time and the second column is population size
- ...
Additional parameters are passed to colik