These functions compute the (log-)likelihood values for various coalescent models, including the constant-\(\Theta\) model and various time-dependent models.
dcoal(bt, theta, log = FALSE)
dcoal.step(bt, theta0, theta1, tau, log = FALSE)
dcoal.linear(bt, theta0, thetaT, log = FALSE)
dcoal.time(bt, theta0, rho, log = FALSE)
dcoal.time2(bt, theta0, rho1, rho2, tau, log = FALSE)a vector of coalescent times (typically from
branching.times).
population parameter THETA.
a logical value specifying whether the probabilities should be returned log-transformed.
THETA parameter for the time-dependent models.
breakpoint in time when the parameters change.
population (exponential) growth rates.
a numeric vector with (log-)likelihood values.
The models are detailed in a vignette: vignette("CoalescentModels").
Griffiths, R. C. and Tavar<U+00E9>, S. (1994) Sampling theory for neutral alleles in a varying environment. Philosophical Transactions of the Royal Society of London. Series B. Biological Sciences, 344, 403--410.
Kuhner, M. K., Yamato, J. and Felsenstein, J. (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429--434.