coalescentMCMC (version 0.4-1)

dcoal: Density Functions of Various Time-Dependent Coalescent Models

Description

These functions compute the (log-)likelihood values for various coalescent models, including the constant-\(\Theta\) model and various time-dependent models.

Usage

dcoal(phy, theta, log = FALSE)
dcoal.step(phy, theta0, theta1, tau, log = FALSE)
dcoal.linear(phy, theta0, thetaT, TMRCA, log = FALSE)
dcoal.time(phy, theta0, rho, log = FALSE)
dcoal.time2(phy, theta0, rho1, rho2, tau, log = FALSE)

Arguments

phy

a tree of class "phylo".

theta

population parameter THETA.

log

a logical value specifying whether the probabilities should be returned log-transformed.

theta0, theta1, thetaT

THETA parameter for the time-dependent models.

tau

breakpoint in time when the parameters change.

TMRCA

time to most recent ancestor.

rho, rho1, rho2

population (exponential) growth rates.

Value

a numeric vector with (log-)likelihood values.

Details

The models are detailed in a vignette: vignette("CoalescentModels").

References

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.

See Also

coalescentMCMC