dcoal {coalescentMCMC}

Density Functions of Some 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(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)

Arguments

bt

a vector of coalescent times (typically from branching.times).

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.

rho, rho1, rho2

population (exponential) growth rates.

Details

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

Value

a numeric vector with (log-)likelihood values.

Author(s)

Emmanuel Paradis

References

Griffiths, R. C. and Tavaré, 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, branching.times