dcoal | R Documentation |
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)
bt |
a vector of coalescent times (typically from
|
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. |
The models are detailed in a vignette: vignette("CoalescentModels")
.
a numeric vector with (log-)likelihood values.
Emmanuel Paradis
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.
coalescentMCMC
, branching.times
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