theta.tree: Population Parameter THETA Using Genealogy
In dwinter/Pegas: Population and Evolutionary Genetics Analysis System

Description Usage Arguments Details Value Author(s) References See Also Examples

This function estimates the population parameter THETA from a genealogy (coded a as phylogenetic tree) under the coalescent.

1	theta.tree(phy, theta, fixed = FALSE, log = TRUE)

`phy`	an object of class `"phylo"`.
`theta`	a numeric vector.
`fixed`	a logical specifying whether to estimate `theta` (the default), or to return the likelihoods for all values in `theta`.
`log`	a logical specifying whether to return the likelihoods on a log scale (the default); ignored if `fixed = FALSE`.

The tree phy is considered as a genealogy, and therefore should be ultrametric. By default, THETA is estimated by maximum likelihood and the value given in theta is used as starting value for the minimisation function (if several values are given as a vector the first one is used). If fixed = TRUE, then the [log-]likelihood values are returned corresponding to each value in theta.

The present implementation does a numerical optimisation of the log-likelihood function (with nlminb) with the first partial derivative as gradient. It is possible to solve the latter and have a direct analytical MLE of THETA (and its standard-error), but this does not seem to be faster.

If fixed = FALSE, a list with two elements:

`theta`	the maximum likelihood estimate of THETA;
`logLik`	the log-likelihood at its maximum.

If fixed = TRUE, a numeric vector with the [log-]likelihood values.

Emmanuel Paradis

Kingman, J. F. C. (1982) The coalescent. Stochastic Processes and their Applications, 13, 235–248.

Kingman, J. F. C. (1982) On the genealogy of large populations. Journal of Applied Probability, 19A, 27–43.

Wakeley, J. (2009) Coalescent Theory: An Introduction. Greenwood Village, CO: Roberts and Company Publishers.

theta.h, theta.s, theta.k

tr <- rcoal(50) # assumes theta = 1
theta.tree(tr, 10)
## profile log-likelihood:
THETA <- seq(0.5, 1.5, 0.01)
logLikelihood <- theta.tree(tr, THETA, fixed = TRUE)
plot(THETA, logLikelihood, type = "l")