Population Parameter THETA Using Genealogy
This function estimates the population parameter THETA from a genealogy (coded a as phylogenetic tree) under the coalescent.
an object of class
a numeric vector.
a logical specifying whether to estimate
a logical specifying whether to use analytical
formulae to estimate
a logical specifying whether to return the likelihoods on a
log scale (the default); ignored if
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
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.
fixed = FALSE, a list with two elements:
the maximum likelihood estimate of THETA;
the log-likelihood at its maximum.
fixed = TRUE, a numeric vector with the [log-]likelihood
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.
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