This function calculates the log-likelihood using the expectation maximization algorithm with Nelder-Mead numerical optimization and beta distribution with one uniform mixture.
Arguments
- parmlist
A list containing initial alpha, mean, and variance values.
- xi
List of observations, in this case allele frequencies.
- niter
Max number of iterates.
- epsilon
Epsilon value for convergence tolerance. When the absolute delta log-likelihood is below this value, convergence is reached.
- trunc
List of two values representing the lower and upper bounds, $c_L$ and $c_U$.
- type
String indicating model type. Options: "free" (estimated parameter(s): alpha, mean, and variance), "fixed" (estimated parameter(s): alpha), "fixed_2" (estimated parameter(s): alpha and variance), or "fixed_3" (estimated parameter(s): variance). If avec is length of 1, fixed and fixed_3 will not be able to return a log-likelihood.