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Expectation maximization - Beta + Beta + Beta Distribution

Source: R/RcppExports.R
emstepB3.Rd

This function is made for the Bclean() function and preforms expectation maximization with Nelder-Mead numerical optimization for beta distribution.

Usage

emstepB3(parmlist, xi, niter, epsilon, trunc)

Arguments

parmlist

A list containing initial alpha, mean, and variance.

xi

Matrix where the first column is total coverage and the second is the count of base A or B.

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 \(c_{U}\).

Value

List of elements including the negative log likelihood, the number of iterates, and the optimized parameter values.

Examples

 if(exists("crazy")){
    xi <- (xm[,2]/xm[,1])
    tcalc <- alphabetacalcvec(mu = c(0.287, 0.50, 0.713),
                              var = c(0.01, 0.01, 0.01))
    set <-  list(avec = c(0.25, 0.25, 0.25, 0.125, 0.125),
                 t1vec = c(tcalc[,1], 0.5, 0.33),
                 t2vec = c(tcalc[,2], 0.33, 0.5))
    checkB <- emstepB3(set,
                       xi,
                       1000,
                       0.1,
                       c(0,0))
}