negTruncLogLike:
Negative truncated log-likelihood function
Description
The negative truncated log-likelihood function to maximize when fitting binomial mixture models to pan-genome data.
Usage
negTruncLogLike(p,y,core.p)
Arguments
p
Vector of parameters (mixing proportions and detection probabilities).
y
Vector of data, the number of gene families observed in 1, 2,...,N genomes.
core.p
The fixed detection probability of core genes.
Value
The negative log-likelihood value is returned, since the optimization algorithm used in binomixEstimate search for minima.
Details
This is the function optimized by binomixMachine when fitting a binomial mixture model to data, and not a function you would call otherwise. This function is only of interest for those who want to explore the computational details of the method.