Creates an objective function
create.likelihood.log(hypothesis, addAttr=FALSE, …)Hypothesis for which to create the objective function
Whether to add attributes to the objective functions. There are two attributes: (1) “hypothesis” referencing the input hypothesis, (ii) ‘functions’ containing the individual objective functions per Locus. The latter contain further attributes.
Any named parameter to modify the hypothesis, e.g.
nUnknowns
A function
The objective function is created from the hypothesis. Itself, it takes as arguments the nuisance parameters and, optionally, the parameters for the penalty function. This particular flavor of the objective returns the sum of the log-likelihood and the sum of log-penalties across loci.
create.likelyhood.vectors, create.likelihood, penalties, Objective Functions