Initialize Covariance Matrices
initializeCovarianceMatrices( parameter, genome, numMixtures, geneAssignment, init.csp.variance = 0.0025 )
parameter: A Parameter object that corresponds to one of the model types. Valid values are "ROC", "PA", and "FONSE".genome: An object of type Genome necessary for the initialization of the Parameter object.numMixtures: The number of mixture elements for the underlying mixture distribution (numMixtures > 0).geneAssignment: A vector holding the initial mixture assignment for each gene. The vector length has to equal the number of genes in the genome. Valid values for the vector range from 1 to numMixtures. It is possible but not advised to leave a mixture element empty.init.csp.variance: initial proposal variance for codon specific parameter, default is 0.0025.parameter Returns the Parameter argument, now modified with initialized mutation, selection, and covariance matrices.