initializeCovarianceMatrices: Initialize Covariance Matrices

In AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework

Description

Initialize Covariance Matrices

Usage

initializeCovarianceMatrices(
  parameter,
  genome,
  numMixtures,
  geneAssignment,
  init.csp.variance = 0.0025
)

Arguments

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.

Value

parameter Returns the Parameter argument, now modified with initialized mutation, selection, and covariance matrices.

AnaCoDa documentation built on Jan. 8, 2021, 2:37 a.m.