R: Initialize Covariance Matrices

initializeCovarianceMatrices {AnaCoDa}

R Documentation

Initialize Covariance Matrices

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.

[Package AnaCoDa version 0.1.4.4 Index]