initializeCovarianceMatrices: Initialize Covariance Matrices

Description Usage Arguments Value

View source: R/parameterObject.R

Description

Initialize Covariance Matrices

Usage

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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.