TycheSVSGeneralSubstitutionModel

public class tyche.evolution.substitutionmodel.TycheSVSGeneralSubstitutionModel extends beastclassic.evolution.substitutionmodel.SVSGeneralSubstitutionModel

Extends SVSGeneralSubstitutionModel so that the rate matrix is stored and restored after rejected proposals.

double storedRateMatrix

BooleanParameter rateIndicator

public void initAndValidate()

Initialize and validate using SVSGeneralSubstitutionModel initAndValidate, and then set up storedRateMatrix.

public void getTransitionProbabilities(Node node, double startTime, double endTime, double rate, double matrix)

Get the transition probabilities, using SVSGeneralSubstitutionModel getTransitionProbabilities, and use rate indicator to address machine accuracy errors.

Parameters:

• node – the current node

• startTime – the start time of the branch

• endTime – the end time of the branch

• rate – the rate of the branch

• matrix – the double array to copy the transition probability matrix into

public void store()

Store the rate matrix so that it can be restored after rejected proposals.

public void restore()

Restore the rate matrix that was stored before the proposal.