getCodonSpecificPosteriorVarianceForCodon {AnaCoDa}

getCodonSpecificPosteriorVarianceForCodon

Description

Method of Parameter class (access via parameter$<function name>, where parameter is an object initialized by initializeParameterObject). Calculate codon-specific parameter (CSP) variance

Arguments

mixtureElement

mixture to calculate CSP variance. Should be between 1 and n, where n is number of mixtures.

samples

number of samples to use for calculating variance

codon

codon to calculate CSP

paramType

CSP to calculate variance for. 0: Mutation (ROC,FONSE) or Alpha (PA, PANSE). 1: Selection (ROC,FONSE), Lambda (PANSE), Lambda^prime (PA). 2: NSERate (PANSE)

unbiased

If TRUE, should calculate variance using unbiased (N-1). Otherwise, used biased (N) correction

withoutReference

If model uses reference codon, then ignore this codon (fixed at 0). Should be TRUE for ROC and FONSE. Should be FALSE for PA and PANSE.

log_scale

If true, calculate posterior mean on log scale. Should only be used for PA and PANSE.

Value

variance over trace for CSP