getCodonSpecificPosteriorVarianceForCodon: getCodonSpecificPosteriorVarianceForCodon

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

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

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