getCodonSpecificQuantilesForCodon function

getCodonSpecificQuantilesForCodon

Method of Parameter class (access via parameter$, where parameter is an object initialized by initializeParameterObject). Calculate quantiles of CSP traces

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)
• probs: vector of two doubles between 0 and 1 indicating range over which to calculate quantiles. <0.0275, 0.975> would give 95% quantiles.
• 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.

Returns

vector representing lower and upper bound of quantile