getCodonSpecificQuantilesForCodon {AnaCoDa} | R Documentation |

## getCodonSpecificQuantilesForCodon

### Description

Method of Parameter class (access via parameter$<function name>, 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. |

### Value

vector representing lower and upper bound of quantile

*AnaCoDa*version 0.1.4.4 Index]