acfCSP {AnaCoDa}

Plots ACF for codon specific parameter traces

Description

The function calculates and by defaults plots the acf and estimates the autocorrelation in the trace

Usage

acfCSP(
  parameter,
  csp = "Mutation",
  numMixtures = 1,
  samples = NULL,
  lag.max = 40,
  plot = TRUE
)

Arguments

parameter

object of class Parameter

csp

indicates which parameter to calculate the autocorrelation. Must be Mutation (the default, ROC, FONSE), Selection (ROC, FONSE), Alpha (PA, PANSE), LambdaPrime (PA, PANSE), NSERate (PA, PANSE)"

numMixtures

indicates the number of CSP mixtures used

samples

number of samples at the end of the trace used to calculate the acf

lag.max

Maximum amount of lag to calculate acf. Default is 10*log10(N), where N i the number of observations.

plot

logical. If TRUE (default) a plot of the acf is created

See Also

acfMCMC