acfCSP function

Plots ACF for codon specific parameter traces

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

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