Rev Language Reference

Trace - Trace of numeric parameter values.

Corresponds to a single column of a log file, usually produced by the `mnModel` monitor in an MCMC or MCMCMC run.

Details

Method description: - `getBurnin()`: Return the number of samples that were discarded as burnin, after thinning. - `getValues()`: Return a vector (e.g. `Real[]`) containing the values of the sampled parameter, after excluding burnin samples. - `setBurnin()`: Modify the number (if >= 1) or fraction (if < 1) of samples to discard as burnin, after thinning. - `size()`, `getNumberSamples()`: Report the number of values stored in `trace`, including (`post = FALSE`) or excluding (`post = TRUE`) burnin samples. - `summarize()`: Display summary statistics of trace.

Example

# Read in a log file as a vector of traces
traces = readTrace("out.log", burnin = 0)

# Get the posterior trace (2nd column in the log file)
posterior = traces[2]
posterior.getBurnin() # will return 0

# Change burnin from 0 to 50 samples
posterior.setBurnin(50)
posterior.getBurnin() # will return 50

# Get summary statistics
posterior.summarize()

Methods

  • getBurnin()
  • getNumberSamples(Bool post)
  • getValues()
  • setBurnin(Probability burnin)
  • size(Bool post)
  • summarize()

See Also

Edit this page