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Calculate effective sample size for MCMC diagnostics

Source: R/diagnostics.R
effective_sample_size.Rd

Calculate effective sample size for MCMC diagnostics

Usage

effective_sample_size(
  results,
  parameter = "logpost",
  method = "autocorrelation"
)

Arguments

results

SNP-Slice results object

parameter

Parameter to analyze. Options include:

  • "logpost": Log posterior probability

  • "kstar": Number of active strains

  • "n_strains": Number of strains with non-zero allocations

  • "ktrunc": Truncation level

  • "mu": Stick-breaking weights (returns ESS for each weight)

  • "A": Allocation matrix (returns overall ESS)

  • "D": Dictionary matrix (returns overall ESS)

  • "all": Calculate ESS for all available parameters

method

Method for ESS calculation. Options:

  • "autocorrelation": Standard autocorrelation-based ESS (default)

  • "batch_means": Batch means method

  • "spectral": Spectral density method

Value

Effective sample size(s) and diagnostic information