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Calculates the Effective Sample Sizes from a parsed BEAST2 log file

Source: R/calc_esses.R
calc_esses.Rd

Calculates the Effective Sample Sizes from a parsed BEAST2 log file

Usage

calc_esses(traces, sample_interval)

Arguments

traces

a dataframe with traces with removed burn-in

sample_interval

the interval in timesteps between samples

Value

the effective sample sizes

Author

Richèl J.C. Bilderbeek

Examples

# Parse an example log file
estimates <- parse_beast_tracelog_file(
  get_tracerer_path("beast2_example_output.log")
)

# Calculate the effective sample sizes of all parameter estimates
calc_esses(estimates, sample_interval = 1000)
#>   posterior likelihood prior treeLikelihood TreeHeight BirthDeath birthRate2
#> 1        11         11    11             11          8         11         11
#>   relativeDeathRate2
#> 1                  7