Calculates the Effective Sample Sizes from a parsed BEAST2 log file

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_all <- parse_beast_log( get_tracerer_path("beast2_example_output.log") ) # Remove burn-ins estimates <- remove_burn_ins(estimates_all, burn_in_fraction = 0.1 ) # Calculate the effective sample sizes of all parameter estimates esses <- calc_esses( estimates, sample_interval = 1000 ) expected <- c(10, 10, 10, 10, 7, 10, 9, 6) testit::assert(all(esses == expected))