Parse TreePPL MCMC output into a tidy data frame

Converts JSON file(s) produced by an MCMC analysis in TreePPL into a single tidy tibble of samples, one row per iteration.

Usage

tp_parse_mcmc(json_path, wide = TRUE)

Arguments

json_path

The full path to the (MCMC) JSON file(s) produced by TreePPL.

wide

Logical. If TRUE (default), return the data frame in wide format, with one column per parameter. If FALSE, return the data frame in long format, with parameter names and values stored in parameter and sample columns.

Value

A tibble with one row per iteration, containing:

run

Run index.

parameter

Parameter name, if present in the input JSON.

sample

Sampled value.

Examples

if (FALSE) { # \dontrun{

# Let's use a quick CRBD model as example
run_mcmc <- tp_run(
sampler = tp_compile(model = "crbd", method = "mcmc", iterations = 10),
data = tp_data(data_input = "crbd"),
n_runs = 2, # this will produce two JSON files as output
n_processes = 2
)

# get the path to the output JSON file; note that the number of JSON
# files produced is equal to n_runs specified above
out_file <- list.files(
  path = tp_tempdir(),
  pattern = "out",
  full.names = TRUE
)

# parse JSON to a tidy data frame
tp_parse_mcmc(json_path = out_file)
} # }