Parse TreePPL SMC output into a tidy data frame

Converts a JSON file from an SMC analysis produced by TreePPL into a single tidy tibble of particles, their samples, and normalized weights. The function internally removes sweeps with an undefined normalizing constant.

Usage

tp_parse_smc(json_path, wide = TRUE)

Arguments

json_path

The full path to the (SMC) JSON file 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 particle, containing:

sweep

Sweep index.

parameter

Parameter name, if present in the input JSON.

sample

Sampled value.

log_weight

Log weight of the particle.

norm_constant

Log normalizing constant for the sweep.

norm_weight

Normalized weight, rescaled so the maximum total log weight across all particles is 1.

Examples

if (FALSE) { # \dontrun{
# fit a CRBD model
run_smc <- tp_run(
  data = tp_data(data_input = "crbd"),
  sampler = tp_compile(
    model = "crbd",
    method = "smc-apf",
    sweeps = 2,
    particles = 10
  )
)

# get the path to the output JSON file:
out_file <- list.files(
  path = tp_tempdir(),
  pattern = "out",
  full.names = TRUE
)

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