Run a TreePPL sampler — tp

Executes a compiled TreePPL sampler on the given data, saves the raw JSON output to disk, prints a run summary, and, when a parser is available for the model/method combination, parses the output into tidy data frames.

Usage

tp_run(
  sampler,
  data,
  dir = NULL,
  out_file_name = "out",
  n_runs = 1,
  n_processes = 3,
  verbose = TRUE,
  ...
)

Arguments

sampler: a sampler produced by tp_compile().
data: input data, produced by tp_data().
dir: the full path to the directory where you want to save the output. Defaults to tp_tempdir().
out_file_name: the name of the output file in JSON format. Defaults to "out".
n_runs: (integer) the number of sweeps (SMC) or runs (MCMC).
n_processes: (integer) the number of parallel processes to use. Cannot be greater than n_runs.
verbose: (logical) Whether to print a run summary on completion. Default is TRUE.
...: See tp_runtime_options() for all supported arguments.

Value

If a parser is available for the model/method combination, a parsed tidy data frame of TreePPL output via tp_parse_smc() or tp_parse_mcmc(). Otherwise, the full path(s) to the raw JSON output file(s), along with a console message explaining that no parser is available.

Details

If the model belongs to a category without an available parser (e.g. "host-repertoire-evolution", "tree-inference"), or if the inference method is neither SMC nor MCMC, no parsing is attempted: a message is printed pointing to the output directory, and the raw output file path(s) are returned instead.

Examples

if (FALSE) { # \dontrun{
# When using SMC
# compile model and create SMC inference machinery
exe_path <- tp_compile(model = "coin", method = "smc-bpf", particles = 2000)

# prepare data
data_path <- tp_data(data_input = "coin")

# run TreePPL
result <- tp_run(exe_path, data_path, n_runs = 2)


# When using MCMC
# compile model and create MCMC inference machinery
exe_path <- tp_compile(model = "coin", method = "mcmc-naive", iterations = 2000)

# prepare data
data_path <- tp_data(data_input = "coin")

# run TreePPL
result <- tp_run(exe_path, data_path)
} # }