morpho.processors.sampling.PyStanSamplingProcessor module

Some template vars

Members: PyStanSamplingProcessor

Functions:

Classes:

PyStan sampling processor Authors: J. Formaggio, J. Johnston, M. Guigue, T. Weiss Date: 06/26/18

Summary

Data:

Reference

class morpho.processors.sampling.PyStanSamplingProcessor.PyStanSamplingProcessor(name)

Bases: morpho.processors.BaseProcessor.BaseProcessor

Sampling processor that will call PyStan.

Parameters:

• model_code (required) – location of the Stan model
• function_files_location – location of the Stan functions
• model_name – name of the cached model
• cache_dir – location of the cache folder (containing cached models)
• input_data – dictionary containing model input data
• iter (required) – total number of iterations (warmup and sampling)
• warmup – number of warmup iterations (default=iter/2)
• chain – number of chains (default=1)
• n_jobs – number of parallel cores running (default=1)
• interestParams – parameters to be saved in the results variable
• no_cache – don’t create cache
• force_recreate – force the cache regeneration
• init – initial values for the parameters
• control – PyStan sampling settings

Input:

data: dictionary containing model input data

Results:

results: dictionary containing the result of the sampling of the parameters of interest

data

gen_arg_dict()

InternalConfigure(params)

Method called by Configure() to set up the object. Must be overridden by child class.

InternalRun()

Method called by Run() to run the object. Must be overridden by child class.