pymcmcstat.structures package¶
pymcmcstat.structures.ParameterSet module¶
Created on Thu Jan 18 10:15:37 2018
@author: prmiles
pymcmcstat.structures.ResultsStructure module¶
Created on Wed Jan 17 09:18:19 2018
@author: prmiles
-
class
pymcmcstat.structures.ResultsStructure.
ResultsStructure
[source]¶ Bases:
object
Results from MCMC simulation.
Description: Class used to organize results of MCMC simulation.
- Attributes:
-
add_basic
(nsimu, covariance, parameters, rejected, simutime, theta)[source]¶ Add basic results from MCMC simulation to structure.
- Args:
- nsimu (
int
): Number of MCMC simulations. - model (
ModelSettings
): MCMC model settings. - covariance (
CovarianceProcedures
): Covariance variables. - parameters (
ModelParameters
): Model parameters. - rejected (
dict
): Dictionary of rejection stats. - simutime (
float
): Simulation run time in seconds. - theta (
ndarray
): Last sampled values.
- nsimu (
-
add_chain
(chain=None)[source]¶ Add chain to results structure.
- Args:
- chain (
ndarray
): Model parameter sampling chain.
- chain (
-
add_dram
(drscale, RDR, total_rejected, drsettings)[source]¶ Add results specific to performing DR algorithm.
- Args:
- drscale (
ndarray
): Reduced scale for sampling in DR algorithm. Default is [5,4,3]. - RDR (
ndarray
): Cholesky decomposition of covariance matrix based on DR. - total_rejected (
int
): Number of rejected samples. - drsettings (
DelayedRejection
): Need access to counters within DR class.
- drscale (
-
add_model
(model=None)[source]¶ Saves subset of features of the model settings in a nested dictionary.
- Args:
- model (
ModelSettings
): MCMC model settings.
- model (
-
add_options
(options=None)[source]¶ Saves subset of features of the simulation options in a nested dictionary.
- Args:
- options (
SimulationOptions
): MCMC simulation options.
- options (
-
add_prior
(mu, sigma, priortype)[source]¶ Add results specific to prior function.
- Args:
Note
This feature is not currently implemented.
-
add_random_number_sequence
(rndseq)[source]¶ Add random number sequence to results structure.
- Args:
- rndseq (
ndarray
): Sequence of sampled random numbers.
- rndseq (
Note
This feature is not currently implemented.
-
add_s2chain
(s2chain=None)[source]¶ Add observiation error chain to results structure.
- Args:
- s2chain (
ndarray
): Sampling chain of observation errors.
- s2chain (
-
add_sschain
(sschain=None)[source]¶ Add sum-of-squares chain to results structure.
- Args:
- sschain (
ndarray
): Calculated sum-of-squares error for each parameter chains set.
- sschain (
-
add_time_stats
(mtime, drtime, adtime)[source]¶ Add time spend using each sampling algorithm.
- Args:
Note
This feature is not currently implemented.
-
add_updatesigma
(updatesigma, sigma2, S20, N0)[source]¶ Add information to results structure related to observation error.
- Args:
If
updatesigma is True
, thenresults['sigma2'] = np.nan results['S20'] = S20 results['N0'] = N0
Otherwise
results['sigma2'] = sigma2 results['S20'] = np.nan results['N0'] = np.nan
-
classmethod
determine_filename
(options)[source]¶ Determine results filename.
If not specified by results_filename in the simulation options, then a default naming format is generated using the date string associated with the initialization of the simulation.
- Args:
- options (
SimulationOptions
): MCMC simulation options.
- options (
- Returns:
- filename (
str
): Filename string.
- filename (
-
export_simulation_results_to_json_file
(results)[source]¶ Export simulation results to a json file.
- Args:
- results (
ResultsStructure
): Dictionary of MCMC simulation results/settings.
- results (