polychron.models.MCMCData Module

MCMCData dataclass

Dataclass containing all of the MCMC results.

This enables lighter-weight "save" behavior

Note

Optional[foo] must be used rather than from __future__ import annotations and foo | None in python 3.9 due to use of get_type_hints

contexts class-attribute instance-attribute

contexts: List[str] = field(default_factory=list)

List of contexts passed in to and returned by run_MCMC, stored in topological order

accept_samples_context class-attribute instance-attribute

accept_samples_context: List[List[float]] = field(default_factory=list)

A list of accepted samples from the MCMC process.

The number of accepted samples is important.

Formerly StartPage.ACCEPT

accept_samples_phi class-attribute instance-attribute

accept_samples_phi: List[List[float]] = field(default_factory=list)

Accepted group boundaries from MCMC simulation

Formerly StartPage.PHI_ACCEPT

A class-attribute instance-attribute

A: int = field(default=0)

The newer limit for the Cal BP range to be considered considered during MCMC, denoting the most recent time.

Formerly StartPage.A

P class-attribute instance-attribute

P: int = field(default=0)

The older limit for the Cal BP range to be considered considered during MCMC

Formerly StartPage.P

all_samples_context class-attribute instance-attribute

all_samples_context: List[List[float]] = field(default_factory=list)

A list of lists containing all samples for contexts from MCMC, including rejected samples.

I.e. accept_samples_context is a subset of this.

Formerly StartPage.ALL_SAMPS_CONT

all_samples_phi class-attribute instance-attribute

all_samples_phi: List[List[float]] = field(default_factory=list)

A list of lists, containing all samples for group boundaries from MCMC, including rejected samples.

I.e. accept_samples_phi is a subset of this.

Formerly StartPage.ALL_SAMPS_PHI

accept_group_limits class-attribute instance-attribute

accept_group_limits: Dict[str, List[float]] = field(default_factory=dict)

A dictionary of group limits from accepted phi samples. Produced in phase_labels.

Formerly StartPage.resultsdict

all_group_limits class-attribute instance-attribute

all_group_limits: Dict[str, List[float]] = field(default_factory=dict)

A dictionary of all_results? returned by MCMC_func, which is used to find the phase lengths during node finding on the results page.

Formerly StartPage.all_results_dict

calibration_curve_name class-attribute instance-attribute

calibration_curve_name: str = 'intcal20_interpolated'

Name of the calibration curve which was used to generate this MCMCData. This enables the correct curve to be displayed on the dating results tab when the curve has been changed, but the model has not been re-calibrated.

save_results_dataframes

save_results_dataframes(path: Path, group_df: DataFrame) -> None

Save some MCMC data to disk, separately from the serialised version of this class

Formerly part of StartPage.save_state_1

Parameters:

Name	Type	Description	Default
path	Path	The path to the directory in which files should be created	required
group_df	DataFrame	A pandas dataframe containing context group information.	required

Todo

• Check if full_results_df include the first 10000 elements or not?

to_json

to_json(pretty: bool = False) -> str

Serialise this object to JSON

Parameters:

Name	Type	Description	Default
pretty	bool	If the json should be prettified or not.	False

Return

JSON string representing the MCMCData instance

save

save(path: Path, group_df: DataFrame, verbose: bool = False) -> None

Save the current state of this file to the specified path

Parameters:

Name	Type	Description	Default
path	Path	The directory in which the files will be saved.	required
group_df	DataFrame	A pandas dataframe containing context group information	required
verbose	bool	If verbose output should be used	False

Raises:

Type	Description
RuntimeError	If the provided path is not a directory
Exception	If other exceptions are raised during saving of files to disk

load_from_disk classmethod

load_from_disk(json_path: Path) -> MCMCData

Get an instance of the MCMCData from serialised json on disk.

Parameters:

Name	Type	Description	Default
json_path	Path	Path to json file to load it from	required

Returns:

Type	Description
MCMCData	MCMCData instance

Raises:

Type	Description
RuntimeError	If the json_path is not an existing file; or the 'polychron_version' key is missing from the json file'; or the 'mcmc_data' key is missing from the json file
JSONDecodeError	If the json_path does not point to a valid json file