CPM Regression

CPMRegression

This class handles the process of performing CPM Regression with cross-validation and permutation testing.

__init__(results_directory, cv=KFold(n_splits=10, shuffle=True, random_state=42), inner_cv=None, edge_selection=UnivariateEdgeSelection(edge_statistic=['pearson'], edge_selection=[PThreshold(threshold=[0.05], correction=[None])]), select_stable_edges=True, stability_threshold=0.8, impute_missing_values=True, n_permutations=0, atlas_labels=None)

Initialize the CPMRegression object.

Parameters:

Name	Type	Description	Default
results_directory	str	Directory to save results.	required
cv	Union[BaseCrossValidator, BaseShuffleSplit]	Outer cross-validation strategy.	KFold(n_splits=10, shuffle=True, random_state=42)
inner_cv	Union[BaseCrossValidator, BaseShuffleSplit]	Inner cross-validation strategy for edge selection.	None
edge_selection	UnivariateEdgeSelection	Method for edge selection.	UnivariateEdgeSelection(edge_statistic=['pearson'], edge_selection=[PThreshold(threshold=[0.05], correction=[None])])
impute_missing_values	bool	Whether to impute missing values.	True
n_permutations	int	Number of permutations to run for permutation testing.	0
atlas_labels	str	CSV file containing atlas and regions labels.	None

calculate_p_values(true_results, perms) staticmethod

Calculate p-values based on true results and permutation results.

:param true_results: DataFrame with the true results. :param perms: DataFrame with the permutation results. :return: DataFrame with the calculated p-values.

estimate(X, y, covariates)

Estimates a model using the provided data and conducts permutation testing. This method first fits the model to the actual data and subsequently performs estimation on permuted data for a specified number of permutations. Finally, it calculates permutation results.

Parameters:

Name	Type	Description	Default
X	Union[DataFrame, ndarray]		required
y	Union[Series, DataFrame, ndarray]		required
covariates	Union[Series, DataFrame, ndarray]		required

load_configuration(results_directory, config_filename)

Load configuration from a file.

:param results_directory: Directory to set for results. :param config_filename: Path to the configuration file.

save_configuration(config_filename)

Saves the current configuration settings to a file in Pickle format. All attributes related to the configuration of the object are serialized and stored in a file with the same base name as the provided filename, but with a .pkl extension.

:param config_filename: The base name of the file where the configuration will be saved. :return: None