Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
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923 lines
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923 lines
49 KiB
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<li class="toctree-l2"><a class="reference internal" href="examples.html#parameters-estimation-example">Parameters Estimation Example</a></li>
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<li class="toctree-l2"><a class="reference internal" href="examples.html#structure-estimation-example">Structure Estimation Example</a></li>
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<a href="#A"><strong>A</strong></a>
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| <a href="#C"><strong>C</strong></a>
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| <a href="#D"><strong>D</strong></a>
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| <a href="#E"><strong>E</strong></a>
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| <a href="#F"><strong>F</strong></a>
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| <a href="#G"><strong>G</strong></a>
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| <a href="#H"><strong>H</strong></a>
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| <a href="#I"><strong>I</strong></a>
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| <a href="#M"><strong>M</strong></a>
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| <a href="#O"><strong>O</strong></a>
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| <a href="#P"><strong>P</strong></a>
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| <a href="#R"><strong>R</strong></a>
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| <a href="#S"><strong>S</strong></a>
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| <a href="#T"><strong>T</strong></a>
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| <a href="#V"><strong>V</strong></a>
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</div>
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<h2 id="A">A</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter">AbstractImporter (class in classes.utility.abstract_importer)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.abstract_sample_path.AbstractSamplePath">AbstractSamplePath (class in classes.structure_graph.abstract_sample_path)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.set_of_cims.SetOfCims.actual_cims">actual_cims() (classes.structure_graph.set_of_cims.SetOfCims property)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.add_edge">add_edge() (classes.structure_graph.structure.Structure method)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.add_edges">add_edges() (classes.structure_graph.network_graph.NetworkGraph method)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.add_nodes">add_nodes() (classes.structure_graph.network_graph.NetworkGraph method)</a>
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</li>
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<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator.adjacency_matrix">adjacency_matrix() (classes.estimators.structure_estimator.StructureEstimator method)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="B">B</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="classes.structure_graph.html#classes.structure_graph.set_of_cims.SetOfCims.build_cims">build_cims() (classes.structure_graph.set_of_cims.SetOfCims method)</a>
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</li>
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<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator.build_complete_graph">build_complete_graph() (classes.estimators.structure_estimator.StructureEstimator static method)</a>
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</li>
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<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.build_list_of_samples_array">build_list_of_samples_array() (classes.utility.abstract_importer.AbstractImporter method)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.build_p_comb_structure_for_a_node">build_p_comb_structure_for_a_node() (classes.structure_graph.network_graph.NetworkGraph static method)</a>
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</li>
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<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator.build_removable_edges_matrix">build_removable_edges_matrix() (classes.estimators.structure_estimator.StructureEstimator method)</a>
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</li>
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<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.build_sorter">build_sorter() (classes.utility.abstract_importer.AbstractImporter method)</a>
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<ul>
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<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.build_sorter">(classes.utility.json_importer.JsonImporter method)</a>
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</li>
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<li><a href="classes.utility.html#classes.utility.sample_importer.SampleImporter.build_sorter">(classes.utility.sample_importer.SampleImporter method)</a>
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</li>
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</ul></li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="classes.structure_graph.html#classes.structure_graph.abstract_sample_path.AbstractSamplePath.build_structure">build_structure() (classes.structure_graph.abstract_sample_path.AbstractSamplePath method)</a>
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<ul>
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<li><a href="classes.structure_graph.html#classes.structure_graph.sample_path.SamplePath.build_structure">(classes.structure_graph.sample_path.SamplePath method)</a>
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</li>
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</ul></li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.build_time_columns_filtering_for_a_node">build_time_columns_filtering_for_a_node() (classes.structure_graph.network_graph.NetworkGraph static method)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.build_time_scalar_indexing_structure_for_a_node">build_time_scalar_indexing_structure_for_a_node() (classes.structure_graph.network_graph.NetworkGraph static method)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.set_of_cims.SetOfCims.build_times_and_transitions_structures">build_times_and_transitions_structures() (classes.structure_graph.set_of_cims.SetOfCims method)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.abstract_sample_path.AbstractSamplePath.build_trajectories">build_trajectories() (classes.structure_graph.abstract_sample_path.AbstractSamplePath method)</a>
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<ul>
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<li><a href="classes.structure_graph.html#classes.structure_graph.sample_path.SamplePath.build_trajectories">(classes.structure_graph.sample_path.SamplePath method)</a>
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</li>
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</ul></li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.build_transition_filtering_for_a_node">build_transition_filtering_for_a_node() (classes.structure_graph.network_graph.NetworkGraph static method)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.build_transition_scalar_indexing_structure_for_a_node">build_transition_scalar_indexing_structure_for_a_node() (classes.structure_graph.network_graph.NetworkGraph static method)</a>
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</li>
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</ul></td>
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</tr></table>
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<h2 id="C">C</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="classes.utility.html#classes.utility.cache.Cache">Cache (class in classes.utility.cache)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix.cim">cim() (classes.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
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</li>
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<li>
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classes
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<ul>
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<li><a href="classes.html#module-classes">module</a>
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</li>
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</ul></li>
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<li>
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classes.estimators
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<ul>
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<li><a href="classes.estimators.html#module-classes.estimators">module</a>
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</li>
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</ul></li>
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<li>
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classes.estimators.fam_score_calculator
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<ul>
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<li><a href="classes.estimators.html#module-classes.estimators.fam_score_calculator">module</a>
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</li>
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</ul></li>
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<li>
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classes.estimators.parameters_estimator
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<ul>
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<li><a href="classes.estimators.html#module-classes.estimators.parameters_estimator">module</a>
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</li>
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</ul></li>
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<li>
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classes.estimators.structure_constraint_based_estimator
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<ul>
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<li><a href="classes.estimators.html#module-classes.estimators.structure_constraint_based_estimator">module</a>
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</li>
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</ul></li>
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<li>
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classes.estimators.structure_estimator
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<ul>
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<li><a href="classes.estimators.html#module-classes.estimators.structure_estimator">module</a>
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</li>
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</ul></li>
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<li>
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classes.estimators.structure_score_based_estimator
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<ul>
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<li><a href="classes.estimators.html#module-classes.estimators.structure_score_based_estimator">module</a>
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</li>
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</ul></li>
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<li>
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classes.optimizers
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<ul>
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<li><a href="classes.optimizers.html#module-classes.optimizers">module</a>
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</li>
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</ul></li>
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<li>
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classes.optimizers.constraint_based_optimizer
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<ul>
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<li><a href="classes.optimizers.html#module-classes.optimizers.constraint_based_optimizer">module</a>
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</li>
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</ul></li>
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<li>
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classes.optimizers.hill_climbing_search
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<ul>
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<li><a href="classes.optimizers.html#module-classes.optimizers.hill_climbing_search">module</a>
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</li>
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</ul></li>
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<li>
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classes.optimizers.optimizer
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<ul>
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<li><a href="classes.optimizers.html#module-classes.optimizers.optimizer">module</a>
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</li>
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</ul></li>
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<li>
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classes.optimizers.tabu_search
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<ul>
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<li><a href="classes.optimizers.html#module-classes.optimizers.tabu_search">module</a>
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</li>
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</ul></li>
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<li>
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classes.structure_graph
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<ul>
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<li><a href="classes.structure_graph.html#module-classes.structure_graph">module</a>
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</li>
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</ul></li>
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<li>
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classes.structure_graph.abstract_sample_path
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<ul>
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<li><a href="classes.structure_graph.html#module-classes.structure_graph.abstract_sample_path">module</a>
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</li>
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</ul></li>
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<li>
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classes.structure_graph.conditional_intensity_matrix
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<ul>
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<li><a href="classes.structure_graph.html#module-classes.structure_graph.conditional_intensity_matrix">module</a>
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</li>
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</ul></li>
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<li>
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classes.structure_graph.network_graph
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<ul>
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<li><a href="classes.structure_graph.html#module-classes.structure_graph.network_graph">module</a>
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</li>
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</ul></li>
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<li>
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classes.structure_graph.sample_path
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<ul>
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<li><a href="classes.structure_graph.html#module-classes.structure_graph.sample_path">module</a>
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</li>
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</ul></li>
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<li>
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classes.structure_graph.set_of_cims
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<ul>
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<li><a href="classes.structure_graph.html#module-classes.structure_graph.set_of_cims">module</a>
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</li>
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</ul></li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li>
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classes.structure_graph.sets_of_cims_container
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<ul>
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<li><a href="classes.structure_graph.html#module-classes.structure_graph.sets_of_cims_container">module</a>
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</li>
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</ul></li>
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<li>
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classes.structure_graph.structure
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<ul>
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<li><a href="classes.structure_graph.html#module-classes.structure_graph.structure">module</a>
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</li>
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</ul></li>
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<li>
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classes.structure_graph.trajectory
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<ul>
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<li><a href="classes.structure_graph.html#module-classes.structure_graph.trajectory">module</a>
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</li>
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</ul></li>
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<li>
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classes.utility
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<ul>
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<li><a href="classes.utility.html#module-classes.utility">module</a>
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</li>
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</ul></li>
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<li>
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classes.utility.abstract_importer
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<ul>
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<li><a href="classes.utility.html#module-classes.utility.abstract_importer">module</a>
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</li>
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</ul></li>
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<li>
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classes.utility.cache
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<ul>
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<li><a href="classes.utility.html#module-classes.utility.cache">module</a>
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</li>
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</ul></li>
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<li>
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classes.utility.decorators
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<ul>
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<li><a href="classes.utility.html#module-classes.utility.decorators">module</a>
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</li>
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</ul></li>
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<li>
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classes.utility.json_importer
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<ul>
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<li><a href="classes.utility.html#module-classes.utility.json_importer">module</a>
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</li>
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</ul></li>
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<li>
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classes.utility.sample_importer
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<ul>
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<li><a href="classes.utility.html#module-classes.utility.sample_importer">module</a>
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</li>
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</ul></li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.clean_structure_edges">clean_structure_edges() (classes.structure_graph.structure.Structure method)</a>
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</li>
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<li><a href="classes.utility.html#classes.utility.cache.Cache.clear">clear() (classes.utility.cache.Cache method)</a>
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</li>
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<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.clear_concatenated_frame">clear_concatenated_frame() (classes.utility.abstract_importer.AbstractImporter method)</a>
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</li>
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<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.clear_data_frame_list">clear_data_frame_list() (classes.utility.json_importer.JsonImporter method)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.clear_indexing_filtering_structures">clear_indexing_filtering_structures() (classes.structure_graph.network_graph.NetworkGraph method)</a>
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|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sample_path.SamplePath.clear_memory">clear_memory() (classes.structure_graph.sample_path.SamplePath method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.complete_test">complete_test() (classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.trajectory.Trajectory.complete_trajectory">complete_trajectory() (classes.structure_graph.trajectory.Trajectory property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix.compute_cim_coefficients">compute_cim_coefficients() (classes.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix method)</a>
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|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.parameters_estimator.ParametersEstimator.compute_parameters">compute_parameters() (classes.estimators.parameters_estimator.ParametersEstimator method)</a>
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|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.parameters_estimator.ParametersEstimator.compute_parameters_for_node">compute_parameters_for_node() (classes.estimators.parameters_estimator.ParametersEstimator method)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.compute_row_delta_in_all_samples_frames">compute_row_delta_in_all_samples_frames() (classes.utility.abstract_importer.AbstractImporter method)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.compute_row_delta_sigle_samples_frame">compute_row_delta_sigle_samples_frame() (classes.utility.abstract_importer.AbstractImporter method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.parameters_estimator.ParametersEstimator.compute_state_res_time_for_node">compute_state_res_time_for_node() (classes.estimators.parameters_estimator.ParametersEstimator static method)</a>
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|
</li>
|
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<li><a href="classes.estimators.html#classes.estimators.parameters_estimator.ParametersEstimator.compute_state_transitions_for_a_node">compute_state_transitions_for_a_node() (classes.estimators.parameters_estimator.ParametersEstimator static method)</a>
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|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.compute_thumb_value">compute_thumb_value() (classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator method)</a>
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|
</li>
|
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<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.concatenated_samples">concatenated_samples() (classes.utility.abstract_importer.AbstractImporter property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix">ConditionalIntensityMatrix (class in classes.structure_graph.conditional_intensity_matrix)</a>
|
|
</li>
|
|
<li><a href="classes.optimizers.html#classes.optimizers.constraint_based_optimizer.ConstraintBasedOptimizer">ConstraintBasedOptimizer (class in classes.optimizers.constraint_based_optimizer)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.contains_edge">contains_edge() (classes.structure_graph.structure.Structure method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.ctpc_algorithm">ctpc_algorithm() (classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator method)</a>
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</li>
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</ul></td>
|
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</tr></table>
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<h2 id="D">D</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.dataset_id">dataset_id() (classes.utility.abstract_importer.AbstractImporter method)</a>
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|
|
|
<ul>
|
|
<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.dataset_id">(classes.utility.json_importer.JsonImporter method)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.sample_importer.SampleImporter.dataset_id">(classes.utility.sample_importer.SampleImporter method)</a>
|
|
</li>
|
|
</ul></li>
|
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</ul></td>
|
|
</tr></table>
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<h2 id="E">E</h2>
|
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<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.edges">edges() (classes.structure_graph.network_graph.NetworkGraph property)</a>
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|
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<ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.edges">(classes.structure_graph.structure.Structure property)</a>
|
|
</li>
|
|
</ul></li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.estimate_parents">estimate_parents() (classes.estimators.structure_score_based_estimator.StructureScoreBasedEstimator method)</a>
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|
</li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.estimate_structure">estimate_structure() (classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator method)</a>
|
|
|
|
<ul>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator.estimate_structure">(classes.estimators.structure_estimator.StructureEstimator method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.estimate_structure">(classes.estimators.structure_score_based_estimator.StructureScoreBasedEstimator method)</a>
|
|
</li>
|
|
</ul></li>
|
|
</ul></td>
|
|
</tr></table>
|
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|
<h2 id="F">F</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.estimators.html#classes.estimators.fam_score_calculator.FamScoreCalculator">FamScoreCalculator (class in classes.estimators.fam_score_calculator)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.parameters_estimator.ParametersEstimator.fast_init">fast_init() (classes.estimators.parameters_estimator.ParametersEstimator method)</a>
|
|
|
|
<ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.fast_init">(classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
</li>
|
|
</ul></li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.file_path">file_path() (classes.utility.abstract_importer.AbstractImporter property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.set_of_cims.SetOfCims.filter_cims_with_mask">filter_cims_with_mask() (classes.structure_graph.set_of_cims.SetOfCims method)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.cache.Cache.find">find() (classes.utility.cache.Cache method)</a>
|
|
</li>
|
|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="G">G</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator.generate_possible_sub_sets_of_size">generate_possible_sub_sets_of_size() (classes.estimators.structure_estimator.StructureEstimator static method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.set_of_cims.SetOfCims.get_cims_number">get_cims_number() (classes.structure_graph.set_of_cims.SetOfCims method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sets_of_cims_container.SetsOfCimsContainer.get_cims_of_node">get_cims_of_node() (classes.structure_graph.sets_of_cims_container.SetsOfCimsContainer method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.fam_score_calculator.FamScoreCalculator.get_fam_score">get_fam_score() (classes.estimators.fam_score_calculator.FamScoreCalculator method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.get_node_id">get_node_id() (classes.structure_graph.structure.Structure method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.get_node_indx">get_node_indx() (classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
|
|
<ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.get_node_indx">(classes.structure_graph.structure.Structure method)</a>
|
|
</li>
|
|
</ul></li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.get_ordered_by_indx_set_of_parents">get_ordered_by_indx_set_of_parents() (classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.get_parents_by_id">get_parents_by_id() (classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.get_positional_node_indx">get_positional_node_indx() (classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
|
|
<ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.get_positional_node_indx">(classes.structure_graph.structure.Structure method)</a>
|
|
</li>
|
|
</ul></li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.get_score_from_graph">get_score_from_graph() (classes.estimators.structure_score_based_estimator.StructureScoreBasedEstimator method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sets_of_cims_container.SetsOfCimsContainer.get_set_of_cims">get_set_of_cims() (classes.structure_graph.sets_of_cims_container.SetsOfCimsContainer method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.get_states_number">get_states_number() (classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
|
|
<ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.get_states_number">(classes.structure_graph.structure.Structure method)</a>
|
|
</li>
|
|
</ul></li>
|
|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="H">H</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.has_edge">has_edge() (classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
</li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sample_path.SamplePath.has_prior_net_structure">has_prior_net_structure() (classes.structure_graph.sample_path.SamplePath property)</a>
|
|
</li>
|
|
<li><a href="classes.optimizers.html#classes.optimizers.hill_climbing_search.HillClimbing">HillClimbing (class in classes.optimizers.hill_climbing_search)</a>
|
|
</li>
|
|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="I">I</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.import_data">import_data() (classes.utility.json_importer.JsonImporter method)</a>
|
|
|
|
<ul>
|
|
<li><a href="classes.utility.html#classes.utility.sample_importer.SampleImporter.import_data">(classes.utility.sample_importer.SampleImporter method)</a>
|
|
</li>
|
|
</ul></li>
|
|
<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.import_sampled_cims">import_sampled_cims() (classes.utility.json_importer.JsonImporter method)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.import_structure">import_structure() (classes.utility.json_importer.JsonImporter method)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.import_trajectories">import_trajectories() (classes.utility.json_importer.JsonImporter method)</a>
|
|
</li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.import_variables">import_variables() (classes.utility.json_importer.JsonImporter method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.independence_test">independence_test() (classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sets_of_cims_container.SetsOfCimsContainer.init_cims_structure">init_cims_structure() (classes.structure_graph.sets_of_cims_container.SetsOfCimsContainer method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.init_graph">init_graph() (classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.parameters_estimator.ParametersEstimator.init_sets_cims_container">init_sets_cims_container() (classes.estimators.parameters_estimator.ParametersEstimator method)</a>
|
|
</li>
|
|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="J">J</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter">JsonImporter (class in classes.utility.json_importer)</a>
|
|
</li>
|
|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="M">M</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.estimators.html#classes.estimators.fam_score_calculator.FamScoreCalculator.marginal_likelihood_q">marginal_likelihood_q() (classes.estimators.fam_score_calculator.FamScoreCalculator method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.fam_score_calculator.FamScoreCalculator.marginal_likelihood_theta">marginal_likelihood_theta() (classes.estimators.fam_score_calculator.FamScoreCalculator method)</a>
|
|
</li>
|
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<li>
|
|
module
|
|
|
|
<ul>
|
|
<li><a href="classes.html#module-classes">classes</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#module-classes.estimators">classes.estimators</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#module-classes.estimators.fam_score_calculator">classes.estimators.fam_score_calculator</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#module-classes.estimators.parameters_estimator">classes.estimators.parameters_estimator</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#module-classes.estimators.structure_constraint_based_estimator">classes.estimators.structure_constraint_based_estimator</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#module-classes.estimators.structure_estimator">classes.estimators.structure_estimator</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#module-classes.estimators.structure_score_based_estimator">classes.estimators.structure_score_based_estimator</a>
|
|
</li>
|
|
<li><a href="classes.optimizers.html#module-classes.optimizers">classes.optimizers</a>
|
|
</li>
|
|
<li><a href="classes.optimizers.html#module-classes.optimizers.constraint_based_optimizer">classes.optimizers.constraint_based_optimizer</a>
|
|
</li>
|
|
<li><a href="classes.optimizers.html#module-classes.optimizers.hill_climbing_search">classes.optimizers.hill_climbing_search</a>
|
|
</li>
|
|
<li><a href="classes.optimizers.html#module-classes.optimizers.optimizer">classes.optimizers.optimizer</a>
|
|
</li>
|
|
<li><a href="classes.optimizers.html#module-classes.optimizers.tabu_search">classes.optimizers.tabu_search</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#module-classes.structure_graph">classes.structure_graph</a>
|
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</li>
|
|
<li><a href="classes.structure_graph.html#module-classes.structure_graph.abstract_sample_path">classes.structure_graph.abstract_sample_path</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#module-classes.structure_graph.conditional_intensity_matrix">classes.structure_graph.conditional_intensity_matrix</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#module-classes.structure_graph.network_graph">classes.structure_graph.network_graph</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#module-classes.structure_graph.sample_path">classes.structure_graph.sample_path</a>
|
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</li>
|
|
<li><a href="classes.structure_graph.html#module-classes.structure_graph.set_of_cims">classes.structure_graph.set_of_cims</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#module-classes.structure_graph.sets_of_cims_container">classes.structure_graph.sets_of_cims_container</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#module-classes.structure_graph.structure">classes.structure_graph.structure</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#module-classes.structure_graph.trajectory">classes.structure_graph.trajectory</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#module-classes.utility">classes.utility</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#module-classes.utility.abstract_importer">classes.utility.abstract_importer</a>
|
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</li>
|
|
<li><a href="classes.utility.html#module-classes.utility.cache">classes.utility.cache</a>
|
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</li>
|
|
<li><a href="classes.utility.html#module-classes.utility.decorators">classes.utility.decorators</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#module-classes.utility.json_importer">classes.utility.json_importer</a>
|
|
</li>
|
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<li><a href="classes.utility.html#module-classes.utility.sample_importer">classes.utility.sample_importer</a>
|
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</li>
|
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</ul></li>
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</ul></td>
|
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</tr></table>
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|
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<h2 id="N">N</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
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<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph">NetworkGraph (class in classes.structure_graph.network_graph)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.nodes">nodes() (classes.structure_graph.network_graph.NetworkGraph property)</a>
|
|
</li>
|
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.nodes_indexes">nodes_indexes() (classes.structure_graph.network_graph.NetworkGraph property)</a>
|
|
|
|
<ul>
|
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<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.nodes_indexes">(classes.structure_graph.structure.Structure property)</a>
|
|
</li>
|
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</ul></li>
|
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.nodes_labels">nodes_labels() (classes.structure_graph.structure.Structure property)</a>
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</li>
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<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.nodes_values">nodes_values() (classes.structure_graph.network_graph.NetworkGraph property)</a>
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<ul>
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<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.nodes_values">(classes.structure_graph.structure.Structure property)</a>
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</li>
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|
</ul></li>
|
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<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.normalize_trajectories">normalize_trajectories() (classes.utility.json_importer.JsonImporter method)</a>
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|
</li>
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</ul></td>
|
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</tr></table>
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<h2 id="O">O</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="classes.estimators.html#classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.one_iteration_of_CTPC_algorithm">one_iteration_of_CTPC_algorithm() (classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator method)</a>
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</li>
|
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<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.one_level_normalizing">one_level_normalizing() (classes.utility.json_importer.JsonImporter method)</a>
|
|
</li>
|
|
<li><a href="classes.optimizers.html#classes.optimizers.constraint_based_optimizer.ConstraintBasedOptimizer.optimize_structure">optimize_structure() (classes.optimizers.constraint_based_optimizer.ConstraintBasedOptimizer method)</a>
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<ul>
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<li><a href="classes.optimizers.html#classes.optimizers.hill_climbing_search.HillClimbing.optimize_structure">(classes.optimizers.hill_climbing_search.HillClimbing method)</a>
|
|
</li>
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<li><a href="classes.optimizers.html#classes.optimizers.optimizer.Optimizer.optimize_structure">(classes.optimizers.optimizer.Optimizer method)</a>
|
|
</li>
|
|
<li><a href="classes.optimizers.html#classes.optimizers.tabu_search.TabuSearch.optimize_structure">(classes.optimizers.tabu_search.TabuSearch method)</a>
|
|
</li>
|
|
</ul></li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.optimizers.html#classes.optimizers.optimizer.Optimizer">Optimizer (class in classes.optimizers.optimizer)</a>
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</li>
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|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="P">P</h2>
|
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<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.p_combs">p_combs() (classes.structure_graph.network_graph.NetworkGraph property)</a>
|
|
|
|
<ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.set_of_cims.SetOfCims.p_combs">(classes.structure_graph.set_of_cims.SetOfCims property)</a>
|
|
</li>
|
|
</ul></li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.estimators.html#classes.estimators.parameters_estimator.ParametersEstimator">ParametersEstimator (class in classes.estimators.parameters_estimator)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.cache.Cache.put">put() (classes.utility.cache.Cache method)</a>
|
|
</li>
|
|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="R">R</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.utility.html#classes.utility.json_importer.JsonImporter.read_json_file">read_json_file() (classes.utility.json_importer.JsonImporter method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator.remove_diagonal_elements">remove_diagonal_elements() (classes.estimators.structure_estimator.StructureEstimator method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.remove_edge">remove_edge() (classes.structure_graph.structure.Structure method)</a>
|
|
</li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.remove_edges">remove_edges() (classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.remove_node">remove_node() (classes.structure_graph.network_graph.NetworkGraph method)</a>
|
|
|
|
<ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.remove_node">(classes.structure_graph.structure.Structure method)</a>
|
|
</li>
|
|
</ul></li>
|
|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="S">S</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.utility.html#classes.utility.sample_importer.SampleImporter">SampleImporter (class in classes.utility.sample_importer)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sample_path.SamplePath">SamplePath (class in classes.structure_graph.sample_path)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator.save_plot_estimated_structure_graph">save_plot_estimated_structure_graph() (classes.estimators.structure_estimator.StructureEstimator method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator.save_results">save_results() (classes.estimators.structure_estimator.StructureEstimator method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.set_of_cims.SetOfCims">SetOfCims (class in classes.structure_graph.set_of_cims)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sets_of_cims_container.SetsOfCimsContainer">SetsOfCimsContainer (class in classes.structure_graph.sets_of_cims_container)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.fam_score_calculator.FamScoreCalculator.single_cim_xu_marginal_likelihood_q">single_cim_xu_marginal_likelihood_q() (classes.estimators.fam_score_calculator.FamScoreCalculator method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.fam_score_calculator.FamScoreCalculator.single_cim_xu_marginal_likelihood_theta">single_cim_xu_marginal_likelihood_theta() (classes.estimators.fam_score_calculator.FamScoreCalculator method)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.fam_score_calculator.FamScoreCalculator.single_internal_cim_xxu_marginal_likelihood_theta">single_internal_cim_xxu_marginal_likelihood_theta() (classes.estimators.fam_score_calculator.FamScoreCalculator method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.trajectory.Trajectory.size">size() (classes.structure_graph.trajectory.Trajectory method)</a>
|
|
</li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.sorter">sorter() (classes.utility.abstract_importer.AbstractImporter property)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator.spurious_edges">spurious_edges() (classes.estimators.structure_estimator.StructureEstimator method)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix.state_residence_times">state_residence_times() (classes.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix.state_transition_matrix">state_transition_matrix() (classes.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure">Structure (class in classes.structure_graph.structure)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sample_path.SamplePath.structure">structure() (classes.structure_graph.sample_path.SamplePath property)</a>
|
|
|
|
<ul>
|
|
<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.structure">(classes.utility.abstract_importer.AbstractImporter property)</a>
|
|
</li>
|
|
</ul></li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator">StructureConstraintBasedEstimator (class in classes.estimators.structure_constraint_based_estimator)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_estimator.StructureEstimator">StructureEstimator (class in classes.estimators.structure_estimator)</a>
|
|
</li>
|
|
<li><a href="classes.estimators.html#classes.estimators.structure_score_based_estimator.StructureScoreBasedEstimator">StructureScoreBasedEstimator (class in classes.estimators.structure_score_based_estimator)</a>
|
|
</li>
|
|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="T">T</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.optimizers.html#classes.optimizers.tabu_search.TabuSearch">TabuSearch (class in classes.optimizers.tabu_search)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.time_filtering">time_filtering() (classes.structure_graph.network_graph.NetworkGraph property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.time_scalar_indexing_strucure">time_scalar_indexing_strucure() (classes.structure_graph.network_graph.NetworkGraph property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.trajectory.Trajectory.times">times() (classes.structure_graph.trajectory.Trajectory property)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.decorators.timing">timing() (in module classes.utility.decorators)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.decorators.timing_write">timing_write() (in module classes.utility.decorators)</a>
|
|
</li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sample_path.SamplePath.total_variables_count">total_variables_count() (classes.structure_graph.sample_path.SamplePath property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.structure.Structure.total_variables_number">total_variables_number() (classes.structure_graph.structure.Structure property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.sample_path.SamplePath.trajectories">trajectories() (classes.structure_graph.sample_path.SamplePath property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.trajectory.Trajectory">Trajectory (class in classes.structure_graph.trajectory)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.trajectory.Trajectory.trajectory">trajectory() (classes.structure_graph.trajectory.Trajectory property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.transition_filtering">transition_filtering() (classes.structure_graph.network_graph.NetworkGraph property)</a>
|
|
</li>
|
|
<li><a href="classes.structure_graph.html#classes.structure_graph.network_graph.NetworkGraph.transition_scalar_indexing_structure">transition_scalar_indexing_structure() (classes.structure_graph.network_graph.NetworkGraph property)</a>
|
|
</li>
|
|
</ul></td>
|
|
</tr></table>
|
|
|
|
<h2 id="V">V</h2>
|
|
<table style="width: 100%" class="indextable genindextable"><tr>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.estimators.html#classes.estimators.fam_score_calculator.FamScoreCalculator.variable_cim_xu_marginal_likelihood_q">variable_cim_xu_marginal_likelihood_q() (classes.estimators.fam_score_calculator.FamScoreCalculator method)</a>
|
|
</li>
|
|
</ul></td>
|
|
<td style="width: 33%; vertical-align: top;"><ul>
|
|
<li><a href="classes.estimators.html#classes.estimators.fam_score_calculator.FamScoreCalculator.variable_cim_xu_marginal_likelihood_theta">variable_cim_xu_marginal_likelihood_theta() (classes.estimators.fam_score_calculator.FamScoreCalculator method)</a>
|
|
</li>
|
|
<li><a href="classes.utility.html#classes.utility.abstract_importer.AbstractImporter.variables">variables() (classes.utility.abstract_importer.AbstractImporter property)</a>
|
|
</li>
|
|
</ul></td>
|
|
</tr></table>
|
|
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|
|
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