API Documentation
=================

This section contains the complete API documentation for py3plex, automatically generated from docstrings.

For auto-generated module documentation, run::

    cd docfiles
    sphinx-apidoc -o AUTOGEN_results -f ../py3plex
    make html

Core Modules
------------

.. automodule:: py3plex.core.multinet
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.. automodule:: py3plex.core.parsers
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.. automodule:: py3plex.core.converters
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.. automodule:: py3plex.core.random_generators
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.. automodule:: py3plex.core.supporting
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.. automodule:: py3plex.core.nx_compat
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HINMINE Network Decomposition
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: py3plex.core.HINMINE.decomposition
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.. automodule:: py3plex.core.HINMINE.IO
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Configuration and Utilities
----------------------------

.. automodule:: py3plex.config
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.. automodule:: py3plex.utils
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.. automodule:: py3plex.exceptions
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Algorithms
----------

Community Detection
~~~~~~~~~~~~~~~~~~~

.. automodule:: py3plex.algorithms.community_detection.community_wrapper
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.. automodule:: py3plex.algorithms.community_detection.multilayer_modularity
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.. automodule:: py3plex.algorithms.community_detection.community_louvain
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.. automodule:: py3plex.algorithms.community_detection.community_measures
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.. automodule:: py3plex.algorithms.community_detection.multilayer_benchmark
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Statistics
~~~~~~~~~~

.. automodule:: py3plex.algorithms.statistics.statistics
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.. automodule:: py3plex.algorithms.statistics.multilayer_statistics
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.. automodule:: py3plex.algorithms.statistics.topology
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.. automodule:: py3plex.algorithms.statistics.enrichment
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.. automodule:: py3plex.algorithms.statistics.correlation_networks
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.. automodule:: py3plex.algorithms.statistics.basic_statistics
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Multilayer Algorithms
~~~~~~~~~~~~~~~~~~~~~

.. automodule:: py3plex.algorithms.multilayer_algorithms.centrality
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.. automodule:: py3plex.algorithms.multilayer_algorithms.multixrank
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.. automodule:: py3plex.algorithms.multilayer_algorithms.entanglement
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.. automodule:: py3plex.algorithms.multilayer_algorithms.supra_matrix_function_centrality
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.. automodule:: py3plex.algorithms.multicentrality
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General Algorithms
~~~~~~~~~~~~~~~~~~

.. automodule:: py3plex.algorithms.general.walkers
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.. automodule:: py3plex.algorithms.general.benchmark_classification
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Node Ranking
~~~~~~~~~~~~

.. automodule:: py3plex.algorithms.node_ranking.node_ranking
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Network Classification
~~~~~~~~~~~~~~~~~~~~~~

.. Note: :noindex: prevents duplicate object descriptions in the documentation index
   since this module is also documented elsewhere.

.. automodule:: py3plex.algorithms.network_classification.label_propagation
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Visualization
-------------

.. automodule:: py3plex.visualization.multilayer
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.. automodule:: py3plex.visualization.drawing_machinery
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.. automodule:: py3plex.visualization.colors
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.. automodule:: py3plex.visualization.layout_algorithms
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.. automodule:: py3plex.visualization.bezier
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.. automodule:: py3plex.visualization.benchmark_visualizations
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Wrappers
--------

.. automodule:: py3plex.wrappers.node2vec_embedding
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.. automodule:: py3plex.wrappers.benchmark_nodes
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I/O Operations
--------------

.. automodule:: py3plex.io.input_output
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For the complete auto-generated API documentation, see the AUTOGEN_results directory after building the docs.
Aggregation and Network Operations
----------------------------------

.. automodule:: py3plex.multinet.aggregation
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Profiling Utilities
-------------------

.. automodule:: py3plex.profiling
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Logging Configuration
---------------------

.. automodule:: py3plex.logging_config
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I/O Schema and Validation
-------------------------

.. Note: :noindex: prevents duplicate object descriptions in the documentation index
   since this module is documented in multiple locations.

.. automodule:: py3plex.io.schema
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.. automodule:: py3plex.io.api
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Hedwig Rule Learning
--------------------

.. automodule:: py3plex.algorithms.hedwig
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.. automodule:: py3plex.algorithms.hedwig.core.example
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.. automodule:: py3plex.algorithms.hedwig.core.predicate
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.. automodule:: py3plex.algorithms.hedwig.core.rule
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Force Atlas 2 Visualization
---------------------------

.. automodule:: py3plex.visualization.fa2.forceatlas2
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.. automodule:: py3plex.visualization.fa2.fa2util
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Embedding Visualization
-----------------------

.. automodule:: py3plex.visualization.embedding_visualization.embedding_visualization
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Network Generation and Benchmarking
-----------------------------------

.. automodule:: py3plex.algorithms.general.network_generation
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Additional Statistics and Analysis
----------------------------------

.. automodule:: py3plex.algorithms.statistics.bayesiantests
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.. automodule:: py3plex.algorithms.statistics.information_theory
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.. automodule:: py3plex.algorithms.statistics.distribution
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Community Detection Advanced
----------------------------

.. automodule:: py3plex.algorithms.community_detection.NoRC
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.. automodule:: py3plex.algorithms.community_detection.community_ranking
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.. automodule:: py3plex.algorithms.community_detection.label_propagation_multilayer
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Node Ranking and Classification
-------------------------------

.. automodule:: py3plex.algorithms.node_ranking
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.. automodule:: py3plex.algorithms.network_classification
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Embeddings and Wrappers
-----------------------

.. automodule:: py3plex.wrappers.train_node2vec_embedding
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.. automodule:: py3plex.wrappers.train_word2vec_embedding
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Network Motifs and Patterns
---------------------------

.. automodule:: py3plex.algorithms.network_patterns.motif_detection
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HINMINE Data Structures
-----------------------

.. automodule:: py3plex.core.HINMINE.dataStructures
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Command-Line Interface
----------------------

.. automodule:: py3plex.cli
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Validation Utilities
--------------------

.. automodule:: py3plex.validation
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Network Comparison and Testing
------------------------------

.. automodule:: py3plex.algorithms.general.network_comparison
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.. automodule:: py3plex.algorithms.general.distances
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.. automodule:: py3plex.algorithms.general.network_slicer
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Hedwig Learning Algorithms
--------------------------

.. automodule:: py3plex.algorithms.hedwig.learners.learner
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.. automodule:: py3plex.algorithms.hedwig.learners.bottomup
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.. automodule:: py3plex.algorithms.hedwig.learners.optimal
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Hedwig Statistics and Scoring
-----------------------------

.. automodule:: py3plex.algorithms.hedwig.stats.scorefunctions
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.. automodule:: py3plex.algorithms.hedwig.stats.validate
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Hedwig Core Components
----------------------

.. automodule:: py3plex.algorithms.hedwig.core.converters
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.. automodule:: py3plex.algorithms.hedwig.core.kb
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.. automodule:: py3plex.algorithms.hedwig.core.settings
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Time Series and Temporal Analysis
---------------------------------

.. automodule:: py3plex.algorithms.temporal.time_series_analysis
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Advanced Visualization
----------------------

.. automodule:: py3plex.visualization.hairballs
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.. automodule:: py3plex.visualization.sankey
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Link Prediction
---------------

.. automodule:: py3plex.algorithms.link_prediction.link_prediction
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