Modify init.py for package imports

.gitignore

@@ -7,3 +7,4 @@ __pycache__
 ./data/
 ./venv/
 ./PyCTBN/.scannerwork
+./results/

PyCTBN.egg-info/PKG-INFO

@@ -1,10 +0,0 @@
-Metadata-Version: 1.0
-Name: PyCTBN
-Version: 1.0
-Summary: A Continuous Time Bayesian Network Library
-Home-page: https://github.com/philipMartini/CTBN_Project
-Author: Filippo Martini
-Author-email: f.martini@campus.unimib.it
-License: MIT
-Description: # CTBN_Project
-Platform: UNKNOWN

PyCTBN.egg-info/SOURCES.txt

@@ -1,22 +0,0 @@
-README.md
-setup.py
-PyCTBN.egg-info/PKG-INFO
-PyCTBN.egg-info/SOURCES.txt
-PyCTBN.egg-info/dependency_links.txt
-PyCTBN.egg-info/not-zip-safe
-PyCTBN.egg-info/requires.txt
-PyCTBN.egg-info/top_level.txt
-classes/__init__.py
-classes/abstract_importer.py
-classes/cache.py
-classes/conditional_intensity_matrix.py
-classes/json_importer.py
-classes/json_importer_mod.py
-classes/network_graph.py
-classes/parameters_estimator.py
-classes/sample_path.py
-classes/set_of_cims.py
-classes/simple_cvs_importer.py
-classes/structure.py
-classes/structure_estimator.py
-classes/trajectory.py

PyCTBN.egg-info/dependency_links.txt

@@ -1,3 +0,0 @@
-https://github.com/numpy/numpy
-https://github.com/pandas-dev/pandas
-https://github.com/networkx/networkx

PyCTBN.egg-info/not-zip-safe

@@ -1 +0,0 @@
-

PyCTBN.egg-info/requires.txt

@@ -1,3 +0,0 @@
-numpy
-pandas
-networkx

PyCTBN.egg-info/top_level.txt

@@ -1 +0,0 @@
-classes

PyCTBN/.scannerwork/report-task.txt

@@ -1,6 +0,0 @@
-projectKey=Ctbn_Project
-serverUrl=http://localhost:9000
-serverVersion=8.4.1.35646
-dashboardUrl=http://localhost:9000/dashboard?id=Ctbn_Project
-ceTaskId=AXPs4gCNB9mzoAo2hiLI
-ceTaskUrl=http://localhost:9000/api/ce/task?id=AXPs4gCNB9mzoAo2hiLI

PyCTBN/__init__.py

@@ -0,0 +1,2 @@
+import PyCTBN.classes
+from PyCTBN.classes import *

PyCTBN/classes/__init__.py

@@ -0,0 +1,11 @@
+from .json_importer import JsonImporter
+from .abstract_importer import AbstractImporter
+from .network_graph import NetworkGraph
+from .sample_path import SamplePath
+from .parameters_estimator import ParametersEstimator
+from .structure import Structure
+from .structure_estimator import StructureEstimator
+from .trajectory import Trajectory
+from .conditional_intensity_matrix import ConditionalIntensityMatrix
+from .cache import Cache
+from .set_of_cims import SetOfCims

PyCTBN/classes/sample_path.py

@@ -19,11 +19,9 @@ class SamplePath(object):
         """Constructor Method
         """
         self._importer = importer
-        if (self._importer._df_variables is None or self._importer._df_structure is None
-                or self._importer._concatenated_samples is None):
+        if (self._importer._df_variables is None or self._importer._concatenated_samples is None):
             raise RuntimeError('The importer object has to contain the all processed data!')
-        if(self._importer._df_variables.empty or self._importer._df_structure.empty
-                or self._importer._concatenated_samples.empty):
+        if(self._importer._df_variables.empty or self._importer._concatenated_samples.empty):
             raise RuntimeError('The importer object has to contain the all processed data!')
         self._trajectories = None
         self._structure = None
@@ -49,7 +47,10 @@ class SamplePath(object):
         labels = self._importer.variables.iloc[:, 0].to_list()
         indxs = self._importer.variables.index.to_numpy()
         vals = self._importer.variables.iloc[:, 1].to_numpy()
-        edges = list(self._importer.structure.to_records(index=False))
+        if self._importer.structure is None or self._importer.structure.empty:
+            edges = []
+        else:
+            edges = list(self._importer.structure.to_records(index=False))
         self._structure = Structure(labels, indxs, vals, edges,
                                        self._total_variables_count)
 

PyCTBN/deprecated/simple_cvs_importer.py

@@ -3,8 +3,8 @@ import glob
 import os
 import typing
 
-from PyCTBN.PyCTBN.abstract_importer import AbstractImporter
-from PyCTBN.PyCTBN.sample_path import SamplePath
+from PyCTBN.classes.abstract_importer import AbstractImporter
+from PyCTBN.classes.sample_path import SamplePath
 
 
 class CSVImporter(AbstractImporter):

PyCTBN/tests/original_ctpc_algorithm.py

@@ -9,7 +9,7 @@ from scipy.stats import chi2 as chi2_dist
 from scipy.stats import f as f_dist
 from tqdm import tqdm
 
-from PyCTBN.PyCTBN.abstract_importer import AbstractImporter
+from PyCTBN.classes.abstract_importer import AbstractImporter
 
 
 class OriginalCTPCAlgorithm(AbstractImporter):

PyCTBN/tests/performance_comparisons.py

@@ -7,9 +7,9 @@ import networkx as nx
 import timeit
 import psutil
 
-from ..PyCTBN.sample_path import SamplePath
-from ..PyCTBN.structure_estimator import StructureEstimator
-from ..PyCTBN.json_importer import JsonImporter
+from ..classes.sample_path import SamplePath
+from ..classes.structure_estimator import StructureEstimator
+from ..classes.json_importer import JsonImporter
 from .original_ctpc_algorithm import OriginalCTPCAlgorithm
 
 

PyCTBN/tests/test_cache.py

@@ -2,8 +2,8 @@
 import unittest
 import numpy as np
 
-from ..PyCTBN.cache import Cache
-from ..PyCTBN.set_of_cims import SetOfCims
+from ..classes.cache import Cache
+from ..classes.set_of_cims import SetOfCims
 
 
 class TestCache(unittest.TestCase):

PyCTBN/tests/test_cim.py

@@ -2,7 +2,7 @@
 import unittest
 import numpy as np
 
-from ..PyCTBN.conditional_intensity_matrix import ConditionalIntensityMatrix
+from ..classes.conditional_intensity_matrix import ConditionalIntensityMatrix
 
 
 class TestConditionalIntensityMatrix(unittest.TestCase):

PyCTBN/tests/test_json_importer.py

@@ -7,7 +7,7 @@ import pandas as pd
 import json
 
 
-from ..PyCTBN.json_importer import JsonImporter
+from ..classes.json_importer import JsonImporter
 
 
 class TestJsonImporter(unittest.TestCase):

PyCTBN/tests/test_networkgraph.py

@@ -6,9 +6,9 @@ import networkx as nx
 import numpy as np
 import itertools
 
-from ..PyCTBN.sample_path import SamplePath
-from ..PyCTBN.network_graph import NetworkGraph
-from ..PyCTBN.json_importer import JsonImporter
+from ..classes.sample_path import SamplePath
+from ..classes.network_graph import NetworkGraph
+from ..classes.json_importer import JsonImporter
 
 
 class TestNetworkGraph(unittest.TestCase):

PyCTBN/tests/test_parameters_estimator.py

@@ -4,11 +4,11 @@ import numpy as np
 import glob
 import os
 
-from ..PyCTBN.network_graph import NetworkGraph
-from ..PyCTBN.sample_path import SamplePath
-from ..PyCTBN.set_of_cims import SetOfCims
-from ..PyCTBN.parameters_estimator import ParametersEstimator
-from ..PyCTBN.json_importer import JsonImporter
+from ..classes.network_graph import NetworkGraph
+from ..classes.sample_path import SamplePath
+from ..classes.set_of_cims import SetOfCims
+from ..classes.parameters_estimator import ParametersEstimator
+from ..classes.json_importer import JsonImporter
 
 
 class TestParametersEstimatior(unittest.TestCase):

PyCTBN/tests/test_sample_path.py

@@ -4,10 +4,10 @@ import glob
 import os
 import random
 
-from ..PyCTBN.json_importer import JsonImporter
-from ..PyCTBN.sample_path import SamplePath
-from ..PyCTBN.trajectory import Trajectory
-from ..PyCTBN.structure import Structure
+from ..classes.json_importer import JsonImporter
+from ..classes.sample_path import SamplePath
+from ..classes.trajectory import Trajectory
+from ..classes.structure import Structure
 
 
 class TestSamplePath(unittest.TestCase):
@@ -57,6 +57,16 @@ class TestSamplePath(unittest.TestCase):
         random.shuffle(importer._sorter)
         self.assertRaises(RuntimeError, s1.build_structure)
 
+    def test_build_saplepath_no_prior_net_structure(self):
+        importer = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        importer.import_data(0)
+        importer._df_structure = None
+        s1 = SamplePath(importer)
+        s1.build_trajectories()
+        s1.build_structure()
+        self.assertFalse(s1.structure.edges)
+
+
 
 if __name__ == '__main__':
     unittest.main()

PyCTBN/tests/test_setofcims.py

@@ -3,7 +3,7 @@ import unittest
 import numpy as np
 import itertools
 
-from ..PyCTBN.set_of_cims import SetOfCims
+from ..classes.set_of_cims import SetOfCims
 
 
 class TestSetOfCims(unittest.TestCase):

PyCTBN/tests/test_structure.py

@@ -1,7 +1,7 @@
 
 import unittest
 import numpy as np
-from ..PyCTBN.structure import Structure
+from ..classes.structure import Structure
 
 
 class TestStructure(unittest.TestCase):

PyCTBN/tests/test_structure_estimator.py

@@ -8,10 +8,10 @@ import networkx as nx
 import numpy as np
 import timeit
 
-from ..PyCTBN.cache import Cache
-from ..PyCTBN.sample_path import SamplePath
-from ..PyCTBN.structure_estimator import StructureEstimator
-from ..PyCTBN.json_importer import JsonImporter
+from ..classes.cache import Cache
+from ..classes.sample_path import SamplePath
+from ..classes.structure_estimator import StructureEstimator
+from ..classes.json_importer import JsonImporter
 
 
 class TestStructureEstimator(unittest.TestCase):

PyCTBN/tests/test_trajectory.py

@@ -2,7 +2,7 @@
 import unittest
 import numpy as np
 
-from ..PyCTBN.trajectory import Trajectory
+from ..classes.trajectory import Trajectory
 
 
 class TestTrajectory(unittest.TestCase):

documentation/PyCTBN.rst

@@ -1,101 +0,0 @@
-PyCTBN package
-==============
-
-Submodules
-----------
-
-PyCTBN.abstract\_importer module
---------------------------------
-
-.. automodule:: PyCTBN.abstract_importer
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.cache module
--------------------
-
-.. automodule:: PyCTBN.cache
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.conditional\_intensity\_matrix module
---------------------------------------------
-
-.. automodule:: PyCTBN.conditional_intensity_matrix
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.json\_importer module
-----------------------------
-
-.. automodule:: PyCTBN.json_importer
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.network\_graph module
-----------------------------
-
-.. automodule:: PyCTBN.network_graph
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.parameters\_estimator module
------------------------------------
-
-.. automodule:: PyCTBN.parameters_estimator
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.sample\_path module
---------------------------
-
-.. automodule:: PyCTBN.sample_path
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.set\_of\_cims module
----------------------------
-
-.. automodule:: PyCTBN.set_of_cims
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.structure module
------------------------
-
-.. automodule:: PyCTBN.structure
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.structure\_estimator module
-----------------------------------
-
-.. automodule:: PyCTBN.structure_estimator
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.trajectory module
-------------------------
-
-.. automodule:: PyCTBN.trajectory
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: PyCTBN
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/_sources/PyCTBN.rst.txt

@@ -1,101 +0,0 @@
-PyCTBN package
-==============
-
-Submodules
-----------
-
-PyCTBN.abstract\_importer module
---------------------------------
-
-.. automodule:: PyCTBN.abstract_importer
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.cache module
--------------------
-
-.. automodule:: PyCTBN.cache
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.conditional\_intensity\_matrix module
---------------------------------------------
-
-.. automodule:: PyCTBN.conditional_intensity_matrix
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.json\_importer module
-----------------------------
-
-.. automodule:: PyCTBN.json_importer
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.network\_graph module
-----------------------------
-
-.. automodule:: PyCTBN.network_graph
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.parameters\_estimator module
------------------------------------
-
-.. automodule:: PyCTBN.parameters_estimator
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.sample\_path module
---------------------------
-
-.. automodule:: PyCTBN.sample_path
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.set\_of\_cims module
----------------------------
-
-.. automodule:: PyCTBN.set_of_cims
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.structure module
------------------------
-
-.. automodule:: PyCTBN.structure
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.structure\_estimator module
-----------------------------------
-
-.. automodule:: PyCTBN.structure_estimator
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-PyCTBN.trajectory module
-------------------------
-
-.. automodule:: PyCTBN.trajectory
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: PyCTBN
-   :members:
-   :undoc-members:
-   :show-inheritance:

documentation/_build/html/genindex.html

@@ -1,665 +0,0 @@
-
-
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
-<html xml:lang="" lang="" version="-//W3C//DTD XHTML 1.1//EN" xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta charset="utf-8">
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-  
-  <title>Index &mdash; PyCTBN 1.0 documentation</title>
-  
-
-  
-
-  
-
-    <link href='https://fonts.googleapis.com/css?family=Lato:400,700,400italic,700italic|Roboto+Slab:400,700|Inconsolata:400,700' rel='stylesheet' type='text/css'/>
-    <link rel="stylesheet" href="_static/css/pdj.css" type="text/css" />
-
-  
-
-  
-
-  
-        <link rel="index" title="Index"
-              href="#"/>
-        <link rel="search" title="Search" href="search.html"/>
-    <link rel="top" title="PyCTBN 1.0 documentation" href="index.html"/>
-
-    <meta http-equiv="content-type" content="text/html; charset=utf-8" />
-    <meta http-equiv="cache-control" content="public" />
-    <meta name="robots" content="follow, all" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <!-- Add jQuery library -->
-    <script type="text/javascript" src="http://code.jquery.com/jquery-latest.min.js"></script>
-    <script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
-
-  </head>
-
-  <body class="wy-body-for-nav" role="document">
-
-  <div class="wy-grid-for-nav">
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-nav-search">
-        <a href="index.html" class="fa fa-home"> PyCTBN </a>
-        <div role="search">
-	  <form id ="rtd-search-form" class="wy-form"
-		action="search.html" method="get">
-	    <input type="text" name="q" placeholder="Search docs" />
-	    <input type="hidden" name="check_keywords" value="yes" />
-	    <input type="hidden" name="area" value="default" />
-	  </form>
-	</div>
-      </div>
-
-      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
-	
-          
-          
-              <p class="caption"><span class="caption-text">Contents:</span></p>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="examples.html#installation-usage">Installation/Usage:</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples.html#implementing-your-own-data-importer">Implementing your own data importer</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples.html#parameters-estimation-example">Parameters Estimation Example</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples.html#structure-estimation-example">Structure Estimation Example</a></li>
-</ul>
-</li>
-</ul>
-
-          
-        
-
-      </div>
-      &nbsp;
-    </nav>
-    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
-
-      <nav class="wy-nav-top" id="barra-mobile" role="navigation" aria-label="top navigation">
-        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-        <a href="#">Porão do Juca</a>
-      </nav>
-
-      <div class="wy-nav-content">
-	<div class="fundo-claro">
-	</div>
-	<div class="fundo-escuro">
-	</div>
-
-        <div class="rst-content">
-          <div role="navigation" aria-label="breadcrumbs navigation">
-	    
-	    <!-- <ul class="wy-breadcrumbs"> -->
-	    <!--   <li><a href="#">Docs</a> &raquo;</li> -->
-
-	    <!--   <li>Features</li> -->
-	    <!--   <li class="wy-breadcrumbs-aside"> -->
-
-	    <!-- 	<a href="_sources/index.txt" rel="nofollow"> View page source</a> -->
-
-	    <!--   </li> -->
-	    <!-- </ul> -->
-	    <!-- <hr/> -->
-	  </div>
-
-          <div role="main" class="">
-
-	    <div id="content" class="hfeed entry-container hentry">
-
-<h1 id="index">Index</h1>
-
-<div class="genindex-jumpbox">
- <a href="#A"><strong>A</strong></a>
- | <a href="#B"><strong>B</strong></a>
- | <a href="#C"><strong>C</strong></a>
- | <a href="#D"><strong>D</strong></a>
- | <a href="#E"><strong>E</strong></a>
- | <a href="#F"><strong>F</strong></a>
- | <a href="#G"><strong>G</strong></a>
- | <a href="#I"><strong>I</strong></a>
- | <a href="#J"><strong>J</strong></a>
- | <a href="#M"><strong>M</strong></a>
- | <a href="#N"><strong>N</strong></a>
- | <a href="#O"><strong>O</strong></a>
- | <a href="#P"><strong>P</strong></a>
- | <a href="#R"><strong>R</strong></a>
- | <a href="#S"><strong>S</strong></a>
- | <a href="#T"><strong>T</strong></a>
- | <a href="#V"><strong>V</strong></a>
- 
-</div>
-<h2 id="A">A</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter">AbstractImporter (class in PyCTBN.abstract_importer)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.actual_cims">actual_cims() (PyCTBN.set_of_cims.SetOfCims property)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.add_edges">add_edges() (PyCTBN.network_graph.NetworkGraph method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.add_nodes">add_nodes() (PyCTBN.network_graph.NetworkGraph method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.adjacency_matrix">adjacency_matrix() (PyCTBN.structure_estimator.StructureEstimator method)</a>
-</li>
-  </ul></td>
-</tr></table>
-
-<h2 id="B">B</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.build_cims">build_cims() (PyCTBN.set_of_cims.SetOfCims method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.build_complete_graph">build_complete_graph() (PyCTBN.structure_estimator.StructureEstimator method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.build_list_of_samples_array">build_list_of_samples_array() (PyCTBN.abstract_importer.AbstractImporter method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_p_comb_structure_for_a_node">build_p_comb_structure_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.build_sorter">build_sorter() (PyCTBN.abstract_importer.AbstractImporter method)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.build_sorter">(PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.build_structure">build_structure() (PyCTBN.sample_path.SamplePath method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_time_columns_filtering_for_a_node">build_time_columns_filtering_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_time_scalar_indexing_structure_for_a_node">build_time_scalar_indexing_structure_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.build_times_and_transitions_structures">build_times_and_transitions_structures() (PyCTBN.set_of_cims.SetOfCims method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.build_trajectories">build_trajectories() (PyCTBN.sample_path.SamplePath method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_transition_filtering_for_a_node">build_transition_filtering_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.build_transition_scalar_indexing_structure_for_a_node">build_transition_scalar_indexing_structure_for_a_node() (PyCTBN.network_graph.NetworkGraph method)</a>
-</li>
-  </ul></td>
-</tr></table>
-
-<h2 id="C">C</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.cache.Cache">Cache (class in PyCTBN.cache)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix.cim">cim() (PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.cache.Cache.clear">clear() (PyCTBN.cache.Cache method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.clear_concatenated_frame">clear_concatenated_frame() (PyCTBN.abstract_importer.AbstractImporter method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.clear_data_frame_list">clear_data_frame_list() (PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.complete_test">complete_test() (PyCTBN.structure_estimator.StructureEstimator method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory.complete_trajectory">complete_trajectory() (PyCTBN.trajectory.Trajectory property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix.compute_cim_coefficients">compute_cim_coefficients() (PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix method)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator.compute_parameters_for_node">compute_parameters_for_node() (PyCTBN.parameters_estimator.ParametersEstimator method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.compute_row_delta_in_all_samples_frames">compute_row_delta_in_all_samples_frames() (PyCTBN.abstract_importer.AbstractImporter method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.compute_row_delta_sigle_samples_frame">compute_row_delta_sigle_samples_frame() (PyCTBN.abstract_importer.AbstractImporter method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator.compute_state_res_time_for_node">compute_state_res_time_for_node() (PyCTBN.parameters_estimator.ParametersEstimator method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator.compute_state_transitions_for_a_node">compute_state_transitions_for_a_node() (PyCTBN.parameters_estimator.ParametersEstimator method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.concatenated_samples">concatenated_samples() (PyCTBN.abstract_importer.AbstractImporter property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix">ConditionalIntensityMatrix (class in PyCTBN.conditional_intensity_matrix)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.ctpc_algorithm">ctpc_algorithm() (PyCTBN.structure_estimator.StructureEstimator method)</a>
-</li>
-  </ul></td>
-</tr></table>
-
-<h2 id="D">D</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.dataset_id">dataset_id() (PyCTBN.abstract_importer.AbstractImporter method)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.dataset_id">(PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-      </ul></li>
-  </ul></td>
-</tr></table>
-
-<h2 id="E">E</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.edges">edges() (PyCTBN.network_graph.NetworkGraph property)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.edges">(PyCTBN.structure.Structure property)</a>
-</li>
-      </ul></li>
-  </ul></td>
-</tr></table>
-
-<h2 id="F">F</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.fast_init">fast_init() (PyCTBN.network_graph.NetworkGraph method)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator.fast_init">(PyCTBN.parameters_estimator.ParametersEstimator method)</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.file_path">file_path() (PyCTBN.abstract_importer.AbstractImporter property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.filter_cims_with_mask">filter_cims_with_mask() (PyCTBN.set_of_cims.SetOfCims method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.cache.Cache.find">find() (PyCTBN.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="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.generate_possible_sub_sets_of_size">generate_possible_sub_sets_of_size() (PyCTBN.structure_estimator.StructureEstimator method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.get_cims_number">get_cims_number() (PyCTBN.set_of_cims.SetOfCims method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.structure.Structure.get_node_id">get_node_id() (PyCTBN.structure.Structure method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_node_indx">get_node_indx() (PyCTBN.network_graph.NetworkGraph method)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.get_node_indx">(PyCTBN.structure.Structure method)</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_ordered_by_indx_set_of_parents">get_ordered_by_indx_set_of_parents() (PyCTBN.network_graph.NetworkGraph method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_parents_by_id">get_parents_by_id() (PyCTBN.network_graph.NetworkGraph method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_positional_node_indx">get_positional_node_indx() (PyCTBN.network_graph.NetworkGraph method)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.get_positional_node_indx">(PyCTBN.structure.Structure method)</a>
-</li>
-      </ul></li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.get_states_number">get_states_number() (PyCTBN.network_graph.NetworkGraph method)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.get_states_number">(PyCTBN.structure.Structure method)</a>
-</li>
-      </ul></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="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_data">import_data() (PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_sampled_cims">import_sampled_cims() (PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_structure">import_structure() (PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_trajectories">import_trajectories() (PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.import_variables">import_variables() (PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.independence_test">independence_test() (PyCTBN.structure_estimator.StructureEstimator 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="PyCTBN.html#PyCTBN.json_importer.JsonImporter">JsonImporter (class in PyCTBN.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>
-    module
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN">PyCTBN</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator</a>
-</li>
-        <li><a href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory</a>
-</li>
-      </ul></li>
-  </ul></td>
-</tr></table>
-
-<h2 id="N">N</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph">NetworkGraph (class in PyCTBN.network_graph)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.nodes">nodes() (PyCTBN.network_graph.NetworkGraph property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.nodes_indexes">nodes_indexes() (PyCTBN.network_graph.NetworkGraph property)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.nodes_indexes">(PyCTBN.structure.Structure property)</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.structure.Structure.nodes_labels">nodes_labels() (PyCTBN.structure.Structure property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.nodes_values">nodes_values() (PyCTBN.network_graph.NetworkGraph property)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.structure.Structure.nodes_values">(PyCTBN.structure.Structure property)</a>
-</li>
-      </ul></li>
-      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.normalize_trajectories">normalize_trajectories() (PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-  </ul></td>
-</tr></table>
-
-<h2 id="O">O</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.one_iteration_of_CTPC_algorithm">one_iteration_of_CTPC_algorithm() (PyCTBN.structure_estimator.StructureEstimator method)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.json_importer.JsonImporter.one_level_normalizing">one_level_normalizing() (PyCTBN.json_importer.JsonImporter method)</a>
-</li>
-  </ul></td>
-</tr></table>
-
-<h2 id="P">P</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.p_combs">p_combs() (PyCTBN.network_graph.NetworkGraph property)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims.p_combs">(PyCTBN.set_of_cims.SetOfCims property)</a>
-</li>
-      </ul></li>
-      <li><a href="PyCTBN.html#PyCTBN.parameters_estimator.ParametersEstimator">ParametersEstimator (class in PyCTBN.parameters_estimator)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.cache.Cache.put">put() (PyCTBN.cache.Cache method)</a>
-</li>
-      <li>
-    PyCTBN
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.abstract_importer
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.abstract_importer">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.cache
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.cache">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.conditional_intensity_matrix
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.json_importer
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.json_importer">module</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li>
-    PyCTBN.network_graph
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.network_graph">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.parameters_estimator
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.parameters_estimator">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.sample_path
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.sample_path">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.set_of_cims
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.set_of_cims">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.structure
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.structure">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.structure_estimator
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.structure_estimator">module</a>
-</li>
-      </ul></li>
-      <li>
-    PyCTBN.trajectory
-
-      <ul>
-        <li><a href="PyCTBN.html#module-PyCTBN.trajectory">module</a>
-</li>
-      </ul></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="PyCTBN.html#PyCTBN.json_importer.JsonImporter.read_json_file">read_json_file() (PyCTBN.json_importer.JsonImporter method)</a>
-</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="PyCTBN.html#PyCTBN.sample_path.SamplePath">SamplePath (class in PyCTBN.sample_path)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator.save_results">save_results() (PyCTBN.structure_estimator.StructureEstimator method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.set_of_cims.SetOfCims">SetOfCims (class in PyCTBN.set_of_cims)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory.size">size() (PyCTBN.trajectory.Trajectory method)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.sorter">sorter() (PyCTBN.abstract_importer.AbstractImporter property)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix.state_residence_times">state_residence_times() (PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix.state_transition_matrix">state_transition_matrix() (PyCTBN.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.structure.Structure">Structure (class in PyCTBN.structure)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.structure">structure() (PyCTBN.abstract_importer.AbstractImporter property)</a>
-
-      <ul>
-        <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.structure">(PyCTBN.sample_path.SamplePath property)</a>
-</li>
-      </ul></li>
-      <li><a href="PyCTBN.html#PyCTBN.structure_estimator.StructureEstimator">StructureEstimator (class in PyCTBN.structure_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="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.time_filtering">time_filtering() (PyCTBN.network_graph.NetworkGraph property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.time_scalar_indexing_strucure">time_scalar_indexing_strucure() (PyCTBN.network_graph.NetworkGraph property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory.times">times() (PyCTBN.trajectory.Trajectory property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.total_variables_count">total_variables_count() (PyCTBN.sample_path.SamplePath property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.structure.Structure.total_variables_number">total_variables_number() (PyCTBN.structure.Structure property)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="PyCTBN.html#PyCTBN.sample_path.SamplePath.trajectories">trajectories() (PyCTBN.sample_path.SamplePath property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory">Trajectory (class in PyCTBN.trajectory)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.trajectory.Trajectory.trajectory">trajectory() (PyCTBN.trajectory.Trajectory property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.transition_filtering">transition_filtering() (PyCTBN.network_graph.NetworkGraph property)</a>
-</li>
-      <li><a href="PyCTBN.html#PyCTBN.network_graph.NetworkGraph.transition_scalar_indexing_structure">transition_scalar_indexing_structure() (PyCTBN.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="PyCTBN.html#PyCTBN.abstract_importer.AbstractImporter.variables">variables() (PyCTBN.abstract_importer.AbstractImporter property)</a>
-</li>
-  </ul></td>
-</tr></table>
-
-
-
-	    </div>
-            <footer>
-  
-
-  <hr/>
-
-  <div role="contentinfo">
-    <p>
-        &copy; Copyright 2020, Alessandro Bregoli, Filippo Martini.
-    </p>
-  </div>
-
-  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/jucacrispim/sphinx_pdj_theme">theme</a> provided by <a href="http://poraodojuca.net">Porão do Juca</a>.
-
-</footer>
-	</div>
-	</div>
-	  
-
-    <script type="text/javascript">
-        var DOCUMENTATION_OPTIONS = {
-            URL_ROOT:'./',
-            VERSION:'1.0',
-            COLLAPSE_INDEX:false,
-            FILE_SUFFIX:'.html',
-            HAS_SOURCE:  true
-        };
-    </script>
-    <script type="text/javascript" src="_static/jquery.js">
-
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-    <script type="text/javascript" src="_static/underscore.js">
-
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-    <script type="text/javascript" src="_static/doctools.js">
-
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-
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-</html>

examples/parameters_estimation_example.py

@@ -3,14 +3,14 @@ import os
 import glob
 
 
-from PyCTBN.PyCTBN.json_importer import JsonImporter
-from PyCTBN.PyCTBN.sample_path import SamplePath
-from PyCTBN.PyCTBN.network_graph import NetworkGraph
-from PyCTBN.PyCTBN.parameters_estimator import ParametersEstimator
+from PyCTBN.classes.json_importer import JsonImporter
+from PyCTBN.classes.sample_path import SamplePath
+from PyCTBN.classes.network_graph import NetworkGraph
+from PyCTBN.classes.parameters_estimator import ParametersEstimator
 
 
 def main():
-    read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
+    read_files = glob.glob(os.path.join('../data', "*.json")) #Take all json files in this dir
     #import data
     importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
     importer.import_data(0)

examples/structure_estimation_example.py

@@ -1,15 +1,15 @@
 import os
 import glob
 
-from PyCTBN.PyCTBN.json_importer import JsonImporter
-from PyCTBN.PyCTBN.sample_path import SamplePath
-from PyCTBN.PyCTBN.structure_estimator import StructureEstimator
+from PyCTBN.classes.json_importer import JsonImporter
+from PyCTBN.classes.sample_path import SamplePath
+from PyCTBN.classes.structure_estimator import StructureEstimator
 
 
 def structure_estimation_example():
 
     # read the json files in ./data path
-    read_files = glob.glob(os.path.join('./data', "*.json"))
+    read_files = glob.glob(os.path.join('../data', "*.json"))
     # initialize a JsonImporter object for the first file
     importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
     # import the data at index 0 of the outer json array

setup.py

@@ -1,5 +1,7 @@
 from setuptools import setup, find_packages
 
+print(find_packages('.', exclude=['PyCTBN.tests']))
+
 setup(name='PyCTBN',
       version='1.0',
       url='https://github.com/philipMartini/PyCTBN',
@@ -7,11 +9,14 @@ setup(name='PyCTBN',
       author=['Alessandro Bregoli', 'Filippo Martini'],
       author_email=['a.bregoli1@campus.unimib.it', 'f.martini@campus.unimib.it'],
       description='A Continuous Time Bayesian Networks Library',
-      packages=find_packages(exclude=['tests', 'data']),
+      packages=find_packages('.', exclude=['PyCTBN.tests']),
+      #packages=['PyCTBN.classes'],
       install_requires=[
           'numpy', 'pandas', 'networkx', 'scipy', 'tqdm'],
       dependency_links=['https://github.com/numpy/numpy', 'https://github.com/pandas-dev/pandas',
                         'https://github.com/networkx/networkx', 'https://github.com/scipy/scipy',
                         'https://github.com/tqdm/tqdm'],
       long_description=open('README.md').read(),
-      zip_safe=False)
+      zip_safe=False,
+      python_requires='>=3.6')
+

sphinx_output/_build/html/_sources/classes.rst.txt

@@ -0,0 +1,101 @@
+classes package
+===============
+
+Submodules
+----------
+
+classes.abstract\_importer module
+---------------------------------
+
+.. automodule:: classes.abstract_importer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.cache module
+--------------------
+
+.. automodule:: classes.cache
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.conditional\_intensity\_matrix module
+---------------------------------------------
+
+.. automodule:: classes.conditional_intensity_matrix
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.json\_importer module
+-----------------------------
+
+.. automodule:: classes.json_importer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.network\_graph module
+-----------------------------
+
+.. automodule:: classes.network_graph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.parameters\_estimator module
+------------------------------------
+
+.. automodule:: classes.parameters_estimator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.sample\_path module
+---------------------------
+
+.. automodule:: classes.sample_path
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.set\_of\_cims module
+----------------------------
+
+.. automodule:: classes.set_of_cims
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.structure module
+------------------------
+
+.. automodule:: classes.structure
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.structure\_estimator module
+-----------------------------------
+
+.. automodule:: classes.structure_estimator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.trajectory module
+-------------------------
+
+.. automodule:: classes.trajectory
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: classes
+   :members:
+   :undoc-members:
+   :show-inheritance:

sphinx_output/_build/html/_sources/examples.rst.txt

@@ -10,7 +10,7 @@ Implementing your own data importer
 .. code-block:: python
 
     """This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format.
-    The net in exam has three ternary nodes.
+    The net in exam has three ternary nodes and no prior net structure.
     """
 
     from .abstract_importer import AbstractImporter
@@ -25,7 +25,6 @@ Implementing your own data importer
             self.read_csv_file()
             self._sorter = self.build_sorter(self._df_samples_list[0])
             self.import_variables()
-            self.import_structure()
             self.compute_row_delta_in_all_samples_frames(self._df_samples_list)
 
         def read_csv_file(self):
@@ -43,10 +42,6 @@ Implementing your own data importer
         def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
             return list(sample_frame.columns)[1:]
 
-        def import_structure(self):
-            data = {'From':['X','Y','Z'], 'To':['Z','Z','Y']}
-            self._df_structure = pd.DataFrame(data)
-
         def dataset_id(self) -> object:
             pass
 

sphinx_output/_build/html/_sources/index.rst.txt

@@ -1,5 +1,5 @@
 .. PyCTBN documentation master file, created by
-   sphinx-quickstart on Mon Dec  7 15:11:12 2020.
+   sphinx-quickstart on Mon Dec 14 20:33:17 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
@@ -10,7 +10,7 @@ Welcome to PyCTBN's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-   PyCTBN
+   classes
    examples
 
 Indices and tables

sphinx_output/_build/html/_sources/modules.rst.txt

@@ -1,7 +1,7 @@
-PyCTBN
-======
+classes
+=======
 
 .. toctree::
    :maxdepth: 4
 
-   PyCTBN
+   classes

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+        padding: 10px 20px;
+        background: #333;
+        color: #FFF;
+    }
+
+    div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p,
+    div.sphinxsidebar h3 a {
+        color: #fff;
+    }
+
+    div.sphinxsidebar a {
+        color: #AAA;
+    }
+
+    div.sphinxsidebar p.logo {
+        display: none;
+    }
+
+    div.document {
+        width: 100%;
+        margin: 0;
+    }
+
+    div.footer {
+        display: none;
+    }
+
+    div.bodywrapper {
+        margin: 0;
+    }
+
+    div.body {
+        min-height: 0;
+        padding: 0;
+    }
+
+    .rtd_doc_footer {
+        display: none;
+    }
+
+    .document {
+        width: auto;
+    }
+
+    .footer {
+        width: auto;
+    }
+
+    .footer {
+        width: auto;
+    }
+
+    .github {
+        display: none;
+    }
+}
+
+
+/* misc. */
+
+.revsys-inline {
+    display: none!important;
+}
+
+/* Make nested-list/multi-paragraph items look better in Releases changelog
+ * pages. Without this, docutils' magical list fuckery causes inconsistent
+ * formatting between different release sub-lists.
+ */
+div#changelog > div.section > ul > li > p:only-child {
+    margin-bottom: 0;
+}
+
+/* Hide fugly table cell borders in ..bibliography:: directive output */
+table.docutils.citation, table.docutils.citation td, table.docutils.citation th {
+  border: none;
+  /* Below needed in some edge cases; if not applied, bottom shadows appear */
+  -moz-box-shadow: none;
+  -webkit-box-shadow: none;
+  box-shadow: none;
+}
+
+
+/* relbar */
+
+.related {
+    line-height: 30px;
+    width: 100%;
+    font-size: 0.9rem;
+}
+
+.related.top {
+    border-bottom: 1px solid #EEE;
+    margin-bottom: 20px;
+}
+
+.related.bottom {
+    border-top: 1px solid #EEE;
+}
+
+.related ul {
+    padding: 0;
+    margin: 0;
+    list-style: none;
+}
+
+.related li {
+    display: inline;
+}
+
+nav#rellinks {
+    float: right;
+}
+
+nav#rellinks li+li:before {
+    content: "|";
+}
+
+nav#breadcrumbs li+li:before {
+    content: "\00BB";
+}
+
+/* Hide certain items when printing */
+@media print {
+    div.related {
+        display: none;
+    }
+}

sphinx_output/_build/html/_static/custom.css

@@ -0,0 +1 @@
+/* This file intentionally left blank. */

sphinx_output/_build/html/examples.html

@@ -27,7 +27,7 @@
               href="genindex.html"/>
         <link rel="search" title="Search" href="search.html"/>
     <link rel="top" title="PyCTBN 1.0 documentation" href="index.html"/>
-        <link rel="prev" title="PyCTBN package" href="PyCTBN.html"/>
+        <link rel="prev" title="classes package" href="classes.html"/>
 
     <meta http-equiv="content-type" content="text/html; charset=utf-8" />
     <meta http-equiv="cache-control" content="public" />
@@ -61,20 +61,20 @@
           
               <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="classes.html">classes package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.abstract_importer">classes.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.cache">classes.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.conditional_intensity_matrix">classes.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.json_importer">classes.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.network_graph">classes.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.parameters_estimator">classes.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.sample_path">classes.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.set_of_cims">classes.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure">classes.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure_estimator">classes.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.trajectory">classes.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes">Module contents</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Examples</a><ul>
@@ -132,7 +132,7 @@
 <div class="section" id="implementing-your-own-data-importer">
 <h2>Implementing your own data importer<a class="headerlink" href="#implementing-your-own-data-importer" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="sd">&quot;&quot;&quot;This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format.</span>
-<span class="sd">The net in exam has three ternary nodes.</span>
+<span class="sd">The net in exam has three ternary nodes and no prior net structure.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">from</span> <span class="nn">.abstract_importer</span> <span class="kn">import</span> <span class="n">AbstractImporter</span>
@@ -147,7 +147,6 @@
         <span class="bp">self</span><span class="o">.</span><span class="n">read_csv_file</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_sorter</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">build_sorter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df_samples_list</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">import_variables</span><span class="p">()</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">import_structure</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">compute_row_delta_in_all_samples_frames</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df_samples_list</span><span class="p">)</span>
 
     <span class="k">def</span> <span class="nf">read_csv_file</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -165,10 +164,6 @@
     <span class="k">def</span> <span class="nf">build_sorter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sample_frame</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">typing</span><span class="o">.</span><span class="n">List</span><span class="p">:</span>
         <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">sample_frame</span><span class="o">.</span><span class="n">columns</span><span class="p">)[</span><span class="mi">1</span><span class="p">:]</span>
 
-    <span class="k">def</span> <span class="nf">import_structure</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="n">data</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;From&#39;</span><span class="p">:[</span><span class="s1">&#39;X&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">,</span><span class="s1">&#39;Z&#39;</span><span class="p">],</span> <span class="s1">&#39;To&#39;</span><span class="p">:[</span><span class="s1">&#39;Z&#39;</span><span class="p">,</span><span class="s1">&#39;Z&#39;</span><span class="p">,</span><span class="s1">&#39;Y&#39;</span><span class="p">]}</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_df_structure</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
-
     <span class="k">def</span> <span class="nf">dataset_id</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">object</span><span class="p">:</span>
         <span class="k">pass</span>
 </pre></div>
@@ -252,7 +247,7 @@
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
       
       
-        <a href="PyCTBN.html" class="btn btn-neutral" title="PyCTBN package"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="classes.html" class="btn btn-neutral" title="classes package"><span class="fa fa-arrow-circle-left"></span> Previous</a>
       
     </div>
   

sphinx_output/_build/html/genindex.html

@@ -0,0 +1,675 @@
+
+
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
+<html xml:lang="" lang="" version="-//W3C//DTD XHTML 1.1//EN" xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+  
+  <title>Index &mdash; PyCTBN 1.0 documentation</title>
+  
+
+  
+
+  
+
+    <link href='https://fonts.googleapis.com/css?family=Lato:400,700,400italic,700italic|Roboto+Slab:400,700|Inconsolata:400,700' rel='stylesheet' type='text/css'/>
+    <link rel="stylesheet" href="_static/css/pdj.css" type="text/css" />
+
+  
+
+  
+
+  
+        <link rel="index" title="Index"
+              href="#"/>
+        <link rel="search" title="Search" href="search.html"/>
+    <link rel="top" title="PyCTBN 1.0 documentation" href="index.html"/>
+
+    <meta http-equiv="content-type" content="text/html; charset=utf-8" />
+    <meta http-equiv="cache-control" content="public" />
+    <meta name="robots" content="follow, all" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <!-- Add jQuery library -->
+    <script type="text/javascript" src="http://code.jquery.com/jquery-latest.min.js"></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
+
+  </head>
+
+  <body class="wy-body-for-nav" role="document">
+
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-nav-search">
+        <a href="index.html" class="fa fa-home"> PyCTBN </a>
+        <div role="search">
+	  <form id ="rtd-search-form" class="wy-form"
+		action="search.html" method="get">
+	    <input type="text" name="q" placeholder="Search docs" />
+	    <input type="hidden" name="check_keywords" value="yes" />
+	    <input type="hidden" name="area" value="default" />
+	  </form>
+	</div>
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+	
+          
+          
+              <p class="caption"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="classes.html">classes package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.abstract_importer">classes.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.cache">classes.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.conditional_intensity_matrix">classes.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.json_importer">classes.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.network_graph">classes.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.parameters_estimator">classes.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.sample_path">classes.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.set_of_cims">classes.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure">classes.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure_estimator">classes.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.trajectory">classes.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes">Module contents</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#installation-usage">Installation/Usage:</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#implementing-your-own-data-importer">Implementing your own data importer</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#parameters-estimation-example">Parameters Estimation Example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="examples.html#structure-estimation-example">Structure Estimation Example</a></li>
+</ul>
+</li>
+</ul>
+
+          
+        
+
+      </div>
+      &nbsp;
+    </nav>
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      <nav class="wy-nav-top" id="barra-mobile" role="navigation" aria-label="top navigation">
+        <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+        <a href="#">Porão do Juca</a>
+      </nav>
+
+      <div class="wy-nav-content">
+	<div class="fundo-claro">
+	</div>
+	<div class="fundo-escuro">
+	</div>
+
+        <div class="rst-content">
+          <div role="navigation" aria-label="breadcrumbs navigation">
+	    
+	    <!-- <ul class="wy-breadcrumbs"> -->
+	    <!--   <li><a href="#">Docs</a> &raquo;</li> -->
+
+	    <!--   <li>Features</li> -->
+	    <!--   <li class="wy-breadcrumbs-aside"> -->
+
+	    <!-- 	<a href="_sources/index.txt" rel="nofollow"> View page source</a> -->
+
+	    <!--   </li> -->
+	    <!-- </ul> -->
+	    <!-- <hr/> -->
+	  </div>
+
+          <div role="main" class="">
+
+	    <div id="content" class="hfeed entry-container hentry">
+
+<h1 id="index">Index</h1>
+
+<div class="genindex-jumpbox">
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#E"><strong>E</strong></a>
+ | <a href="#F"><strong>F</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#I"><strong>I</strong></a>
+ | <a href="#J"><strong>J</strong></a>
+ | <a href="#M"><strong>M</strong></a>
+ | <a href="#N"><strong>N</strong></a>
+ | <a href="#O"><strong>O</strong></a>
+ | <a href="#P"><strong>P</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#V"><strong>V</strong></a>
+ 
+</div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter">AbstractImporter (class in classes.abstract_importer)</a>
+</li>
+      <li><a href="classes.html#classes.set_of_cims.SetOfCims.actual_cims">actual_cims() (classes.set_of_cims.SetOfCims property)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.add_edges">add_edges() (classes.network_graph.NetworkGraph method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.add_nodes">add_nodes() (classes.network_graph.NetworkGraph method)</a>
+</li>
+      <li><a href="classes.html#classes.structure_estimator.StructureEstimator.adjacency_matrix">adjacency_matrix() (classes.structure_estimator.StructureEstimator method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.set_of_cims.SetOfCims.build_cims">build_cims() (classes.set_of_cims.SetOfCims method)</a>
+</li>
+      <li><a href="classes.html#classes.structure_estimator.StructureEstimator.build_complete_graph">build_complete_graph() (classes.structure_estimator.StructureEstimator static method)</a>
+</li>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.build_list_of_samples_array">build_list_of_samples_array() (classes.abstract_importer.AbstractImporter method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.build_p_comb_structure_for_a_node">build_p_comb_structure_for_a_node() (classes.network_graph.NetworkGraph static method)</a>
+</li>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.build_sorter">build_sorter() (classes.abstract_importer.AbstractImporter method)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.json_importer.JsonImporter.build_sorter">(classes.json_importer.JsonImporter method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.sample_path.SamplePath.build_structure">build_structure() (classes.sample_path.SamplePath method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.build_time_columns_filtering_for_a_node">build_time_columns_filtering_for_a_node() (classes.network_graph.NetworkGraph static method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.build_time_scalar_indexing_structure_for_a_node">build_time_scalar_indexing_structure_for_a_node() (classes.network_graph.NetworkGraph static method)</a>
+</li>
+      <li><a href="classes.html#classes.set_of_cims.SetOfCims.build_times_and_transitions_structures">build_times_and_transitions_structures() (classes.set_of_cims.SetOfCims method)</a>
+</li>
+      <li><a href="classes.html#classes.sample_path.SamplePath.build_trajectories">build_trajectories() (classes.sample_path.SamplePath method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.build_transition_filtering_for_a_node">build_transition_filtering_for_a_node() (classes.network_graph.NetworkGraph static method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.build_transition_scalar_indexing_structure_for_a_node">build_transition_scalar_indexing_structure_for_a_node() (classes.network_graph.NetworkGraph static method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.cache.Cache">Cache (class in classes.cache)</a>
+</li>
+      <li><a href="classes.html#classes.conditional_intensity_matrix.ConditionalIntensityMatrix.cim">cim() (classes.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
+</li>
+      <li>
+    classes
+
+      <ul>
+        <li><a href="classes.html#module-classes">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.abstract_importer
+
+      <ul>
+        <li><a href="classes.html#module-classes.abstract_importer">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.cache
+
+      <ul>
+        <li><a href="classes.html#module-classes.cache">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.conditional_intensity_matrix
+
+      <ul>
+        <li><a href="classes.html#module-classes.conditional_intensity_matrix">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.json_importer
+
+      <ul>
+        <li><a href="classes.html#module-classes.json_importer">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.network_graph
+
+      <ul>
+        <li><a href="classes.html#module-classes.network_graph">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.parameters_estimator
+
+      <ul>
+        <li><a href="classes.html#module-classes.parameters_estimator">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.sample_path
+
+      <ul>
+        <li><a href="classes.html#module-classes.sample_path">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.set_of_cims
+
+      <ul>
+        <li><a href="classes.html#module-classes.set_of_cims">module</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li>
+    classes.structure
+
+      <ul>
+        <li><a href="classes.html#module-classes.structure">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.structure_estimator
+
+      <ul>
+        <li><a href="classes.html#module-classes.structure_estimator">module</a>
+</li>
+      </ul></li>
+      <li>
+    classes.trajectory
+
+      <ul>
+        <li><a href="classes.html#module-classes.trajectory">module</a>
+</li>
+      </ul></li>
+      <li><a href="classes.html#classes.cache.Cache.clear">clear() (classes.cache.Cache method)</a>
+</li>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.clear_concatenated_frame">clear_concatenated_frame() (classes.abstract_importer.AbstractImporter method)</a>
+</li>
+      <li><a href="classes.html#classes.json_importer.JsonImporter.clear_data_frame_list">clear_data_frame_list() (classes.json_importer.JsonImporter method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.clear_indexing_filtering_structures">clear_indexing_filtering_structures() (classes.network_graph.NetworkGraph method)</a>
+</li>
+      <li><a href="classes.html#classes.structure_estimator.StructureEstimator.complete_test">complete_test() (classes.structure_estimator.StructureEstimator method)</a>
+</li>
+      <li><a href="classes.html#classes.trajectory.Trajectory.complete_trajectory">complete_trajectory() (classes.trajectory.Trajectory property)</a>
+</li>
+      <li><a href="classes.html#classes.conditional_intensity_matrix.ConditionalIntensityMatrix.compute_cim_coefficients">compute_cim_coefficients() (classes.conditional_intensity_matrix.ConditionalIntensityMatrix method)</a>
+</li>
+      <li><a href="classes.html#classes.parameters_estimator.ParametersEstimator.compute_parameters_for_node">compute_parameters_for_node() (classes.parameters_estimator.ParametersEstimator method)</a>
+</li>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.compute_row_delta_in_all_samples_frames">compute_row_delta_in_all_samples_frames() (classes.abstract_importer.AbstractImporter method)</a>
+</li>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.compute_row_delta_sigle_samples_frame">compute_row_delta_sigle_samples_frame() (classes.abstract_importer.AbstractImporter method)</a>
+</li>
+      <li><a href="classes.html#classes.parameters_estimator.ParametersEstimator.compute_state_res_time_for_node">compute_state_res_time_for_node() (classes.parameters_estimator.ParametersEstimator static method)</a>
+</li>
+      <li><a href="classes.html#classes.parameters_estimator.ParametersEstimator.compute_state_transitions_for_a_node">compute_state_transitions_for_a_node() (classes.parameters_estimator.ParametersEstimator static method)</a>
+</li>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.concatenated_samples">concatenated_samples() (classes.abstract_importer.AbstractImporter property)</a>
+</li>
+      <li><a href="classes.html#classes.conditional_intensity_matrix.ConditionalIntensityMatrix">ConditionalIntensityMatrix (class in classes.conditional_intensity_matrix)</a>
+</li>
+      <li><a href="classes.html#classes.structure_estimator.StructureEstimator.ctpc_algorithm">ctpc_algorithm() (classes.structure_estimator.StructureEstimator method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.dataset_id">dataset_id() (classes.abstract_importer.AbstractImporter method)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.json_importer.JsonImporter.dataset_id">(classes.json_importer.JsonImporter method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.edges">edges() (classes.network_graph.NetworkGraph property)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.structure.Structure.edges">(classes.structure.Structure property)</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<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.html#classes.network_graph.NetworkGraph.fast_init">fast_init() (classes.network_graph.NetworkGraph method)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.parameters_estimator.ParametersEstimator.fast_init">(classes.parameters_estimator.ParametersEstimator method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.file_path">file_path() (classes.abstract_importer.AbstractImporter property)</a>
+</li>
+      <li><a href="classes.html#classes.set_of_cims.SetOfCims.filter_cims_with_mask">filter_cims_with_mask() (classes.set_of_cims.SetOfCims method)</a>
+</li>
+      <li><a href="classes.html#classes.cache.Cache.find">find() (classes.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.html#classes.structure_estimator.StructureEstimator.generate_possible_sub_sets_of_size">generate_possible_sub_sets_of_size() (classes.structure_estimator.StructureEstimator static method)</a>
+</li>
+      <li><a href="classes.html#classes.set_of_cims.SetOfCims.get_cims_number">get_cims_number() (classes.set_of_cims.SetOfCims method)</a>
+</li>
+      <li><a href="classes.html#classes.structure.Structure.get_node_id">get_node_id() (classes.structure.Structure method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.get_node_indx">get_node_indx() (classes.network_graph.NetworkGraph method)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.structure.Structure.get_node_indx">(classes.structure.Structure method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.get_ordered_by_indx_set_of_parents">get_ordered_by_indx_set_of_parents() (classes.network_graph.NetworkGraph method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.get_parents_by_id">get_parents_by_id() (classes.network_graph.NetworkGraph method)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.get_positional_node_indx">get_positional_node_indx() (classes.network_graph.NetworkGraph method)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.structure.Structure.get_positional_node_indx">(classes.structure.Structure method)</a>
+</li>
+      </ul></li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.get_states_number">get_states_number() (classes.network_graph.NetworkGraph method)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.structure.Structure.get_states_number">(classes.structure.Structure method)</a>
+</li>
+      </ul></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.html#classes.json_importer.JsonImporter.import_data">import_data() (classes.json_importer.JsonImporter method)</a>
+</li>
+      <li><a href="classes.html#classes.json_importer.JsonImporter.import_sampled_cims">import_sampled_cims() (classes.json_importer.JsonImporter method)</a>
+</li>
+      <li><a href="classes.html#classes.json_importer.JsonImporter.import_structure">import_structure() (classes.json_importer.JsonImporter method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.json_importer.JsonImporter.import_trajectories">import_trajectories() (classes.json_importer.JsonImporter method)</a>
+</li>
+      <li><a href="classes.html#classes.json_importer.JsonImporter.import_variables">import_variables() (classes.json_importer.JsonImporter method)</a>
+</li>
+      <li><a href="classes.html#classes.structure_estimator.StructureEstimator.independence_test">independence_test() (classes.structure_estimator.StructureEstimator 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.html#classes.json_importer.JsonImporter">JsonImporter (class in classes.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>
+    module
+
+      <ul>
+        <li><a href="classes.html#module-classes">classes</a>
+</li>
+        <li><a href="classes.html#module-classes.abstract_importer">classes.abstract_importer</a>
+</li>
+        <li><a href="classes.html#module-classes.cache">classes.cache</a>
+</li>
+        <li><a href="classes.html#module-classes.conditional_intensity_matrix">classes.conditional_intensity_matrix</a>
+</li>
+        <li><a href="classes.html#module-classes.json_importer">classes.json_importer</a>
+</li>
+        <li><a href="classes.html#module-classes.network_graph">classes.network_graph</a>
+</li>
+        <li><a href="classes.html#module-classes.parameters_estimator">classes.parameters_estimator</a>
+</li>
+        <li><a href="classes.html#module-classes.sample_path">classes.sample_path</a>
+</li>
+        <li><a href="classes.html#module-classes.set_of_cims">classes.set_of_cims</a>
+</li>
+        <li><a href="classes.html#module-classes.structure">classes.structure</a>
+</li>
+        <li><a href="classes.html#module-classes.structure_estimator">classes.structure_estimator</a>
+</li>
+        <li><a href="classes.html#module-classes.trajectory">classes.trajectory</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="N">N</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph">NetworkGraph (class in classes.network_graph)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.nodes">nodes() (classes.network_graph.NetworkGraph property)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.nodes_indexes">nodes_indexes() (classes.network_graph.NetworkGraph property)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.structure.Structure.nodes_indexes">(classes.structure.Structure property)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.structure.Structure.nodes_labels">nodes_labels() (classes.structure.Structure property)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.nodes_values">nodes_values() (classes.network_graph.NetworkGraph property)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.structure.Structure.nodes_values">(classes.structure.Structure property)</a>
+</li>
+      </ul></li>
+      <li><a href="classes.html#classes.json_importer.JsonImporter.normalize_trajectories">normalize_trajectories() (classes.json_importer.JsonImporter method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="O">O</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.structure_estimator.StructureEstimator.one_iteration_of_CTPC_algorithm">one_iteration_of_CTPC_algorithm() (classes.structure_estimator.StructureEstimator method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.json_importer.JsonImporter.one_level_normalizing">one_level_normalizing() (classes.json_importer.JsonImporter method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.p_combs">p_combs() (classes.network_graph.NetworkGraph property)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.set_of_cims.SetOfCims.p_combs">(classes.set_of_cims.SetOfCims property)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.parameters_estimator.ParametersEstimator">ParametersEstimator (class in classes.parameters_estimator)</a>
+</li>
+      <li><a href="classes.html#classes.cache.Cache.put">put() (classes.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.html#classes.json_importer.JsonImporter.read_json_file">read_json_file() (classes.json_importer.JsonImporter method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.remove_node">remove_node() (classes.network_graph.NetworkGraph method)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.structure.Structure.remove_node">(classes.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.html#classes.sample_path.SamplePath">SamplePath (class in classes.sample_path)</a>
+</li>
+      <li><a href="classes.html#classes.structure_estimator.StructureEstimator.save_results">save_results() (classes.structure_estimator.StructureEstimator method)</a>
+</li>
+      <li><a href="classes.html#classes.set_of_cims.SetOfCims">SetOfCims (class in classes.set_of_cims)</a>
+</li>
+      <li><a href="classes.html#classes.trajectory.Trajectory.size">size() (classes.trajectory.Trajectory method)</a>
+</li>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.sorter">sorter() (classes.abstract_importer.AbstractImporter property)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.conditional_intensity_matrix.ConditionalIntensityMatrix.state_residence_times">state_residence_times() (classes.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
+</li>
+      <li><a href="classes.html#classes.conditional_intensity_matrix.ConditionalIntensityMatrix.state_transition_matrix">state_transition_matrix() (classes.conditional_intensity_matrix.ConditionalIntensityMatrix property)</a>
+</li>
+      <li><a href="classes.html#classes.structure.Structure">Structure (class in classes.structure)</a>
+</li>
+      <li><a href="classes.html#classes.abstract_importer.AbstractImporter.structure">structure() (classes.abstract_importer.AbstractImporter property)</a>
+
+      <ul>
+        <li><a href="classes.html#classes.sample_path.SamplePath.structure">(classes.sample_path.SamplePath property)</a>
+</li>
+      </ul></li>
+      <li><a href="classes.html#classes.structure_estimator.StructureEstimator">StructureEstimator (class in classes.structure_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.html#classes.network_graph.NetworkGraph.time_filtering">time_filtering() (classes.network_graph.NetworkGraph property)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.time_scalar_indexing_strucure">time_scalar_indexing_strucure() (classes.network_graph.NetworkGraph property)</a>
+</li>
+      <li><a href="classes.html#classes.trajectory.Trajectory.times">times() (classes.trajectory.Trajectory property)</a>
+</li>
+      <li><a href="classes.html#classes.sample_path.SamplePath.total_variables_count">total_variables_count() (classes.sample_path.SamplePath property)</a>
+</li>
+      <li><a href="classes.html#classes.structure.Structure.total_variables_number">total_variables_number() (classes.structure.Structure property)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="classes.html#classes.sample_path.SamplePath.trajectories">trajectories() (classes.sample_path.SamplePath property)</a>
+</li>
+      <li><a href="classes.html#classes.trajectory.Trajectory">Trajectory (class in classes.trajectory)</a>
+</li>
+      <li><a href="classes.html#classes.trajectory.Trajectory.trajectory">trajectory() (classes.trajectory.Trajectory property)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.transition_filtering">transition_filtering() (classes.network_graph.NetworkGraph property)</a>
+</li>
+      <li><a href="classes.html#classes.network_graph.NetworkGraph.transition_scalar_indexing_structure">transition_scalar_indexing_structure() (classes.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.html#classes.abstract_importer.AbstractImporter.variables">variables() (classes.abstract_importer.AbstractImporter property)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+
+
+	    </div>
+            <footer>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2020, Alessandro Bregoli, Filippo Martini.
+    </p>
+  </div>
+
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/jucacrispim/sphinx_pdj_theme">theme</a> provided by <a href="http://poraodojuca.net">Porão do Juca</a>.
+
+</footer>
+	</div>
+	</div>
+	  
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'1.0',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js">
+
+    </script>
+    <script type="text/javascript" src="_static/underscore.js">
+
+    </script>
+    <script type="text/javascript" src="_static/doctools.js">
+
+    </script>
+    <script type="text/javascript" src="_static/language_data.js">
+
+    </script>
+
+  
+
+   <script type="text/javascript"
+           src="_static/js/theme.js"></script>
+
+   <script type="text/javascript"
+           src="_static/js/pdj.js"></script>
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
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+  </script>
+   
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+  </body>
+</html>

sphinx_output/_build/html/index.html

@@ -27,7 +27,7 @@
               href="genindex.html"/>
         <link rel="search" title="Search" href="search.html"/>
     <link rel="top" title="PyCTBN 1.0 documentation" href="#"/>
-        <link rel="next" title="PyCTBN package" href="PyCTBN.html"/>
+        <link rel="next" title="classes package" href="classes.html"/>
 
     <meta http-equiv="content-type" content="text/html; charset=utf-8" />
     <meta http-equiv="cache-control" content="public" />
@@ -61,20 +61,20 @@
           
               <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="classes.html">classes package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.abstract_importer">classes.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.cache">classes.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.conditional_intensity_matrix">classes.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.json_importer">classes.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.network_graph">classes.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.parameters_estimator">classes.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.sample_path">classes.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.set_of_cims">classes.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure">classes.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure_estimator">classes.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.trajectory">classes.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes">Module contents</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
@@ -129,20 +129,20 @@
 <div class="toctree-wrapper compound">
 <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="classes.html">classes package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.abstract_importer">classes.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.cache">classes.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.conditional_intensity_matrix">classes.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.json_importer">classes.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.network_graph">classes.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.parameters_estimator">classes.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.sample_path">classes.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.set_of_cims">classes.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure">classes.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure_estimator">classes.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.trajectory">classes.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes">Module contents</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
@@ -170,7 +170,7 @@
   
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
       
-        <a href="PyCTBN.html" class="btn btn-neutral float-right" title="PyCTBN package">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="classes.html" class="btn btn-neutral float-right" title="classes package">Next <span class="fa fa-arrow-circle-right"></span></a>
       
       
     </div>

sphinx_output/_build/html/modules.html

@@ -8,7 +8,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
   
-  <title>PyCTBN &mdash; PyCTBN 1.0 documentation</title>
+  <title>classes &mdash; PyCTBN 1.0 documentation</title>
   
 
   
@@ -60,20 +60,20 @@
           
               <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="classes.html">classes package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.abstract_importer">classes.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.cache">classes.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.conditional_intensity_matrix">classes.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.json_importer">classes.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.network_graph">classes.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.parameters_estimator">classes.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.sample_path">classes.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.set_of_cims">classes.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure">classes.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure_estimator">classes.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.trajectory">classes.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes">Module contents</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
@@ -123,24 +123,24 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn">
-<h1>PyCTBN<a class="headerlink" href="#pyctbn" title="Permalink to this headline">¶</a></h1>
+  <div class="section" id="classes">
+<h1>classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="classes.html">classes package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.abstract_importer">classes.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.cache">classes.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.conditional_intensity_matrix">classes.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.json_importer">classes.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.network_graph">classes.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.parameters_estimator">classes.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.sample_path">classes.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.set_of_cims">classes.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure">classes.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure_estimator">classes.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.trajectory">classes.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes">Module contents</a></li>
 </ul>
 </li>
 </ul>

sphinx_output/_build/html/py-modindex.html

@@ -63,20 +63,20 @@
           
               <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="classes.html">classes package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.abstract_importer">classes.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.cache">classes.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.conditional_intensity_matrix">classes.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.json_importer">classes.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.network_graph">classes.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.parameters_estimator">classes.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.sample_path">classes.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.set_of_cims">classes.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure">classes.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure_estimator">classes.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.trajectory">classes.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes">Module contents</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>
@@ -130,73 +130,73 @@
    <h1>Python Module Index</h1>
 
    <div class="modindex-jumpbox">
-   <a href="#cap-p"><strong>p</strong></a>
+   <a href="#cap-c"><strong>c</strong></a>
    </div>
 
    <table class="indextable modindextable">
      <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
-     <tr class="cap" id="cap-p"><td></td><td>
-       <strong>p</strong></td><td></td></tr>
+     <tr class="cap" id="cap-c"><td></td><td>
+       <strong>c</strong></td><td></td></tr>
      <tr>
        <td><img src="_static/minus.png" class="toggler"
               id="toggle-1" style="display: none" alt="-" /></td>
        <td>
-       <a href="PyCTBN.html#module-PyCTBN"><code class="xref">PyCTBN</code></a></td><td>
+       <a href="classes.html#module-classes"><code class="xref">classes</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.abstract_importer"><code class="xref">PyCTBN.abstract_importer</code></a></td><td>
+       <a href="classes.html#module-classes.abstract_importer"><code class="xref">classes.abstract_importer</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.cache"><code class="xref">PyCTBN.cache</code></a></td><td>
+       <a href="classes.html#module-classes.cache"><code class="xref">classes.cache</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix"><code class="xref">PyCTBN.conditional_intensity_matrix</code></a></td><td>
+       <a href="classes.html#module-classes.conditional_intensity_matrix"><code class="xref">classes.conditional_intensity_matrix</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.json_importer"><code class="xref">PyCTBN.json_importer</code></a></td><td>
+       <a href="classes.html#module-classes.json_importer"><code class="xref">classes.json_importer</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.network_graph"><code class="xref">PyCTBN.network_graph</code></a></td><td>
+       <a href="classes.html#module-classes.network_graph"><code class="xref">classes.network_graph</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.parameters_estimator"><code class="xref">PyCTBN.parameters_estimator</code></a></td><td>
+       <a href="classes.html#module-classes.parameters_estimator"><code class="xref">classes.parameters_estimator</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.sample_path"><code class="xref">PyCTBN.sample_path</code></a></td><td>
+       <a href="classes.html#module-classes.sample_path"><code class="xref">classes.sample_path</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.set_of_cims"><code class="xref">PyCTBN.set_of_cims</code></a></td><td>
+       <a href="classes.html#module-classes.set_of_cims"><code class="xref">classes.set_of_cims</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.structure"><code class="xref">PyCTBN.structure</code></a></td><td>
+       <a href="classes.html#module-classes.structure"><code class="xref">classes.structure</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.structure_estimator"><code class="xref">PyCTBN.structure_estimator</code></a></td><td>
+       <a href="classes.html#module-classes.structure_estimator"><code class="xref">classes.structure_estimator</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="PyCTBN.html#module-PyCTBN.trajectory"><code class="xref">PyCTBN.trajectory</code></a></td><td>
+       <a href="classes.html#module-classes.trajectory"><code class="xref">classes.trajectory</code></a></td><td>
        <em></em></td></tr>
    </table>
 

sphinx_output/_build/html/search.html

@@ -60,20 +60,20 @@
           
               <p class="caption"><span class="caption-text">Contents:</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="PyCTBN.html">PyCTBN package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.abstract_importer">PyCTBN.abstract_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.cache">PyCTBN.cache module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.conditional_intensity_matrix">PyCTBN.conditional_intensity_matrix module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.json_importer">PyCTBN.json_importer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.network_graph">PyCTBN.network_graph module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.parameters_estimator">PyCTBN.parameters_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.sample_path">PyCTBN.sample_path module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.set_of_cims">PyCTBN.set_of_cims module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure">PyCTBN.structure module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.structure_estimator">PyCTBN.structure_estimator module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN.trajectory">PyCTBN.trajectory module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="PyCTBN.html#module-PyCTBN">Module contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="classes.html">classes package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.abstract_importer">classes.abstract_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.cache">classes.cache module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.conditional_intensity_matrix">classes.conditional_intensity_matrix module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.json_importer">classes.json_importer module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.network_graph">classes.network_graph module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.parameters_estimator">classes.parameters_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.sample_path">classes.sample_path module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.set_of_cims">classes.set_of_cims module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure">classes.structure module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.structure_estimator">classes.structure_estimator module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes.trajectory">classes.trajectory module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="classes.html#module-classes">Module contents</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a><ul>

sphinx_output/classes.rst

@@ -0,0 +1,101 @@
+classes package
+===============
+
+Submodules
+----------
+
+classes.abstract\_importer module
+---------------------------------
+
+.. automodule:: classes.abstract_importer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.cache module
+--------------------
+
+.. automodule:: classes.cache
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.conditional\_intensity\_matrix module
+---------------------------------------------
+
+.. automodule:: classes.conditional_intensity_matrix
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.json\_importer module
+-----------------------------
+
+.. automodule:: classes.json_importer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.network\_graph module
+-----------------------------
+
+.. automodule:: classes.network_graph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.parameters\_estimator module
+------------------------------------
+
+.. automodule:: classes.parameters_estimator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.sample\_path module
+---------------------------
+
+.. automodule:: classes.sample_path
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.set\_of\_cims module
+----------------------------
+
+.. automodule:: classes.set_of_cims
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.structure module
+------------------------
+
+.. automodule:: classes.structure
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.structure\_estimator module
+-----------------------------------
+
+.. automodule:: classes.structure_estimator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+classes.trajectory module
+-------------------------
+
+.. automodule:: classes.trajectory
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: classes
+   :members:
+   :undoc-members:
+   :show-inheritance:

sphinx_output/examples.rst

@@ -10,7 +10,7 @@ Implementing your own data importer
 .. code-block:: python
 
     """This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format.
-    The net in exam has three ternary nodes.
+    The net in exam has three ternary nodes and no prior net structure.
     """
 
     from .abstract_importer import AbstractImporter
@@ -25,7 +25,6 @@ Implementing your own data importer
             self.read_csv_file()
             self._sorter = self.build_sorter(self._df_samples_list[0])
             self.import_variables()
-            self.import_structure()
             self.compute_row_delta_in_all_samples_frames(self._df_samples_list)
 
         def read_csv_file(self):
@@ -43,10 +42,6 @@ Implementing your own data importer
         def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
             return list(sample_frame.columns)[1:]
 
-        def import_structure(self):
-            data = {'From':['X','Y','Z'], 'To':['Z','Z','Y']}
-            self._df_structure = pd.DataFrame(data)
-
         def dataset_id(self) -> object:
             pass
 

sphinx_output/index.rst

@@ -1,5 +1,5 @@
 .. PyCTBN documentation master file, created by
-   sphinx-quickstart on Mon Dec  7 15:11:12 2020.
+   sphinx-quickstart on Mon Dec 14 20:33:17 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
@@ -10,7 +10,7 @@ Welcome to PyCTBN's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-   PyCTBN
+   classes
    examples
 
 Indices and tables

sphinx_output/modules.rst

@@ -1,7 +1,7 @@
-PyCTBN
-======
+classes
+=======
 
 .. toctree::
    :maxdepth: 4
 
-   PyCTBN
+   classes