Added building shell file and updated documentation

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e2aa039006b0eeb2c81bf5879f34a604
+config: 8ebcdd3a94cc8c783fb6bee52f77602b
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/genindex.html

@@ -93,13 +93,15 @@ <h1 id="index">Index</h1>
  | <a href="#G"><strong>G</strong></a>
  | <a href="#H"><strong>H</strong></a>
  | <a href="#I"><strong>I</strong></a>
+ | <a href="#K"><strong>K</strong></a>
  | <a href="#L"><strong>L</strong></a>
  | <a href="#M"><strong>M</strong></a>
  | <a href="#N"><strong>N</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>
  | <a href="#W"><strong>W</strong></a>
 
 </div>
@@ -143,6 +145,8 @@ <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="modules/Criteria.html#survivors.criteria.chi2_sf">chi2_sf() (in module survivors.criteria)</a>
+</li>
+      <li><a href="modules/External.html#survivors.external.nonparametric.KaplanMeier.count_confidence_interval">count_confidence_interval() (survivors.external.nonparametric.KaplanMeier method)</a>
 </li>
       <li><a href="modules/External.html#survivors.external.parametric.CoxPH">CoxPH (class in survivors.external.parametric)</a>
 </li>
@@ -159,6 +163,10 @@ <h2 id="C">C</h2>
 
 <h2 id="D">D</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="modules/Tree.html#survivors.tree.decision_tree.CRAID.delete_leaves_by_span">delete_leaves_by_span() (survivors.tree.decision_tree.CRAID method)</a>
+</li>
+  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="modules/Metrics.html#survivors.metrics.DESCEND_METRICS">DESCEND_METRICS (in module survivors.metrics)</a>
 </li>
@@ -178,11 +186,15 @@ <h2 id="F">F</h2>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="modules/Ensemble.html#survivors.ensemble.base_ensemble.FastBaseEnsemble">FastBaseEnsemble (class in survivors.ensemble.base_ensemble)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="modules/Tree.html#survivors.tree.node.Node.find_best_split">find_best_split() (survivors.tree.node.Node method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="modules/Criteria.html#survivors.criteria.find_inverse_gamma">find_inverse_gamma() (in module survivors.criteria)</a>
+</li>
+      <li><a href="modules/Ensemble.html#survivors.ensemble.bootstrap.ParallelBootstrapCRAID.fit_tree">fit_tree() (survivors.ensemble.bootstrap.ParallelBootstrapCRAID static method)</a>
+</li>
+      <li><a href="modules/External.html#survivors.external.nonparametric.FullProbKM">FullProbKM (class in survivors.external.nonparametric)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -195,12 +207,20 @@ <h2 id="G">G</h2>
       <li><a href="modules/Constants.html#survivors.constants.get_bins">get_bins() (in module survivors.constants)</a>
 </li>
       <li><a href="modules/Tree.html#survivors.tree.node.Node.get_comb_fast">get_comb_fast() (survivors.tree.node.Node method)</a>
+</li>
+      <li><a href="modules/Tree.html#survivors.tree.node.Node.get_description">get_description() (survivors.tree.node.Node method)</a>
+</li>
+      <li><a href="modules/Tree.html#survivors.tree.node.Node.get_figure">get_figure() (survivors.tree.node.Node method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="modules/Experiments.html#survivors.experiments.grid.get_fit_eval_func">get_fit_eval_func() (in module survivors.experiments.grid)</a>
 </li>
       <li><a href="modules/Metrics.html#survivors.metrics.get_hazard_func">get_hazard_func() (in module survivors.metrics)</a>
+</li>
+      <li><a href="modules/Experiments.html#survivors.experiments.grid.get_name_file">get_name_file() (in module survivors.experiments.grid)</a>
+</li>
+      <li><a href="modules/Tree.html#survivors.tree.decision_tree.CRAID.get_spanning_leaf_numbers">get_spanning_leaf_numbers() (survivors.tree.decision_tree.CRAID method)</a>
 </li>
       <li><a href="modules/Metrics.html#survivors.metrics.get_survival_func">get_survival_func() (in module survivors.metrics)</a>
 </li>
@@ -212,8 +232,22 @@ <h2 id="G">G</h2>
 <h2 id="H">H</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="modules/External.html#survivors.external.nonparametric.BaseLeafModeLL.hazard_class">hazard_class (survivors.external.nonparametric.BaseLeafModeLL attribute)</a>
+      <li><a href="modules/External.html#survivors.external.nonparametric.BaseLeafModel.hazard_class">hazard_class (survivors.external.nonparametric.BaseLeafModel attribute)</a>
+
+      <ul>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseLeafModeLL.hazard_class">(survivors.external.nonparametric.BaseLeafModeLL attribute)</a>
 </li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseLeafModelOnlyHazard.hazard_class">(survivors.external.nonparametric.BaseLeafModelOnlyHazard attribute)</a>
+</li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseMeaningLeafModel.hazard_class">(survivors.external.nonparametric.BaseMeaningLeafModel attribute)</a>
+</li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseMixLeafModel.hazard_class">(survivors.external.nonparametric.BaseMixLeafModel attribute)</a>
+</li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseNormalizedLeafModel.hazard_class">(survivors.external.nonparametric.BaseNormalizedLeafModel attribute)</a>
+</li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.StableLeafModel.hazard_class">(survivors.external.nonparametric.StableLeafModel attribute)</a>
+</li>
+      </ul></li>
   </ul></td>
 </tr></table>
 
@@ -233,6 +267,18 @@ <h2 id="I">I</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="K">K</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="modules/External.html#survivors.external.nonparametric.KaplanMeier">KaplanMeier (class in survivors.external.nonparametric)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="modules/External.html#survivors.external.nonparametric.KaplanMeierZeroAfter">KaplanMeierZeroAfter (class in survivors.external.nonparametric)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="L">L</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -315,6 +361,8 @@ <h2 id="M">M</h2>
 <h2 id="N">N</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="modules/External.html#survivors.external.nonparametric.NelsonAalen">NelsonAalen (class in survivors.external.nonparametric)</a>
+</li>
       <li><a href="modules/Tree.html#survivors.tree.node.Node">Node (class in survivors.tree.node)</a>
 </li>
   </ul></td>
@@ -339,10 +387,10 @@ <h2 id="P">P</h2>
 </li>
       <li><a href="modules/Visualize.html#survivors.visualize.comparison.plot_metric_comparison">plot_metric_comparison() (in module survivors.visualize.comparison)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="modules/Visualize.html#survivors.visualize.base.plot_survival_function">plot_survival_function() (in module survivors.visualize.base)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="modules/Criteria.html#survivors.criteria.polyval">polyval() (in module survivors.criteria)</a>
 </li>
       <li><a href="modules/Tree.html#survivors.tree.decision_tree.CRAID.predict">predict() (survivors.tree.decision_tree.CRAID method)</a>
@@ -352,6 +400,10 @@ <h2 id="P">P</h2>
 </li>
       </ul></li>
       <li><a href="modules/Tree.html#survivors.tree.decision_tree.CRAID.predict_at_times">predict_at_times() (survivors.tree.decision_tree.CRAID method)</a>
+</li>
+      <li><a href="modules/Tree.html#survivors.tree.node.Node.predict_scheme">predict_scheme() (survivors.tree.node.Node method)</a>
+</li>
+      <li><a href="modules/Experiments.html#survivors.experiments.grid.prepare_sample">prepare_sample() (in module survivors.experiments.grid)</a>
 </li>
       <li><a href="modules/Tree.html#survivors.tree.node.Rule.print">print() (survivors.tree.node.Rule method)</a>
 </li>
@@ -373,10 +425,34 @@ <h2 id="R">R</h2>
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="modules/Tree.html#survivors.tree.node.Node.set_dot_edges">set_dot_edges() (survivors.tree.node.Node method)</a>
+</li>
+      <li><a href="modules/Tree.html#survivors.tree.node.Node.set_dot_node">set_dot_node() (survivors.tree.node.Node method)</a>
+</li>
       <li><a href="modules/Tree.html#survivors.tree.node.Node.split">split() (survivors.tree.node.Node method)</a>
 </li>
-      <li><a href="modules/External.html#survivors.external.nonparametric.BaseLeafModeLL.survival_class">survival_class (survivors.external.nonparametric.BaseLeafModeLL attribute)</a>
+      <li><a href="modules/External.html#survivors.external.leaf_model.StableLeafModel">StableLeafModel (class in survivors.external.leaf_model)</a>
+
+      <ul>
+        <li><a href="modules/External.html#survivors.external.nonparametric.StableLeafModel">(class in survivors.external.nonparametric)</a>
+</li>
+      </ul></li>
+      <li><a href="modules/External.html#survivors.external.nonparametric.BaseLeafModel.survival_class">survival_class (survivors.external.nonparametric.BaseLeafModel attribute)</a>
+
+      <ul>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseLeafModeLL.survival_class">(survivors.external.nonparametric.BaseLeafModeLL attribute)</a>
+</li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseLeafModelOnlySurv.survival_class">(survivors.external.nonparametric.BaseLeafModelOnlySurv attribute)</a>
+</li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseMeaningLeafModel.survival_class">(survivors.external.nonparametric.BaseMeaningLeafModel attribute)</a>
 </li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseMixLeafModel.survival_class">(survivors.external.nonparametric.BaseMixLeafModel attribute)</a>
+</li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.BaseNormalizedLeafModel.survival_class">(survivors.external.nonparametric.BaseNormalizedLeafModel attribute)</a>
+</li>
+        <li><a href="modules/External.html#survivors.external.nonparametric.StableLeafModel.survival_class">(survivors.external.nonparametric.StableLeafModel attribute)</a>
+</li>
+      </ul></li>
       <li>
     survivors.constants
 
@@ -405,6 +481,8 @@ <h2 id="S">S</h2>
         <li><a href="modules/Ensemble.html#module-survivors.ensemble.base_ensemble">module</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     survivors.ensemble.bootstrap
 
@@ -426,8 +504,6 @@ <h2 id="S">S</h2>
         <li><a href="modules/External.html#module-survivors.external.leaf_model">module</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     survivors.external.nonparametric
 
@@ -485,9 +561,21 @@ <h2 id="T">T</h2>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="modules/Constants.html#survivors.constants.TIME_NAME">TIME_NAME (in module survivors.constants)</a>
 </li>
+      <li><a href="modules/Tree.html#survivors.tree.decision_tree.CRAID.translate">translate() (survivors.tree.decision_tree.CRAID method)</a>
+
+      <ul>
+        <li><a href="modules/Tree.html#survivors.tree.node.Node.translate">(survivors.tree.node.Node method)</a>
+</li>
+        <li><a href="modules/Tree.html#survivors.tree.node.Rule.translate">(survivors.tree.node.Rule method)</a>
+</li>
+      </ul></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="modules/Tree.html#survivors.tree.node.Rule.translate">translate() (survivors.tree.node.Rule method)</a>
+      <li><a href="modules/Tree.html#survivors.tree.decision_tree.CRAID.visualize">visualize() (survivors.tree.decision_tree.CRAID method)</a>
 </li>
   </ul></td>
 </tr></table>

docs/_build/html/modules/Ensemble.html

@@ -62,7 +62,10 @@
 <li class="toctree-l3"><a class="reference internal" href="#survivors.ensemble.base_ensemble.BaseEnsemble"><code class="docutils literal notranslate"><span class="pre">BaseEnsemble</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#survivors.ensemble.base_ensemble.FastBaseEnsemble"><code class="docutils literal notranslate"><span class="pre">FastBaseEnsemble</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#survivors.ensemble.bootstrap.BootstrapCRAID"><code class="docutils literal notranslate"><span class="pre">BootstrapCRAID</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="#survivors.ensemble.bootstrap.ParallelBootstrapCRAID"><code class="docutils literal notranslate"><span class="pre">ParallelBootstrapCRAID</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#survivors.ensemble.bootstrap.ParallelBootstrapCRAID"><code class="docutils literal notranslate"><span class="pre">ParallelBootstrapCRAID</span></code></a><ul>
+<li class="toctree-l4"><a class="reference internal" href="#survivors.ensemble.bootstrap.ParallelBootstrapCRAID.fit_tree"><code class="docutils literal notranslate"><span class="pre">ParallelBootstrapCRAID.fit_tree()</span></code></a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="Datasets.html">Datasets</a></li>
@@ -179,7 +182,15 @@ <h2>Methods<a class="headerlink" href="#id2" title="Link to this heading"></a
 <dl class="py class">
 <dt class="sig sig-object py" id="survivors.ensemble.bootstrap.ParallelBootstrapCRAID">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">survivors.ensemble.bootstrap.</span></span><span class="sig-name descname"><span class="pre">ParallelBootstrapCRAID</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#survivors.ensemble.bootstrap.ParallelBootstrapCRAID" title="Link to this definition"></a></dt>
-<dd></dd></dl>
+<dd><p>Parallel realization of BootstrapCRAID.
+Trees are built in parallel, and the number of processes is specified via n_jobs.</p>
+<dl class="py method">
+<dt class="sig sig-object py" id="survivors.ensemble.bootstrap.ParallelBootstrapCRAID.fit_tree">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">fit_tree</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x_sub</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#survivors.ensemble.bootstrap.ParallelBootstrapCRAID.fit_tree" title="Link to this definition"></a></dt>
+<dd><p>An atomic out-of-class tree construction operation for parallelization.</p>
+</dd></dl>
+
+</dd></dl>
 
 </section>
 

docs/_build/html/modules/Experiments.html

@@ -64,6 +64,8 @@
 <li class="toctree-l3"><a class="reference internal" href="#survivors.experiments.grid.Experiments"><code class="docutils literal notranslate"><span class="pre">Experiments</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#survivors.experiments.grid.generate_sample"><code class="docutils literal notranslate"><span class="pre">generate_sample()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="#survivors.experiments.grid.get_fit_eval_func"><code class="docutils literal notranslate"><span class="pre">get_fit_eval_func()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#survivors.experiments.grid.get_name_file"><code class="docutils literal notranslate"><span class="pre">get_name_file()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="#survivors.experiments.grid.prepare_sample"><code class="docutils literal notranslate"><span class="pre">prepare_sample()</span></code></a></li>
 </ul>
 </li>
 </ul>
@@ -217,6 +219,18 @@ <h2>Returns<a class="headerlink" href="#returns" title="Link to this heading">
 </section>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="survivors.experiments.grid.get_name_file">
+<span class="sig-prename descclassname"><span class="pre">survivors.experiments.grid.</span></span><span class="sig-name descname"><span class="pre">get_name_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">method</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mode</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fold</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#survivors.experiments.grid.get_name_file" title="Link to this definition"></a></dt>
+<dd><p>Creating a name to cache the model without considering variables independent for reproducibility.</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="survivors.experiments.grid.prepare_sample">
+<span class="sig-prename descclassname"><span class="pre">survivors.experiments.grid.</span></span><span class="sig-name descname"><span class="pre">prepare_sample</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">train_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">test_index</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#survivors.experiments.grid.prepare_sample" title="Link to this definition"></a></dt>
+<dd><p>Constructing a set of bins on target variables and clipping.</p>
+</dd></dl>
+
 </section>