reorganized caveats into standalone section

uclamii · Nov 8, 2024 · 4992976 · 4992976
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diff --git a/docs/.doctrees/caveats.doctree b/docs/.doctrees/caveats.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/references copy.doctree b/docs/.doctrees/references copy.doctree
diff --git a/docs/.doctrees/usage_guide.doctree b/docs/.doctrees/usage_guide.doctree
diff --git a/docs/_sources/caveats.rst.txt b/docs/_sources/caveats.rst.txt
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -41,6 +41,13 @@ Model Tuner Documentation
    usage_guide
 
 
+.. toctree::
+   :maxdepth: 4
+   :caption: Caveats
+
+   caveats
+
+
 .. toctree::
    :maxdepth: 4
    :caption: About Model Tuner

diff --git a/docs/_sources/references copy.rst.txt b/docs/_sources/references copy.rst.txt
@@ -0,0 +1,30 @@
+.. _references:   
+
+.. _target-link:
+
+.. raw:: html
+
+   <div class="no-click">
+
+.. image:: /../assets/ModelTunerTarget.png
+   :alt: Model Tuner Logo
+   :align: left
+   :width: 250px
+
+.. raw:: html
+
+   </div>
+
+.. raw:: html
+
+   <div style="height: 150px;"></div>
+
+\
+
+
+
+References
+==========
+
+El-Sadr, W., & Abrams, D. (1998). `AIDS Clinical Trials Group Study 175`. UCI Machine Learning Repository.  
+https://doi.org/10.24432/C5G896.
diff --git a/docs/_sources/usage_guide.rst.txt b/docs/_sources/usage_guide.rst.txt
diff --git a/docs/about.html b/docs/about.html
@@ -27,7 +27,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Changelog" href="changelog.html" />
-    <link rel="prev" title="iPython Notebooks" href="usage_guide.html" /> 
+    <link rel="prev" title="Zero Variance Columns" href="caveats.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -59,11 +59,23 @@
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#key-methods-and-functionalities">Key Methods and Functionalities</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#helper-functions">Helper Functions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#input-parameters">Input Parameters</a></li>
-<li class="toctree-l1"><a class="reference internal" href="usage_guide.html#caveats">Caveats</a></li>
-<li class="toctree-l1"><a class="reference internal" href="usage_guide.html#model-calibration">Model Calibration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#binary-classification">Binary Classification</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#regression">Regression</a></li>
 </ul>
+<p class="caption" role="heading"><span class="caption-text">Caveats</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html">Zero Variance Columns</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#dependent-variable">Dependent Variable</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#imputation-before-scaling">Imputation Before Scaling</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#column-stratification-with-cross-validation">Column Stratification with Cross-Validation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#goal-of-calibration">Goal of Calibration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#calibration-curve">Calibration Curve</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#brier-score">Brier Score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#platt-scaling">Platt Scaling</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#isotonic-regression">Isotonic Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#example-calibration-in-logistic-regression">Example: Calibration in Logistic Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#summary">Summary</a></li>
+</ul>
 <p class="caption" role="heading"><span class="caption-text">About Model Tuner</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">GitHub Repository</a></li>
@@ -130,7 +142,7 @@ <h1>Citing Model Tuner<a class="headerlink" href="#citing-model-tuner" title="Li
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="usage_guide.html" class="btn btn-neutral float-left" title="iPython Notebooks" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="caveats.html" class="btn btn-neutral float-left" title="Zero Variance Columns" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="changelog.html" class="btn btn-neutral float-right" title="Changelog" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

diff --git a/docs/caveats.html b/docs/caveats.html
diff --git a/docs/changelog.html b/docs/changelog.html
@@ -59,11 +59,23 @@
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#key-methods-and-functionalities">Key Methods and Functionalities</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#helper-functions">Helper Functions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#input-parameters">Input Parameters</a></li>
-<li class="toctree-l1"><a class="reference internal" href="usage_guide.html#caveats">Caveats</a></li>
-<li class="toctree-l1"><a class="reference internal" href="usage_guide.html#model-calibration">Model Calibration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#binary-classification">Binary Classification</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#regression">Regression</a></li>
 </ul>
+<p class="caption" role="heading"><span class="caption-text">Caveats</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html">Zero Variance Columns</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#dependent-variable">Dependent Variable</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#imputation-before-scaling">Imputation Before Scaling</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#column-stratification-with-cross-validation">Column Stratification with Cross-Validation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#goal-of-calibration">Goal of Calibration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#calibration-curve">Calibration Curve</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#brier-score">Brier Score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#platt-scaling">Platt Scaling</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#isotonic-regression">Isotonic Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#example-calibration-in-logistic-regression">Example: Calibration in Logistic Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#summary">Summary</a></li>
+</ul>
 <p class="caption" role="heading"><span class="caption-text">About Model Tuner</span></p>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="about.html">GitHub Repository</a></li>

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -56,11 +56,23 @@
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#key-methods-and-functionalities">Key Methods and Functionalities</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#helper-functions">Helper Functions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#input-parameters">Input Parameters</a></li>
-<li class="toctree-l1"><a class="reference internal" href="usage_guide.html#caveats">Caveats</a></li>
-<li class="toctree-l1"><a class="reference internal" href="usage_guide.html#model-calibration">Model Calibration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#binary-classification">Binary Classification</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#regression">Regression</a></li>
 </ul>
+<p class="caption" role="heading"><span class="caption-text">Caveats</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html">Zero Variance Columns</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#dependent-variable">Dependent Variable</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#imputation-before-scaling">Imputation Before Scaling</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#column-stratification-with-cross-validation">Column Stratification with Cross-Validation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#goal-of-calibration">Goal of Calibration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#calibration-curve">Calibration Curve</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#brier-score">Brier Score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#platt-scaling">Platt Scaling</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#isotonic-regression">Isotonic Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#example-calibration-in-logistic-regression">Example: Calibration in Logistic Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#summary">Summary</a></li>
+</ul>
 <p class="caption" role="heading"><span class="caption-text">About Model Tuner</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="about.html">GitHub Repository</a></li>

diff --git a/docs/getting_started.html b/docs/getting_started.html
@@ -64,11 +64,23 @@
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#key-methods-and-functionalities">Key Methods and Functionalities</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#helper-functions">Helper Functions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#input-parameters">Input Parameters</a></li>
-<li class="toctree-l1"><a class="reference internal" href="usage_guide.html#caveats">Caveats</a></li>
-<li class="toctree-l1"><a class="reference internal" href="usage_guide.html#model-calibration">Model Calibration</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#binary-classification">Binary Classification</a></li>
 <li class="toctree-l1"><a class="reference internal" href="usage_guide.html#regression">Regression</a></li>
 </ul>
+<p class="caption" role="heading"><span class="caption-text">Caveats</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html">Zero Variance Columns</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#dependent-variable">Dependent Variable</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#imputation-before-scaling">Imputation Before Scaling</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#column-stratification-with-cross-validation">Column Stratification with Cross-Validation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#goal-of-calibration">Goal of Calibration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#calibration-curve">Calibration Curve</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#brier-score">Brier Score</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#platt-scaling">Platt Scaling</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#isotonic-regression">Isotonic Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#example-calibration-in-logistic-regression">Example: Calibration in Logistic Regression</a></li>
+<li class="toctree-l1"><a class="reference internal" href="caveats.html#summary">Summary</a></li>
+</ul>
 <p class="caption" role="heading"><span class="caption-text">About Model Tuner</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="about.html">GitHub Repository</a></li>