doc update part 2

jdtuck · Jul 21, 2023 · b1f0a0e · b1f0a0e
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diff --git a/doc/build/html/.buildinfo b/doc/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: cff1e5dc319d7ac07f594719d3407034
+config: 94cabc678eb0f7c74fefabe67532679c
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/build/html/.doctrees/environment.pickle b/doc/build/html/.doctrees/environment.pickle
diff --git a/doc/build/html/.doctrees/time_warping.doctree b/doc/build/html/.doctrees/time_warping.doctree
diff --git a/doc/build/html/_modules/index.html b/doc/build/html/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Overview: module code &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -97,7 +97,6 @@ <h1>All modules for which code is available</h1>
 <li><a href="kmeans.html">kmeans</a></li>
 <li><a href="pcr_regression.html">pcr_regression</a></li>
 <li><a href="regression.html">regression</a></li>
-<li><a href="time_warping.html">time_warping</a></li>
 <li><a href="tolerance.html">tolerance</a></li>
 <li><a href="umap_metric.html">umap_metric</a></li>
 <li><a href="utility_functions.html">utility_functions</a></li>

diff --git a/doc/build/html/_static/documentation_options.js b/doc/build/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '2.4.1',
+    VERSION: '2.4.2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/doc/build/html/boxplots.html b/doc/build/html/boxplots.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Elastic Functional Boxplots &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Elastic Functional Boxplots &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -105,7 +105,7 @@
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>warp_data</strong> (<a class="reference internal" href="time_warping.html#time_warping.fdawarp" title="time_warping.fdawarp"><em>fdawarp</em></a>) – fdawarp class with alignment data</p></li>
+<li><p><strong>warp_data</strong> (<em>fdawarp</em>) – fdawarp class with alignment data</p></li>
 <li><p><strong>Q1</strong> – First quartile</p></li>
 <li><p><strong>Q3</strong> – Second quartile</p></li>
 <li><p><strong>Q1a</strong> – First quantile based on alpha</p></li>
@@ -154,7 +154,7 @@
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>warp_data</strong> (<a class="reference internal" href="time_warping.html#time_warping.fdawarp" title="time_warping.fdawarp"><em>fdawarp</em></a>) – fdawarp class with alignment data</p></li>
+<li><p><strong>warp_data</strong> (<em>fdawarp</em>) – fdawarp class with alignment data</p></li>
 <li><p><strong>Q1</strong> – First quartile</p></li>
 <li><p><strong>Q3</strong> – Second quartile</p></li>
 <li><p><strong>Q1a</strong> – First quantile based on alpha</p></li>

diff --git a/doc/build/html/curve_functions.html b/doc/build/html/curve_functions.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Curve Functions &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Curve Functions &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

diff --git a/doc/build/html/curve_statistics.html b/doc/build/html/curve_statistics.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Curve Registration &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Curve Registration &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

diff --git a/doc/build/html/fPCA.html b/doc/build/html/fPCA.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Functional Principal Component Analysis &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Functional Principal Component Analysis &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

diff --git a/doc/build/html/fPLS.html b/doc/build/html/fPLS.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Functional Principal Least Squares &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Functional Principal Least Squares &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

diff --git a/doc/build/html/genindex.html b/doc/build/html/genindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Index &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -97,11 +97,9 @@ <h1 id="index">Index</h1>
  | <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="#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="#O"><strong>O</strong></a>
  | <a href="#P"><strong>P</strong></a>
  | <a href="#Q"><strong>Q</strong></a>
@@ -116,12 +114,6 @@ <h1 id="index">Index</h1>
 <h2 id="A">A</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="time_warping.html#time_warping.align_fPCA">align_fPCA() (in module time_warping)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="time_warping.html#time_warping.align_fPLS">align_fPLS() (in module time_warping)</a>
-</li>
       <li><a href="boxplots.html#boxplots.ampbox">ampbox (class in boxplots)</a>
 </li>
   </ul></td>
@@ -285,15 +277,13 @@ <h2 id="F">F</h2>
       <li><a href="fPCA.html#fPCA.fdajpca">fdajpca (class in fPCA)</a>
 </li>
       <li><a href="fPCA.html#fPCA.fdavpca">fdavpca (class in fPCA)</a>
-</li>
-      <li><a href="time_warping.html#time_warping.fdawarp">fdawarp (class in time_warping)</a>
 </li>
       <li><a href="curve_functions.html#curve_functions.find_basis_normal">find_basis_normal() (in module curve_functions)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="geodesic.html#geodesic.find_basis_normal_path">find_basis_normal_path() (in module geodesic)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="curve_functions.html#curve_functions.find_best_rotation">find_best_rotation() (in module curve_functions)</a>
 </li>
       <li><a href="curve_functions.html#curve_functions.find_rotation_and_seed_coord">find_rotation_and_seed_coord() (in module curve_functions)</a>
@@ -322,8 +312,6 @@ <h2 id="F">F</h2>
 <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="time_warping.html#time_warping.fdawarp.gauss_model">gauss_model() (time_warping.fdawarp method)</a>
-</li>
       <li><a href="utility_functions.html#utility_functions.geigen">geigen() (in module utility_functions)</a>
 </li>
       <li><a href="geodesic.html#geodesic.geod_dist_path_strt">geod_dist_path_strt() (in module geodesic)</a>
@@ -379,14 +367,6 @@ <h2 id="I">I</h2>
   </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="time_warping.html#time_warping.fdawarp.joint_gauss_model">joint_gauss_model() (time_warping.fdawarp method)</a>
-</li>
-  </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>
@@ -458,8 +438,6 @@ <h2 id="M">M</h2>
         <li><a href="pcr_regression.html#module-pcr_regression">pcr_regression</a>
 </li>
         <li><a href="regression.html#module-regression">regression</a>
-</li>
-        <li><a href="time_warping.html#module-time_warping">time_warping</a>
 </li>
         <li><a href="tolerance.html#module-tolerance">tolerance</a>
 </li>
@@ -470,21 +448,11 @@ <h2 id="M">M</h2>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="time_warping.html#time_warping.fdawarp.multiple_align_functions">multiple_align_functions() (time_warping.fdawarp method)</a>
-</li>
       <li><a href="tolerance.html#tolerance.mvtol_region">mvtol_region() (in module tolerance)</a>
 </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="time_warping.html#time_warping.normal">normal() (in module time_warping)</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>
@@ -504,12 +472,6 @@ <h2 id="O">O</h2>
 <h2 id="P">P</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="time_warping.html#time_warping.pairwise_align_bayes">pairwise_align_bayes() (in module time_warping)</a>
-</li>
-      <li><a href="time_warping.html#time_warping.pairwise_align_bayes_infHMC">pairwise_align_bayes_infHMC() (in module time_warping)</a>
-</li>
-      <li><a href="time_warping.html#time_warping.pairwise_align_functions">pairwise_align_functions() (in module time_warping)</a>
-</li>
       <li><a href="curve_functions.html#curve_functions.parallel_translate">parallel_translate() (in module curve_functions)</a>
 </li>
       <li><a href="geodesic.html#geodesic.path_straightening">path_straightening() (in module geodesic)</a>
@@ -539,8 +501,6 @@ <h2 id="P">P</h2>
         <li><a href="fPCA.html#fPCA.fdajpca.plot">(fPCA.fdajpca method)</a>
 </li>
         <li><a href="fPCA.html#fPCA.fdavpca.plot">(fPCA.fdavpca method)</a>
-</li>
-        <li><a href="time_warping.html#time_warping.fdawarp.plot">(time_warping.fdawarp method)</a>
 </li>
       </ul></li>
   </ul></td>
@@ -588,11 +548,7 @@ <h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="elastic_glm_regression.html#elastic_glm_regression.rand">rand() (in module elastic_glm_regression)</a>
-
-      <ul>
-        <li><a href="time_warping.html#time_warping.rand">(in module time_warping)</a>
 </li>
-      </ul></li>
       <li><a href="curve_statistics.html#curve_stats.randn">randn() (in module curve_stats)</a>
 </li>
       <li><a href="utility_functions.html#utility_functions.randomGamma">randomGamma() (in module utility_functions)</a>
@@ -641,8 +597,6 @@ <h2 id="S">S</h2>
       <li><a href="utility_functions.html#utility_functions.SqrtMeanInverse">SqrtMeanInverse() (in module utility_functions)</a>
 </li>
       <li><a href="utility_functions.html#utility_functions.SqrtMedian">SqrtMedian() (in module utility_functions)</a>
-</li>
-      <li><a href="time_warping.html#time_warping.fdawarp.srsf_align">srsf_align() (time_warping.fdawarp method)</a>
 </li>
       <li><a href="utility_functions.html#utility_functions.srsf_to_f">srsf_to_f() (in module utility_functions)</a>
 </li>
@@ -653,15 +607,6 @@ <h2 id="S">S</h2>
 
 <h2 id="T">T</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li>
-    time_warping
-
-      <ul>
-        <li><a href="time_warping.html#module-time_warping">module</a>
-</li>
-      </ul></li>
-  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     tolerance

diff --git a/doc/build/html/geodesic.html b/doc/build/html/geodesic.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>SRVF Geodesic Computation &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>SRVF Geodesic Computation &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

diff --git a/doc/build/html/index.html b/doc/build/html/index.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Welcome to fdasrsf’s documentation! &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Welcome to fdasrsf’s documentation! &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

diff --git a/doc/build/html/objects.inv b/doc/build/html/objects.inv
diff --git a/doc/build/html/pcr_regression.html b/doc/build/html/pcr_regression.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Elastic Principal Component Regression &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Elastic Principal Component Regression &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

diff --git a/doc/build/html/py-modindex.html b/doc/build/html/py-modindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Python Module Index &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Python Module Index &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -195,11 +195,6 @@ <h1>Python Module Index</h1>
      <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
      <tr class="cap" id="cap-t"><td></td><td>
        <strong>t</strong></td><td></td></tr>
-     <tr>
-       <td></td>
-       <td>
-       <a href="time_warping.html#module-time_warping"><code class="xref">time_warping</code></a></td><td>
-       <em></em></td></tr>
      <tr>
        <td></td>
        <td>

diff --git a/doc/build/html/regression.html b/doc/build/html/regression.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Elastic Regression &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Elastic Regression &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>

diff --git a/doc/build/html/search.html b/doc/build/html/search.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; fdasrsf 2.4.1 documentation</title>
+  <title>Search &mdash; fdasrsf 2.4.2 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
 

diff --git a/doc/build/html/searchindex.js b/doc/build/html/searchindex.js