update docs for release

jdtuck · Jul 7, 2022 · c390e1f · c390e1f
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diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,3 +1,4 @@
+v2.3.11,  2022-07-07 -- bugfixes
 v2.3.10,  2022-03-28 -- bugfixes
 v2.3.7,  2022-01-17 -- bugfixes
 v2.3.6,  2021-12-24 -- bugfixes

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ using functional component analysis and regression.
 
 ### Installation
 ------------------------------------------------------------------------------
-v2.3.10 is on pip and can be installed using
+v2.3.11 is on pip and can be installed using
 > `pip install fdasrsf`
 
 or conda

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: 8c8a8493cbaa9348947da12bfa448214
+config: d739618e4d24e43e7381a70976db80c0
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/build/html/.doctrees/boxplots.doctree b/doc/build/html/.doctrees/boxplots.doctree
diff --git a/doc/build/html/.doctrees/curve_functions.doctree b/doc/build/html/.doctrees/curve_functions.doctree
diff --git a/doc/build/html/.doctrees/curve_statistics.doctree b/doc/build/html/.doctrees/curve_statistics.doctree
diff --git a/doc/build/html/.doctrees/environment.pickle b/doc/build/html/.doctrees/environment.pickle
diff --git a/doc/build/html/.doctrees/fPCA.doctree b/doc/build/html/.doctrees/fPCA.doctree
diff --git a/doc/build/html/.doctrees/fPLS.doctree b/doc/build/html/.doctrees/fPLS.doctree
diff --git a/doc/build/html/.doctrees/geodesic.doctree b/doc/build/html/.doctrees/geodesic.doctree
diff --git a/doc/build/html/.doctrees/index.doctree b/doc/build/html/.doctrees/index.doctree
diff --git a/doc/build/html/.doctrees/pcr_regression.doctree b/doc/build/html/.doctrees/pcr_regression.doctree
diff --git a/doc/build/html/.doctrees/regression.doctree b/doc/build/html/.doctrees/regression.doctree
diff --git a/doc/build/html/.doctrees/time_warping.doctree b/doc/build/html/.doctrees/time_warping.doctree
diff --git a/doc/build/html/.doctrees/tolerance.doctree b/doc/build/html/.doctrees/tolerance.doctree
diff --git a/doc/build/html/.doctrees/umap_metric.doctree b/doc/build/html/.doctrees/umap_metric.doctree
diff --git a/doc/build/html/.doctrees/utility_functions.doctree b/doc/build/html/.doctrees/utility_functions.doctree
diff --git a/doc/build/html/_modules/fPCA.html b/doc/build/html/_modules/fPCA.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>fPCA &mdash; fdasrsf 2.3.8 documentation</title>
+  <title>fPCA &mdash; fdasrsf 2.3.11 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]>
@@ -13,6 +13,7 @@
         <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/jquery.js"></script>
         <script src="../_static/underscore.js"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
         <script src="../_static/doctools.js"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../_static/js/theme.js"></script>
@@ -344,7 +345,7 @@ <h1>Source code for fPCA</h1><div class="highlight"><pre>
         <span class="n">c</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">N2</span><span class="p">,</span><span class="n">no</span><span class="p">))</span>
         <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">no</span><span class="p">):</span>
             <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">N2</span><span class="p">):</span>
-                <span class="n">c</span><span class="p">[</span><span class="n">i</span><span class="p">,</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">vec</span><span class="p">[:,</span><span class="n">i</span><span class="p">]</span><span class="o">-</span><span class="n">vm</span><span class="p">,</span><span class="n">U</span><span class="p">[:,</span><span class="n">k</span><span class="p">]))</span>
+                <span class="n">c</span><span class="p">[</span><span class="n">i</span><span class="p">,</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">vec</span><span class="p">[:,</span><span class="n">i</span><span class="p">]</span><span class="o">-</span><span class="n">vm</span><span class="p">,</span><span class="n">U</span><span class="p">[:,</span><span class="n">k</span><span class="p">])</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">gam_pca</span> <span class="o">=</span> <span class="n">gam_pca</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">psi_pca</span> <span class="o">=</span> <span class="n">psi_pca</span>

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 2.3.8 documentation</title>
+  <title>Overview: module code &mdash; fdasrsf 2.3.11 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]>
@@ -13,6 +13,7 @@
         <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/jquery.js"></script>
         <script src="../_static/underscore.js"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
         <script src="../_static/doctools.js"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../_static/js/theme.js"></script>

diff --git a/doc/build/html/_modules/time_warping.html b/doc/build/html/_modules/time_warping.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>time_warping &mdash; fdasrsf 2.3.8 documentation</title>
+  <title>time_warping &mdash; fdasrsf 2.3.11 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]>
@@ -13,6 +13,7 @@
         <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
         <script src="../_static/jquery.js"></script>
         <script src="../_static/underscore.js"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
         <script src="../_static/doctools.js"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../_static/js/theme.js"></script>
@@ -330,23 +331,22 @@ <h1>Source code for time_warping</h1><div class="highlight"><pre>
                 <span class="k">break</span>
 
         <span class="c1"># Last Step with centering of gam</span>
+        <span class="n">r</span> <span class="o">+=</span> <span class="mi">1</span>
+        <span class="k">if</span> <span class="n">parallel</span><span class="p">:</span>
+            <span class="n">out</span> <span class="o">=</span> <span class="n">Parallel</span><span class="p">(</span><span class="n">n_jobs</span><span class="o">=</span><span class="n">cores</span><span class="p">)(</span><span class="n">delayed</span><span class="p">(</span><span class="n">uf</span><span class="o">.</span><span class="n">optimum_reparam</span><span class="p">)(</span><span class="n">mq</span><span class="p">[:,</span> <span class="n">r</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">time</span><span class="p">,</span>
+                <span class="n">q</span><span class="p">[:,</span> <span class="n">n</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">omethod</span><span class="p">,</span> <span class="n">lam</span><span class="p">,</span> <span class="n">grid_dim</span><span class="p">)</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">N</span><span class="p">))</span>
+            <span class="n">gam</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">out</span><span class="p">)</span>
+            <span class="n">gam</span> <span class="o">=</span> <span class="n">gam</span><span class="o">.</span><span class="n">transpose</span><span class="p">()</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">N</span><span class="p">):</span>
+                <span class="n">gam</span><span class="p">[:,</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">uf</span><span class="o">.</span><span class="n">optimum_reparam</span><span class="p">(</span><span class="n">mq</span><span class="p">[:,</span> <span class="n">r</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">time</span><span class="p">,</span> <span class="n">q</span><span class="p">[:,</span> <span class="n">k</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">omethod</span><span class="p">,</span>
+                        <span class="n">lam</span><span class="p">,</span> <span class="n">grid_dim</span><span class="p">)</span>
 
-        <span class="k">if</span> <span class="n">center</span><span class="p">:</span>
-            <span class="n">r</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="k">if</span> <span class="n">parallel</span><span class="p">:</span>
-                <span class="n">out</span> <span class="o">=</span> <span class="n">Parallel</span><span class="p">(</span><span class="n">n_jobs</span><span class="o">=</span><span class="n">cores</span><span class="p">)(</span><span class="n">delayed</span><span class="p">(</span><span class="n">uf</span><span class="o">.</span><span class="n">optimum_reparam</span><span class="p">)(</span><span class="n">mq</span><span class="p">[:,</span> <span class="n">r</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">time</span><span class="p">,</span>
-                    <span class="n">q</span><span class="p">[:,</span> <span class="n">n</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">omethod</span><span class="p">,</span> <span class="n">lam</span><span class="p">,</span> <span class="n">grid_dim</span><span class="p">)</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">N</span><span class="p">))</span>
-                <span class="n">gam</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">out</span><span class="p">)</span>
-                <span class="n">gam</span> <span class="o">=</span> <span class="n">gam</span><span class="o">.</span><span class="n">transpose</span><span class="p">()</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">N</span><span class="p">):</span>
-                    <span class="n">gam</span><span class="p">[:,</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">uf</span><span class="o">.</span><span class="n">optimum_reparam</span><span class="p">(</span><span class="n">mq</span><span class="p">[:,</span> <span class="n">r</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">time</span><span class="p">,</span> <span class="n">q</span><span class="p">[:,</span> <span class="n">k</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="n">omethod</span><span class="p">,</span>
-                            <span class="n">lam</span><span class="p">,</span> <span class="n">grid_dim</span><span class="p">)</span>
-
-            <span class="n">gam_dev</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">M</span><span class="p">,</span> <span class="n">N</span><span class="p">))</span>
-            <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">N</span><span class="p">):</span>
-                <span class="n">gam_dev</span><span class="p">[:,</span> <span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">gradient</span><span class="p">(</span><span class="n">gam</span><span class="p">[:,</span> <span class="n">k</span><span class="p">],</span> <span class="mi">1</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="n">M</span> <span class="o">-</span> <span class="mi">1</span><span class="p">))</span>
+        <span class="n">gam_dev</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">M</span><span class="p">,</span> <span class="n">N</span><span class="p">))</span>
+        <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">N</span><span class="p">):</span>
+            <span class="n">gam_dev</span><span class="p">[:,</span> <span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">gradient</span><span class="p">(</span><span class="n">gam</span><span class="p">[:,</span> <span class="n">k</span><span class="p">],</span> <span class="mi">1</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="n">M</span> <span class="o">-</span> <span class="mi">1</span><span class="p">))</span>
 
+        <span class="k">if</span> <span class="n">center</span><span class="p">:</span>
             <span class="n">gamI</span> <span class="o">=</span> <span class="n">uf</span><span class="o">.</span><span class="n">SqrtMeanInverse</span><span class="p">(</span><span class="n">gam</span><span class="p">)</span>
             <span class="n">gamI_dev</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">gradient</span><span class="p">(</span><span class="n">gamI</span><span class="p">,</span> <span class="mi">1</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="n">M</span> <span class="o">-</span> <span class="mi">1</span><span class="p">))</span>
             <span class="n">time0</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">time</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">time</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">*</span> <span class="n">gamI</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">time</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
@@ -365,6 +365,7 @@ <h1>Source code for time_warping</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">fn</span> <span class="o">=</span> <span class="n">f</span><span class="p">[:,</span> <span class="p">:,</span> <span class="n">r</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">qn</span> <span class="o">=</span> <span class="n">q</span><span class="p">[:,</span> <span class="p">:,</span> <span class="n">r</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">q0</span> <span class="o">=</span> <span class="n">q</span><span class="p">[:,</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">gamI</span> <span class="o">=</span> <span class="n">gamI</span>
         <span class="n">mean_f0</span> <span class="o">=</span> <span class="n">f0</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
         <span class="n">std_f0</span> <span class="o">=</span> <span class="n">f0</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
         <span class="n">mean_fn</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">fn</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>