Skip to content

Commit

Permalink
update docs
Browse files Browse the repository at this point in the history
  • Loading branch information
@jdtuck
jdtuck committed Aug 21, 2023
1 parent 9ce2d44 commit f817b0f
Show file tree
Hide file tree
Showing 36 changed files with 783 additions and 358 deletions.
2 changes: 1 addition & 1 deletion doc/build/html/.buildinfo
View file
@@ -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: 94cabc678eb0f7c74fefabe67532679c
config: 294076d25accd1bfb90128f0dcd5f81d
tags: 645f666f9bcd5a90fca523b33c5a78b7
Binary file modified doc/build/html/.doctrees/curve_functions.doctree
View file
Binary file not shown.
Binary file modified doc/build/html/.doctrees/curve_statistics.doctree
View file
Binary file not shown.
Binary file modified doc/build/html/.doctrees/environment.pickle
View file
Binary file not shown.
Binary file modified doc/build/html/.doctrees/time_warping.doctree
View file
Binary file not shown.
218 changes: 65 additions & 153 deletions doc/build/html/_modules/curve_functions.html
View file

Large diffs are not rendered by default.

248 changes: 95 additions & 153 deletions doc/build/html/_modules/curve_stats.html
View file

Large diffs are not rendered by default.

3 changes: 2 additions & 1 deletion doc/build/html/_modules/index.html
View file
Expand Up @@ -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 2.4.2 documentation</title>
<title>Overview: module code &mdash; fdasrsf 2.4.3 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]>
Expand Down Expand Up @@ -97,6 +97,7 @@ <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>
Expand Down
43 changes: 21 additions & 22 deletions doc/build/html/_modules/time_warping.html
View file

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion doc/build/html/_static/documentation_options.js
View file
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '2.4.2',
VERSION: '2.4.3',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
Expand Down
6 changes: 3 additions & 3 deletions doc/build/html/boxplots.html
View file
Expand Up @@ -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 2.4.2 documentation</title>
<title>Elastic Functional Boxplots &mdash; fdasrsf 2.4.3 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]>
Expand Down Expand Up @@ -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> (<em>fdawarp</em>) – fdawarp class with alignment data</p></li>
<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>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>
Expand Down Expand Up @@ -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> (<em>fdawarp</em>) – fdawarp class with alignment data</p></li>
<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>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>
Expand Down
5 changes: 3 additions & 2 deletions doc/build/html/curve_functions.html
View file
Expand Up @@ -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 2.4.2 documentation</title>
<title>Curve Functions &mdash; fdasrsf 2.4.3 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]>
Expand Down Expand Up @@ -383,7 +383,7 @@

<dl class="py function">
<dt class="sig sig-object py" id="curve_functions.find_rotation_and_seed_unique">
<span class="sig-prename descclassname"><span class="pre">curve_functions.</span></span><span class="sig-name descname"><span class="pre">find_rotation_and_seed_unique</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">q1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">q2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">closed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rotation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'DP'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/curve_functions.html#find_rotation_and_seed_unique"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#curve_functions.find_rotation_and_seed_unique" title="Permalink to this definition"></a></dt>
<span class="sig-prename descclassname"><span class="pre">curve_functions.</span></span><span class="sig-name descname"><span class="pre">find_rotation_and_seed_unique</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">q1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">q2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">closed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lam</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rotation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'DP'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/curve_functions.html#find_rotation_and_seed_unique"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#curve_functions.find_rotation_and_seed_unique" title="Permalink to this definition"></a></dt>
<dd><p>This function returns a candidate list of optimally oriented and
registered (seed) shapes w.r.t. beta1</p>
<dl class="field-list simple">
Expand All @@ -393,6 +393,7 @@
<li><p><strong>beta2</strong> – numpy ndarray of shape (2,M) of M samples</p></li>
<li><p><strong>closed</strong> – Open (0) or Closed (1)</p></li>
<li><p><strong>rotation</strong> – find rotation (default=True)</p></li>
<li><p><strong>lam</strong> – controls the elasticity (default = 0)</p></li>
<li><p><strong>method</strong> – method to apply optimization (default=”DP”) options are “DP” or “RBFGS”</p></li>
</ul>
</dd>
Expand Down
16 changes: 12 additions & 4 deletions doc/build/html/curve_statistics.html
View file
Expand Up @@ -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 2.4.2 documentation</title>
<title>Curve Registration &mdash; fdasrsf 2.4.3 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]>
Expand Down Expand Up @@ -119,6 +119,7 @@
:param coef: pca coefficients
:param pca principal directions
:param qun: cost function
:param lambda: lambda
:param samples: random samples
:param gamr: random warping functions
:param cent: center
Expand All @@ -138,18 +139,24 @@

<dl class="py method">
<dt class="sig sig-object py" id="curve_stats.fdacurve.karcher_mean">
<span class="sig-name descname"><span class="pre">karcher_mean</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rotation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parallel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cores</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-</span> <span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'DP'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/curve_stats.html#fdacurve.karcher_mean"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#curve_stats.fdacurve.karcher_mean" title="Permalink to this definition"></a></dt>
<span class="sig-name descname"><span class="pre">karcher_mean</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rotation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parallel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lam</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cores</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-</span> <span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'DP'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/curve_stats.html#fdacurve.karcher_mean"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#curve_stats.fdacurve.karcher_mean" title="Permalink to this definition"></a></dt>
<dd><p>This calculates the mean of a set of curves
:param rotation: compute optimal rotation (default = T)
:param parallel: run in parallel (default = F)
:param lam: controls the elasticity (default = 0)
:param cores: number of cores for parallel (default = -1 (all))
:param method: method to apply optimization (default=”DP”) options are “DP” or “RBFGS”</p>
</dd></dl>

<dl class="py method">
<dt class="sig sig-object py" id="curve_stats.fdacurve.plot">
<span class="sig-name descname"><span class="pre">plot</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/curve_stats.html#fdacurve.plot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#curve_stats.fdacurve.plot" title="Permalink to this definition"></a></dt>
<span class="sig-name descname"><span class="pre">plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">multivariate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/curve_stats.html#fdacurve.plot"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#curve_stats.fdacurve.plot" title="Permalink to this definition"></a></dt>
<dd><p>plot curve mean results</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>multivariate</strong> – plot as multivariate functions instead of curves (default=False)</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
Expand Down Expand Up @@ -180,9 +187,10 @@

<dl class="py method">
<dt class="sig sig-object py" id="curve_stats.fdacurve.srvf_align">
<span class="sig-name descname"><span class="pre">srvf_align</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rotation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parallel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cores</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-</span> <span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'DP'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/curve_stats.html#fdacurve.srvf_align"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#curve_stats.fdacurve.srvf_align" title="Permalink to this definition"></a></dt>
<span class="sig-name descname"><span class="pre">srvf_align</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rotation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lam</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parallel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cores</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-</span> <span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'DP'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/curve_stats.html#fdacurve.srvf_align"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#curve_stats.fdacurve.srvf_align" title="Permalink to this definition"></a></dt>
<dd><p>This aligns a set of curves to the mean and computes mean if not computed
:param rotation: compute optimal rotation (default = T)
:param lam: controls the elasticity (default = 0)
:param parallel: run in parallel (default = F)
:param cores: number of cores for parallel (default = -1 (all))
:param method: method to apply optimization (default=”DP”) options are “DP” or “RBFGS”</p>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/fPCA.html
View file
Expand Up @@ -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 2.4.2 documentation</title>
<title>Functional Principal Component Analysis &mdash; fdasrsf 2.4.3 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]>
Expand Down
2 changes: 1 addition & 1 deletion doc/build/html/fPLS.html
View file
Expand Up @@ -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 2.4.2 documentation</title>
<title>Functional Principal Least Squares &mdash; fdasrsf 2.4.3 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]>
Expand Down

0 comments on commit f817b0f

Please sign in to comment.