From ffc3d056b25b188dc40735dac5d2bd77d5f8862f Mon Sep 17 00:00:00 2001
From: Maria Rizzo <mrizzo@bgsu.edu>
Date: Tue, 27 Aug 2024 15:44:22 -0400
Subject: [PATCH] updates

---
 docs/news/index.html           |   2 +-
 docs/pkgdown.yml               |   2 +-
 docs/reference/indep.test.html | 245 ---------------------------------
 3 files changed, 2 insertions(+), 247 deletions(-)
 delete mode 100644 docs/reference/indep.test.html
diff --git a/docs/news/index.html b/docs/news/index.html
index 27e1310..152d9e1 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -48,7 +48,7 @@ <h1 data-toc-skip>Changelog <small></small></h1>
     </div>
 
     <div class="section level2">
-<h2 class="page-header" data-toc-text="1.7-12" id="energy-17-12">energy 1.7-12<a class="anchor" aria-label="anchor" href="#energy-17-12"></a></h2>
+<h2 class="page-header" data-toc-text="1.7-12" id="energy-17-12">energy 1.7-12<small>2024-08-23</small><a class="anchor" aria-label="anchor" href="#energy-17-12"></a></h2>
 <ul><li>User level changes
 <ul><li>Defunct functions indep.e and indep.etest removed (previously replaced by mvI and mvI.test)</li>
 <li>indep.test is now deprecated.</li>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 8ad4f0e..bd8f09e 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: '3.3'
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-25T21:32Z
+last_built: 2024-08-27T19:42Z
diff --git a/docs/reference/indep.test.html b/docs/reference/indep.test.html
deleted file mode 100644
index 9b71293..0000000
--- a/docs/reference/indep.test.html
+++ /dev/null
@@ -1,245 +0,0 @@
-<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Energy-tests of Independence — indep.test • energy</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Energy-tests of Independence — indep.test"><meta property="og:description" content="Computes a multivariate nonparametric test of independence.
- The default method implements the distance covariance test
- dcov.test."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-        <a class="navbar-link" href="../index.html">energy</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.7-11</span>
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-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav"><li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li>
-  <a href="../news/index.html">Changelog</a>
-</li>
-      </ul><ul class="nav navbar-nav navbar-right"><li>
-  <a href="https://github.com/mariarizzo/energy/" class="external-link">
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-      </header><div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Energy-tests of Independence</h1>
-    
-    <div class="hidden name"><code>indep.test.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    <p>Computes a multivariate nonparametric test of independence.
- The default method implements the distance covariance test
- <code><a href="dcov.test.html">dcov.test</a></code>.</p>
-    </div>
-
-    <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">indep.test</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"dcov"</span>,<span class="st">"mvI"</span><span class="op">)</span>, index <span class="op">=</span> <span class="fl">1</span>, <span class="va">R</span><span class="op">)</span></span></code></pre></div>
-    </div>
-
-    <div id="arguments">
-    <h2>Arguments</h2>
-    <dl><dt>x</dt>
-<dd><p>matrix: first sample, observations in rows</p></dd>
-
-  <dt>y</dt>
-<dd><p>matrix: second sample, observations in rows</p></dd>
-
-  <dt>method</dt>
-<dd><p>a character string giving the name of the test</p></dd>
-
-  <dt>index</dt>
-<dd><p>exponent on Euclidean distances</p></dd>
-
-  <dt>R</dt>
-<dd><p>number of replicates</p></dd>
-
-</dl></div>
-    <div id="details">
-    <h2>Details</h2>
-    <p><code>indep.test</code> with the default <code>method = "dcov"</code> computes
- the distance
- covariance test of independence. <code>index</code> is an exponent on
- the Euclidean distances. Valid choices for <code>index</code> are in (0,2],
- with default value 1 (Euclidean distance). The arguments are passed
- to the <code>dcov.test</code> function. See the help topic <code><a href="dcov.test.html">dcov.test</a></code> for
- the description and documentation and also see the references below.</p>
-<p><code>indep.test</code> with <code>method = "mvI"</code>
- computes the coefficient \(\mathcal I_n\) and performs a nonparametric
- \(\mathcal E\)-test of independence. The arguments are passed to
- <code>mvI.test</code>. The
- <code>index</code> argument is ignored (<code>index = 1</code> is applied).
- See the help topic <code><a href="mvI.test.html">mvI.test</a></code> and also
- see the reference (2006) below for details.</p>
-<p>The test decision is obtained via
- bootstrap, with <code>R</code> replicates.
- The sample sizes (number of rows) of the two samples must agree, and
- samples must not contain missing values.</p>
-<p>These energy tests of independence are based on related theoretical
- results, but different test statistics.
- The <code>dcov</code> method is faster than <code>mvI</code> method by
- approximately a factor of O(n).</p>
-    </div>
-    <div id="value">
-    <h2>Value</h2>
-    <p></p>
-<p><code>indep.test</code> returns a list with class</p>
-<p></p>
-<p><code>htest</code> containing</p>
-<dl><dt>     method</dt>
-<dd><p>description of test</p></dd>
-
- <dt>  statistic</dt>
-<dd><p>observed value of the
- test statistic \(n \mathcal V_n^2\)
- or \(n \mathcal I_n^2\)</p></dd>
-
-    <dt>  estimate</dt>
-<dd><p>\(\mathcal V_n\) or \(\mathcal I_n\)</p></dd>
-
-    <dt>  estimates</dt>
-<dd><p>a vector [dCov(x,y), dCor(x,y), dVar(x), dVar(y)]
-    (method dcov)</p></dd>
-
-   <dt> replicates</dt>
-<dd><p>replicates of the test statistic</p></dd>
-
-   <dt>    p.value</dt>
-<dd><p>approximate p-value of the test</p></dd>
-
- <dt>  data.name</dt>
-<dd><p>description of data</p></dd>
-
- </dl></div>
-    <div id="note">
-    <h2>Note</h2>
-    <p>As of energy-1.1-0,
-<code>indep.etest</code> is deprecated and replaced by <code>indep.test</code>, which
-has methods for two different energy tests of independence.  <code>indep.test</code> applies
-the distance covariance test (see <code>dcov.test</code>) by default (<code>method = "dcov"</code>).
-The original <code>indep.etest</code> applied the independence coefficient
-\(\mathcal I_n\), which is now obtained by <code>method = "mvI"</code>.</p>
-    </div>
-    <div id="see-also">
-    <h2>See also</h2>
-    <div class="dont-index"><p><code> <a href="dcov.test.html">dcov.test</a> </code>
- <code> <a href="mvI.test.html">mvI.test</a> </code>
- <code> <a href="dcov.html">dcov</a> </code>
- <code> <a href="mvI.test.html">mvI</a> </code></p></div>
-    </div>
-    <div id="references">
-    <h2>References</h2>
-    <p>Szekely, G.J. and Rizzo, M.L. (2009),
-  Brownian Distance Covariance,
- <em>Annals of Applied Statistics</em>, Vol. 3 No. 4, pp.
- 1236-1265. (Also see discussion and rejoinder.)
- <br><a href="https://doi.org/10.1214/09-AOAS312" class="external-link">doi:10.1214/09-AOAS312</a></p>
-<p>Szekely, G.J., Rizzo, M.L., and Bakirov, N.K. (2007),
-  Measuring and Testing Dependence by Correlation of Distances,
- <em>Annals of Statistics</em>, Vol. 35 No. 6, pp. 2769-2794.
- <br><a href="https://doi.org/10.1214/009053607000000505" class="external-link">doi:10.1214/009053607000000505</a></p>
-<p>Bakirov, N.K., Rizzo, M.L., and Szekely, G.J. (2006), A Multivariate
- Nonparametric Test of Independence, <em>Journal of Multivariate Analysis</em>
- 93/1, 58-80, <br><a href="https://doi.org/10.1016/j.jmva.2005.10.005" class="external-link">doi:10.1016/j.jmva.2005.10.005</a></p>
-    </div>
-    <div id="author">
-    <h2>Author</h2>
-    <p>Maria L. Rizzo <a href="mailto:mrizzo@bgsu.edu">mrizzo@bgsu.edu</a> and
-Gabor J. Szekely</p>
-    </div>
-
-    <div id="ref-examples">
-    <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
-<span class="r-in"><span> <span class="co">## independent multivariate data</span></span></span>
-<span class="r-in"><span> <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">60</span><span class="op">)</span>, nrow<span class="op">=</span><span class="fl">20</span>, ncol<span class="op">=</span><span class="fl">3</span><span class="op">)</span></span></span>
-<span class="r-in"><span> <span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">40</span><span class="op">)</span>, nrow<span class="op">=</span><span class="fl">20</span>, ncol<span class="op">=</span><span class="fl">2</span><span class="op">)</span></span></span>
-<span class="r-in"><span> <span class="fu">indep.test</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span>, method <span class="op">=</span> <span class="st">"dcov"</span>, R <span class="op">=</span> <span class="fl">99</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 	dCov independence test (permutation test)</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> data:  index 1, replicates 99</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> nV^2 = 3.2897, p-value = 0.79</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> sample estimates:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>      dCov </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 0.4055658 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in"><span> <span class="fu">indep.test</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span>, method <span class="op">=</span> <span class="st">"mvI"</span>, R <span class="op">=</span> <span class="fl">99</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 	mvI energy test of independence</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> data:  x (20 by 3), y(20 by 2), replicates 99</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> nI^2 = 1.0105, p-value = 0.3838</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> sample estimates:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>         I </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 0.2247749 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span> <span class="co">## dependent multivariate data</span></span></span>
-<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://www.stats.ox.ac.uk/pub/MASS4/" class="external-link">MASS</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
-<span class="r-in"><span>   <span class="va">Sigma</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">.1</span>, <span class="fl">0</span>, <span class="fl">0</span> , <span class="fl">1</span>, <span class="fl">0</span>, <span class="fl">0</span> ,<span class="fl">.1</span>, <span class="fl">1</span><span class="op">)</span>, <span class="fl">3</span>, <span class="fl">3</span><span class="op">)</span></span></span>
-<span class="r-in"><span>   <span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/MASS/man/mvrnorm.html" class="external-link">mvrnorm</a></span><span class="op">(</span><span class="fl">30</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-in"><span>   <span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/MASS/man/mvrnorm.html" class="external-link">mvrnorm</a></span><span class="op">(</span><span class="fl">30</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">0</span><span class="op">)</span>, <span class="va">Sigma</span><span class="op">)</span> <span class="op">*</span> <span class="va">x</span></span></span>
-<span class="r-in"><span>   <span class="fu">indep.test</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span>, R <span class="op">=</span> <span class="fl">99</span><span class="op">)</span>    <span class="co">#dcov method</span></span></span>
-<span class="r-in"><span>   <span class="fu">indep.test</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span>, method <span class="op">=</span> <span class="st">"mvI"</span>, R <span class="op">=</span> <span class="fl">99</span><span class="op">)</span></span></span>
-<span class="r-in"><span>    <span class="op">}</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: MASS</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 	mvI energy test of independence</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> data:  x (30 by 3), y(30 by 3), replicates 99</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> nI^2 = 1.2646, p-value = 0.0101</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> sample estimates:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>         I </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 0.2053116 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in"><span>  <span class="co"># }</span></span></span>
-</code></pre></div>
-    </div>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
-    </nav></div>
-</div>
-
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-      <footer><div class="copyright">
-  <p></p><p>Developed by Maria Rizzo, Gabor Szekely.</p>
-</div>
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