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| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-13 05:19:08 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-13 05:19:08 +0100 |
| commit | 8d1a84ac2190538ed3bac53a303064e281595868 (patch) | |
| tree | acb894d85ab7ec87c4911c355a5264a77e08e34b /docs/dev/reference/ilr.html | |
| parent | 51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff) | |
| parent | 4200e566ad2600f56bc3987669aeab88582139eb (diff) | |
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'docs/dev/reference/ilr.html')
| -rw-r--r-- | docs/dev/reference/ilr.html | 235 |
1 files changed, 97 insertions, 138 deletions
diff --git a/docs/dev/reference/ilr.html b/docs/dev/reference/ilr.html index 452647d6..c1396303 100644 --- a/docs/dev/reference/ilr.html +++ b/docs/dev/reference/ilr.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <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>Function to perform isometric log-ratio transformation — ilr • mkin</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> - 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- - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ transformations." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ transformations." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to perform isometric log-ratio transformation</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/ilr.R'><code>R/ilr.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ilr.R" class="external-link"><code>R/ilr.R</code></a></small> <div class="hidden name"><code>ilr.Rd</code></div> </div> @@ -149,86 +94,100 @@ transformations." /> transformations.</p> </div> - <pre class="usage"><span class='fu'>ilr</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> - -<span class='fu'>invilr</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">invilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>A numeric vector. Naturally, the forward transformation is only -sensible for vectors with all elements being greater than zero.</p></td> - </tr> - </table> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>A numeric vector. Naturally, the forward transformation is only +sensible for vectors with all elements being greater than zero.</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + - <p>The result of the forward or backward transformation. The returned +<p>The result of the forward or backward transformation. The returned components always sum to 1 for the case of the inverse log-ratio transformation.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>Another implementation can be found in R package + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p>Another implementation can be found in R package <code>robCompositions</code>.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>René Lehmann and Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># Order matters</span> -<span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] -1.628174 -2.820079</div><div class='input'><span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 1.628174 2.820079</div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> -<span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0 0</div><div class='input'><span class='co'># Almost equal entries give small numbers</span> -<span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] -0.2034219 0.1174457</div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> -<span class='fu'>invilr</span><span class='op'>(</span><span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'>ilr</span><span class='op'>(</span><span class='fl'>2.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> -<span class='fu'>invilr</span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01</div><div class='input'><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span>, <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04</div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> -<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span>, <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 1</div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> -<span class='va'>a</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span><span class='op'>)</span> -<span class='va'>b</span> <span class='op'><-</span> <span class='fu'>invilr</span><span class='op'>(</span><span class='va'>a</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>)</span> <span class='co'># Four elements</span> -</div><div class='output co'>#> [1] 4</div><div class='input'><span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, <span class='fl'>1</span> <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># Gives c(0.1, 0.3, 0.5)</span> -</div><div class='output co'>#> [1] 0.1 0.3 0.5</div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Order matters</span></span></span> +<span class="r-in"><span><span class="fu">ilr</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">0.1</span>, <span class="fl">1</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] -1.628174 -2.820079</span> +<span class="r-in"><span><span class="fu">ilr</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">10</span>, <span class="fl">1</span>, <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1.628174 2.820079</span> +<span class="r-in"><span><span class="co"># Equal entries give ilr transformations with zeros as elements</span></span></span> +<span class="r-in"><span><span class="fu">ilr</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">3</span>, <span class="fl">3</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0 0</span> +<span class="r-in"><span><span class="co"># Almost equal entries give small numbers</span></span></span> +<span class="r-in"><span><span class="fu">ilr</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">0.3</span>, <span class="fl">0.4</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] -0.2034219 0.1174457</span> +<span class="r-in"><span><span class="co"># Only the ratio between the numbers counts, not their sum</span></span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</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">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.70 0.29 0.01</span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</span><span class="op">(</span><span class="fl">2.1</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">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.70 0.29 0.01</span> +<span class="r-in"><span><span class="co"># Inverse transformation of larger numbers gives unequal elements</span></span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="op">-</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 7.213536e-07 9.999993e-01</span> +<span class="r-in"><span><span class="fu">invilr</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="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 7.207415e-07 9.991507e-01 8.486044e-04</span> +<span class="r-in"><span><span class="co"># The sum of the elements of the inverse ilr is 1</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">invilr</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="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1</span> +<span class="r-in"><span><span class="co"># This is why we do not need all elements of the inverse transformation to go back:</span></span></span> +<span class="r-in"><span><span class="va">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">0.1</span>, <span class="fl">0.3</span>, <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu">invilr</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">b</span><span class="op">)</span> <span class="co"># Four elements</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 4</span> +<span class="r-in"><span><span class="fu">ilr</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="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="fl">1</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="co"># Gives c(0.1, 0.3, 0.5)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.1 0.3 0.5</span> +<span class="r-in"><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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |