diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-02-28 15:05:58 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-02-28 15:05:58 +0100 |
| commit | b3ca0aa552916b10a7d6d642138aecf744aed3de (patch) | |
| tree | 6ffaa424b58b7e40cd1f4ef71b610c1f4aaeb9a0 /docs/dev/reference/tffm0.html | |
| parent | 37bffdcfab0ca4e0de638b1a63e808b1d29d3f15 (diff) | |
Update docs
Diffstat (limited to 'docs/dev/reference/tffm0.html')
| -rw-r--r-- | docs/dev/reference/tffm0.html | 178 |
1 files changed, 55 insertions, 123 deletions
diff --git a/docs/dev/reference/tffm0.html b/docs/dev/reference/tffm0.html index c7b5b6de..8988b5a2 100644 --- a/docs/dev/reference/tffm0.html +++ b/docs/dev/reference/tffm0.html @@ -1,46 +1,5 @@ -<!-- 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>Transform formation fractions as in the first published mkin version — tffm0 • 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> - -<!-- 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="Transform formation fractions as in the first published mkin version — tffm0" /> -<meta property="og:description" content="The transformed fractions can be restricted between 0 and 1 in model +<!-- 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>Transform formation fractions as in the first published mkin version — tffm0 • 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><!-- 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="Transform formation fractions as in the first published mkin version — tffm0"><meta property="og:description" content="The transformed fractions can be restricted between 0 and 1 in model optimisations. Therefore this transformation was used originally in mkin. It was later replaced by the ilr transformation because the ilr transformed fractions can assumed to follow normal distribution. As the ilr @@ -49,28 +8,14 @@ the nlmixr modelling language, this transformation is currently used for translating mkin models with formation fractions to more than one target compartment for fitting with nlmixr in nlmixr_model. However, this implementation cannot be used there, as it is not accessible -from RxODE." /> - - -<meta name="robots" content="noindex"> - -<!-- 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]> +from RxODE."><meta name="robots" content="noindex"><!-- 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]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <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"> @@ -86,8 +31,7 @@ from RxODE." /> </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"> @@ -96,8 +40,7 @@ from RxODE." /> <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> @@ -121,106 +64,95 @@ from RxODE." /> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</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>Transform formation fractions as in the first published mkin version</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/tffm0.R'><code>R/tffm0.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/tffm0.R" class="external-link"><code>R/tffm0.R</code></a></small> <div class="hidden name"><code>tffm0.Rd</code></div> </div> <div class="ref-description"> <p>The transformed fractions can be restricted between 0 and 1 in model optimisations. Therefore this transformation was used originally in mkin. It -was later replaced by the <a href='ilr.html'>ilr</a> transformation because the ilr transformed +was later replaced by the <a href="ilr.html">ilr</a> transformation because the ilr transformed fractions can assumed to follow normal distribution. As the ilr -transformation is not available in <a href='https://nlmixrdevelopment.github.io/RxODE/reference/RxODE.html'>RxODE</a> and can therefore not be used in +transformation is not available in <a href="https://nlmixrdevelopment.github.io/RxODE/reference/RxODE.html" class="external-link">RxODE</a> and can therefore not be used in the nlmixr modelling language, this transformation is currently used for translating mkin models with formation fractions to more than one target -compartment for fitting with nlmixr in <a href='nlmixr.mmkin.html'>nlmixr_model</a>. However, +compartment for fitting with nlmixr in <a href="nlmixr.mmkin.html">nlmixr_model</a>. However, this implementation cannot be used there, as it is not accessible from RxODE.</p> </div> - <pre class="usage"><span class='fu'>tffm0</span><span class='op'>(</span><span class='va'>ff</span><span class='op'>)</span> - -<span class='fu'>invtffm0</span><span class='op'>(</span><span class='va'>ff_trans</span><span class='op'>)</span></pre> - - <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>ff</th> - <td><p>Vector of untransformed formation fractions. The sum -must be smaller or equal to one</p></td> - </tr> - <tr> - <th>ff_trans</th> - <td><p>Vector of transformed formation fractions that can be -restricted to the interval from 0 to 1</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A vector of the transformed formation fractions</p> -<p>A vector of backtransformed formation fractions for natural use in degradation models</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>ff_example</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'>0.10983681</span>, <span class='fl'>0.09035905</span>, <span class='fl'>0.08399383</span> -<span class='op'>)</span> -<span class='va'>ff_example_trans</span> <span class='op'><-</span> <span class='fu'>tffm0</span><span class='op'>(</span><span class='va'>ff_example</span><span class='op'>)</span> -<span class='fu'>invtffm0</span><span class='op'>(</span><span class='va'>ff_example_trans</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.10983681 0.09035905 0.08399383</div></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">tffm0</span><span class="op">(</span><span class="va">ff</span><span class="op">)</span> + +<span class="fu">invtffm0</span><span class="op">(</span><span class="va">ff_trans</span><span class="op">)</span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>ff</dt> +<dd><p>Vector of untransformed formation fractions. The sum +must be smaller or equal to one</p></dd> +<dt>ff_trans</dt> +<dd><p>Vector of transformed formation fractions that can be +restricted to the interval from 0 to 1</p></dd> +</dl></div> + <div id="value"> + <h2>Value</h2> + <p>A vector of the transformed formation fractions +A vector of backtransformed formation fractions for natural use in degradation models</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">ff_example</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> +<span class="r-in"> <span class="fl">0.10983681</span>, <span class="fl">0.09035905</span>, <span class="fl">0.08399383</span></span> +<span class="r-in"><span class="op">)</span></span> +<span class="r-in"><span class="va">ff_example_trans</span> <span class="op"><-</span> <span class="fu">tffm0</span><span class="op">(</span><span class="va">ff_example</span><span class="op">)</span></span> +<span class="r-in"><span class="fu">invtffm0</span><span class="op">(</span><span class="va">ff_example_trans</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.10983681 0.09035905 0.08399383</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> 2.0.2.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |