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It was +later replaced by the ilr transformation because the ilr transformed +fractions can assumed to follow normal distribution. As the ilr +transformation is not available in RxODE and can therefore not be used in +the nlmixr modelling language, the original 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."><!-- 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><body data-spy="scroll" data-target="#toc"> + + + <div class="container template-reference-topic"> + <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"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <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"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</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/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> + </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/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </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/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>This transformation was used originally in mkin, in order to implement a +constraint for the sum of formation fractions to be smaller than 1. It 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" class="external-link">RxODE</a> and can therefore not be used in +the nlmixr modelling language, the original 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, this +implementation cannot be used there, as it is not accessible from RxODE.</p> + </div> + + <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="details"> + <h2>Details</h2> + <p>If the transformed formation fractions are restricted to the interval +between 0 and 1, the sum of backtransformed values is restricted +to this interval.</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> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> + + + + + + + </body></html> + |