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authorJohannes Ranke <jranke@uni-bremen.de>2022-03-02 18:03:54 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-03-02 18:03:54 +0100
commit2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch)
treef286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/tffm0.html
parent351248d07f810ccb6c497633a02cd48ee35526e6 (diff)
Make tests more platform independent, update docs
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+constraint for the sum of formation fractions to be smaller than 1. 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]>
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+ <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">&lt;-</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">&lt;-</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">#&gt;</span> [1] 0.10983681 0.09035905 0.08399383</span>
+</code></pre></div>
+ </div>
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