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authorJohannes Ranke <jranke@uni-bremen.de>2022-02-28 15:05:58 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-02-28 15:05:58 +0100
commitb3ca0aa552916b10a7d6d642138aecf744aed3de (patch)
tree6ffaa424b58b7e40cd1f4ef71b610c1f4aaeb9a0 /docs/dev/reference/tffm0.html
parent37bffdcfab0ca4e0de638b1a63e808b1d29d3f15 (diff)
Update docs
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-rw-r--r--docs/dev/reference/tffm0.html178
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diff --git a/docs/dev/reference/tffm0.html b/docs/dev/reference/tffm0.html
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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." />
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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/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'>&lt;-</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'>&lt;-</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'>#&gt; [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">&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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