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-rw-r--r--docs/reference/DFOP.solution.html2
-rw-r--r--docs/reference/FOMC.solution.html2
-rw-r--r--docs/reference/HS.solution.html33
-rw-r--r--docs/reference/SFO.solution.html2
-rw-r--r--docs/reference/SFORB.solution.html22
-rw-r--r--docs/reference/create_deg_func.html198
-rw-r--r--docs/reference/index.html4
-rw-r--r--docs/reference/logistic.solution.html63
-rw-r--r--docs/reference/mkinmod.html16
-rw-r--r--docs/reference/mkinpredict.html48
-rw-r--r--docs/reference/nlme-1.pngbin70555 -> 71651 bytes
-rw-r--r--docs/reference/nlme.html75
12 files changed, 347 insertions, 118 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 46e0cc91..84e33f9e 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -73,7 +73,7 @@ two exponential decline functions." />
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 6c1f5229..369398d5 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -73,7 +73,7 @@ a decreasing rate constant." />
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index ad33d948..2684ee60 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -73,7 +73,7 @@ between them." />
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
@@ -152,6 +152,22 @@ between them.</p>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
+ <th>t</th>
+ <td><p>Time.</p></td>
+ </tr>
+ <tr>
+ <th>parent_0</th>
+ <td><p>Starting value for the response variable at time zero.</p></td>
+ </tr>
+ <tr>
+ <th>k1</th>
+ <td><p>First kinetic constant.</p></td>
+ </tr>
+ <tr>
+ <th>k2</th>
+ <td><p>Second kinetic constant.</p></td>
+ </tr>
+ <tr>
<th>tb</th>
<td><p>Break point. Before this time, exponential decline according to
<code>k1</code> is calculated, after this time, exponential decline proceeds
@@ -159,6 +175,21 @@ according to <code>k2</code>.</p></td>
</tr>
</table>
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The value of the response variable at time <code>t</code>.</p>
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
+FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ Version 1.1, 18 December 2014
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Other parent solutions:
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 93da04eb..9664deb3 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -72,7 +72,7 @@
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index c9f1b471..504f209f 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -76,7 +76,7 @@ and no substance in the bound fraction." />
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
@@ -158,6 +158,14 @@ and no substance in the bound fraction.</p>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
+ <th>t</th>
+ <td><p>Time.</p></td>
+ </tr>
+ <tr>
+ <th>parent_0</th>
+ <td><p>Starting value for the response variable at time zero.</p></td>
+ </tr>
+ <tr>
<th>k_12</th>
<td><p>Kinetic constant describing transfer from free to bound.</p></td>
</tr>
@@ -176,6 +184,18 @@ fraction.</p></td>
<p>The value of the response variable, which is the sum of free and
bound fractions at time <code>t</code>.</p>
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
+FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ Version 1.1, 18 December 2014
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Other parent solutions:
diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html
new file mode 100644
index 00000000..e14857cc
--- /dev/null
+++ b/docs/reference/create_deg_func.html
@@ -0,0 +1,198 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
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+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+<!-- Bootstrap -->
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+
+<!-- clipboard.js -->
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+
+<!-- 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>
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+<meta property="og:title" content="Create degradation functions for known analytical solutions — create_deg_func" />
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+ <a href="../articles/mkin.html">Introduction to mkin</a>
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+ </li>
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+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
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+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
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+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
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+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
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+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Create degradation functions for known analytical solutions</h1>
+ <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/create_deg_func.R'><code>R/create_deg_func.R</code></a></small>
+ <div class="hidden name"><code>create_deg_func.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Create degradation functions for known analytical solutions</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>create_deg_func</span>(<span class='no'>spec</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"min"</span>, <span class='st'>"max"</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>spec</th>
+ <td><p>List of model specifications as contained in mkinmod objects</p></td>
+ </tr>
+ <tr>
+ <th>use_of_ff</th>
+ <td><p>Minimum or maximum use of formation fractions</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Degradation function to be attached to mkinmod objects</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'>
+<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
+ <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div></pre>
+ </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>
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+
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+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index f77881fe..75820166 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
@@ -609,7 +609,7 @@ kinetic models fitted with mkinfit</p></td>
</tr><tr>
<td>
- <p><code><a href="logistic.solution.html">logistic.solution()</a></code> <code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
+ <p><code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
</td>
<td><p>Logistic kinetics</p></td>
</tr>
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 9697d420..b0ec77b1 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -41,8 +41,6 @@
<meta property="og:title" content="Logistic kinetics — logistic.solution" />
<meta property="og:description" content="Function describing exponential decline from a defined starting value, with
-an increasing rate constant, supposedly caused by microbial growth
-Function describing exponential decline from a defined starting value, with
an increasing rate constant, supposedly caused by microbial growth" />
@@ -75,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
@@ -139,20 +137,16 @@ an increasing rate constant, supposedly caused by microbial growth" />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Logistic kinetics</h1>
- <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/logistic.solution.R'><code>R/logistic.solution.R</code></a>, <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
+ <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
<div class="hidden name"><code>logistic.solution.Rd</code></div>
</div>
<div class="ref-description">
<p>Function describing exponential decline from a defined starting value, with
an increasing rate constant, supposedly caused by microbial growth</p>
-<p>Function describing exponential decline from a defined starting value, with
-an increasing rate constant, supposedly caused by microbial growth</p>
</div>
- <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)
-
-<span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
+ <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -177,10 +171,6 @@ an increasing rate constant, supposedly caused by microbial growth</p>
<th>r</th>
<td><p>Growth rate of the increase in the rate constant.</p></td>
</tr>
- <tr>
- <th>parent.0</th>
- <td><p>Starting value for the response variable at time zero.</p></td>
- </tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -190,11 +180,14 @@ an increasing rate constant, supposedly caused by microbial growth</p>
<p>The solution of the logistic model reduces to the
<code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p>
-<p>The solution of the logistic model reduces to the
- <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
- <p>FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+ <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+ and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+ EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
+FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
and Degradation Kinetics from Environmental Fate Studies on Pesticides in
EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
Version 1.1, 18 December 2014
@@ -248,44 +241,6 @@ an increasing rate constant, supposedly caused by microbial growth</p>
#&gt; r 1.1821120
#&gt; sigma 7.3256566</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; DT50 DT90 DT50_k0 DT50_kmax
#&gt; parent 36.86533 62.41511 4297.853 10.83349</div><div class='input'>
-
- <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
- <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
- <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>),
- <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
- <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>),
- <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>),
- <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>),
- <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
- <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"k0 = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span>),
- <span class='st'>", r = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span>)),
- <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>)</div><div class='img'><img src='logistic.solution-3.png' alt='' width='700' height='433' /></div><div class='input'>
- <span class='co'># Fit with synthetic data</span>
- <span class='no'>logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"logistic"</span>))
-
- <span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
- <span class='no'>parms_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>kmax</span> <span class='kw'>=</span> <span class='fl'>0.08</span>, <span class='kw'>k0</span> <span class='kw'>=</span> <span class='fl'>0.0001</span>, <span class='kw'>r</span> <span class='kw'>=</span> <span class='fl'>0.2</span>)
- <span class='no'>d_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>logistic</span>,
- <span class='no'>parms_logistic</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>),
- <span class='no'>sampling_times</span>)
- <span class='no'>d_2_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_logistic</span>,
- <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>),
- <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
-
- <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02
-#&gt; kmax 6.398190e-02 0.0143201031 4.467978 3.841829e-04 3.929235e-02
-#&gt; k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08
-#&gt; r 2.263946e-01 0.1718110715 1.317695 1.061044e-01 4.335843e-02
-#&gt; sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00
-#&gt; Upper
-#&gt; parent_0 109.9341588
-#&gt; kmax 0.1041853
-#&gt; k0 0.4448749
-#&gt; r 1.1821120
-#&gt; sigma 7.3256566</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; DT50 DT90 DT50_k0 DT50_kmax
-#&gt; parent 36.86533 62.41511 4297.853 10.83349</div><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index d1204e2e..2f2e89d9 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -75,7 +75,7 @@ list of lists can be given in the speclist argument." />
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
@@ -152,7 +152,7 @@ list of lists can be given in the speclist argument.</p>
<pre class="usage"><span class='fu'>mkinmod</span>(
<span class='no'>...</span>,
- <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>,
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>,
<span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
@@ -252,15 +252,15 @@ in the FOCUS and NAFTA guidance documents are used.</p>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file66a9718e919b.c 2&gt; file66a9718e919b.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB fileb6a4eaab60.c 2&gt; fileb6a4eaab60.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
#&gt; 3:
#&gt; 4: static double parms [3];
-#&gt; 5: #define k_parent_sink parms[0]
-#&gt; 6: #define k_parent_m1 parms[1]
-#&gt; 7: #define k_m1_sink parms[2]
+#&gt; 5: #define k_parent parms[0]
+#&gt; 6: #define f_parent_to_m1 parms[1]
+#&gt; 7: #define k_m1 parms[2]
#&gt; 8:
#&gt; 9: void initpar(void (* odeparms)(int *, double *)) {
#&gt; 10: int N = 3;
@@ -270,8 +270,8 @@ in the FOCUS and NAFTA guidance documents are used.</p>
#&gt; 14:
#&gt; 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
#&gt; 16:
-#&gt; 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
-#&gt; 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
+#&gt; 17: f[0] = - k_parent * y[0];
+#&gt; 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];
#&gt; 19: }</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='co'># If we have several parallel metabolites</span>
<span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 689fb7c7..21c13156 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." />
</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">0.9.49.11</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
@@ -268,8 +268,29 @@ solver is used.</p></td>
<pre class="examples"><div class='input'>
<span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
<span class='co'># Compare solution types</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
- <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, k) { parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)</span></div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt; time degradinol
+#&gt; 1 0 100.0000000
+#&gt; 2 1 74.0818221
+#&gt; 3 2 54.8811636
+#&gt; 4 3 40.6569660
+#&gt; 5 4 30.1194212
+#&gt; 6 5 22.3130160
+#&gt; 7 6 16.5298888
+#&gt; 8 7 12.2456428
+#&gt; 9 8 9.0717953
+#&gt; 10 9 6.7205513
+#&gt; 11 10 4.9787068
+#&gt; 12 11 3.6883167
+#&gt; 13 12 2.7323722
+#&gt; 14 13 2.0241911
+#&gt; 15 14 1.4995577
+#&gt; 16 15 1.1108997
+#&gt; 17 16 0.8229747
+#&gt; 18 17 0.6096747
+#&gt; 19 18 0.4516581
+#&gt; 20 19 0.3345965
+#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#&gt; time degradinol
#&gt; 1 0 100.0000000
#&gt; 2 1 74.0818221
@@ -291,7 +312,7 @@ solver is used.</p></td>
#&gt; 18 17 0.6096747
#&gt; 19 18 0.4516581
#&gt; 20 19 0.3345965
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; time degradinol
#&gt; 1 0 100.0000000
#&gt; 2 1 74.0818221
@@ -313,7 +334,7 @@ solver is used.</p></td>
#&gt; 18 17 0.6096747
#&gt; 19 18 0.4516581
#&gt; 20 19 0.3345965
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#&gt; time degradinol
#&gt; 1 0 100.0000000
#&gt; 2 1 74.0818221
@@ -337,25 +358,26 @@ solver is used.</p></td>
#&gt; 20 19 0.3345965
#&gt; 21 20 0.2478752</div><div class='input'>
<span class='co'># Compare integration methods to analytical solution</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
- <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, k) { parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)</span></div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
-#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 21 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
<span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
#&gt; 21 20 0.2480043</div><div class='input'><span class='co'># rk4 is not as precise here</span>
<span class='co'># The number of output times used to make a lot of difference until the</span>
<span class='co'># default for atol was adjusted</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
<span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#&gt; time degradinol
-#&gt; 201 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+#&gt; 201 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
<span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#&gt; time degradinol
#&gt; 2001 20 0.2478752</div><div class='input'>
<span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span>
<span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) {
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) {
<span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(
<span class='kw'>eigen</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
@@ -371,7 +393,7 @@ solver is used.</p></td>
}</div><div class='output co'>#&gt; <span class='message'>Lade nötiges Paket: rbenchmark</span></div><div class='output co'>#&gt; test replications elapsed relative user.self sys.self user.child
#&gt; 3 deSolve 10 0.229 28.625 0.229 0 0
#&gt; 2 deSolve_compiled 10 0.008 1.000 0.008 0 0
-#&gt; 1 eigen 10 0.025 3.125 0.026 0 0
+#&gt; 1 eigen 10 0.026 3.250 0.025 0 0
#&gt; sys.child
#&gt; 3 0
#&gt; 2 0
diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png
index 68ccb43f..8db1f999 100644
--- a/docs/reference/nlme-1.png
+++ b/docs/reference/nlme-1.png
Binary files differ
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index 70c6b63c..b92d2141 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -10,23 +10,27 @@
<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+<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">
@@ -40,7 +44,6 @@
an mmkin row object. An mmkin row object is essentially a list of mkinfit
objects that have been obtained by fitting the same model to a list of
datasets." />
-<meta name="twitter:card" content="summary" />
@@ -58,7 +61,7 @@ datasets." />
</head>
- <body>
+ <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -72,7 +75,7 @@ datasets." />
</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">0.9.49.10</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
</span>
</div>
@@ -116,7 +119,12 @@ datasets." />
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin/">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
@@ -131,7 +139,7 @@ datasets." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Helper functions to create nlme models from mmkin row objects</h1>
-
+ <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nlme.R'><code>R/nlme.R</code></a></small>
<div class="hidden name"><code>nlme.Rd</code></div>
</div>
@@ -177,15 +185,15 @@ datasets.</p>
<pre class="examples"><div class='input'><span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
<span class='no'>m_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
<span class='no'>d_SFO_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>98</span>), <span class='no'>sampling_times</span>)
<span class='no'>d_SFO_1_long</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>d_SFO_1</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)
<span class='no'>d_SFO_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.05</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.05</span>),
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>102</span>), <span class='no'>sampling_times</span>)
<span class='no'>d_SFO_2_long</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>d_SFO_2</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)
<span class='no'>d_SFO_3</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>103</span>), <span class='no'>sampling_times</span>)
<span class='no'>d_SFO_3_long</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>d_SFO_3</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)
@@ -214,42 +222,37 @@ datasets.</p>
#&gt; Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
#&gt; Data: grouped_data
#&gt; AIC BIC logLik
-#&gt; 298.2781 307.7372 -144.1391
+#&gt; 252.7798 262.1358 -121.3899
#&gt;
#&gt; Random effects:
#&gt; Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
#&gt; Level: ds
#&gt; Structure: Diagonal
-#&gt; parent_0 log_k_parent_sink Residual
-#&gt; StdDev: 0.9374733 0.7098105 3.83543
+#&gt; parent_0 log_k_parent_sink Residual
+#&gt; StdDev: 0.0006768135 0.6800777 2.489397
#&gt;
#&gt; Fixed effects: parent_0 + log_k_parent_sink ~ 1
-#&gt; Value Std.Error DF t-value p-value
-#&gt; parent_0 101.76838 1.1445444 45 88.91606 0
-#&gt; log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0
+#&gt; Value Std.Error DF t-value p-value
+#&gt; parent_0 101.74884 0.6456014 44 157.60321 0
+#&gt; log_k_parent_sink -3.05575 0.4015811 44 -7.60929 0
#&gt; Correlation:
#&gt; prnt_0
-#&gt; log_k_parent_sink 0.034
+#&gt; log_k_parent_sink 0.026
#&gt;
#&gt; Standardized Within-Group Residuals:
#&gt; Min Q1 Med Q3 Max
-#&gt; -2.6169360 -0.2185329 0.0574070 0.5720937 3.0459868
+#&gt; -2.1317488 -0.6878121 0.0828385 0.8592270 2.9529864
#&gt;
-#&gt; Number of Observations: 49
-#&gt; Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span>(<span class='no'>m_nlme</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0</span>:<span class='fl'>1</span>), <span class='kw'>layout</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>1</span>))</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'># augPred does not seem to work on fits with more than one state
+#&gt; Number of Observations: 48
+#&gt; Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span>(<span class='no'>m_nlme</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0</span>:<span class='fl'>1</span>), <span class='kw'>layout</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>1</span>))</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'># augPred does not seem to work on fits with more than one state
# variable
</div></pre>
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@@ -260,7 +263,7 @@ datasets.</p>
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