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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-14 21:47:45 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-14 21:47:45 +0100
commit9275bcb39b5ee25753ef489d334b4906401970b3 (patch)
tree9ddaaf518f8655f38a44f1a0516335989085d490 /docs/dev/reference/mkinpredict.html
parentd6168b0851a52adeaed8099e41a960d79acedae9 (diff)
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@@ -1,69 +1,14 @@
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kinetic model as specified by mkinmod, using a specific set of
-kinetic parameters and initial values for the state variables." />
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@@ -74,23 +19,21 @@ kinetic parameters and initial values for the state variables." />
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- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span>
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+ <ul class="nav navbar-nav"><li>
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+ <ul class="dropdown-menu" role="menu"><li>
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@@ -100,12 +43,18 @@ kinetic parameters and initial values for the state variables." />
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <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/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
@@ -114,343 +63,358 @@ kinetic parameters and initial values for the state variables." />
<li>
<a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
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+ </header><div class="row">
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<h1>Produce predictions from a kinetic model using specific parameters</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinpredict.R'><code>R/mkinpredict.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinpredict.R" class="external-link"><code>R/mkinpredict.R</code></a></small>
<div class="hidden name"><code>mkinpredict.Rd</code></div>
</div>
<div class="ref-description">
<p>This function produces a time series for all the observed variables in a
-kinetic model as specified by <code><a href='mkinmod.html'>mkinmod</a></code>, using a specific set of
+kinetic model as specified by <a href="mkinmod.html">mkinmod</a>, using a specific set of
kinetic parameters and initial values for the state variables.</p>
</div>
- <pre class="usage"><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>odeparms</span>, <span class='va'>odeini</span>, <span class='va'>outtimes</span>, <span class='va'>...</span><span class='op'>)</span>
-
-<span class='co'># S3 method for mkinmod</span>
-<span class='fu'>mkinpredict</span><span class='op'>(</span>
- <span class='va'>x</span>,
- odeparms <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent_sink <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>,
- odeini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>,
- outtimes <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>120</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>,
- solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>,
- use_compiled <span class='op'>=</span> <span class='st'>"auto"</span>,
- method.ode <span class='op'>=</span> <span class='st'>"lsoda"</span>,
- atol <span class='op'>=</span> <span class='fl'>1e-08</span>,
- rtol <span class='op'>=</span> <span class='fl'>1e-10</span>,
- map_output <span class='op'>=</span> <span class='cn'>TRUE</span>,
- na_stop <span class='op'>=</span> <span class='cn'>TRUE</span>,
- <span class='va'>...</span>
-<span class='op'>)</span>
-
-<span class='co'># S3 method for mkinfit</span>
-<span class='fu'>mkinpredict</span><span class='op'>(</span>
- <span class='va'>x</span>,
- odeparms <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>bparms.ode</span>,
- odeini <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>bparms.state</span>,
- outtimes <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>120</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>,
- solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>,
- use_compiled <span class='op'>=</span> <span class='st'>"auto"</span>,
- method.ode <span class='op'>=</span> <span class='st'>"lsoda"</span>,
- atol <span class='op'>=</span> <span class='fl'>1e-08</span>,
- rtol <span class='op'>=</span> <span class='fl'>1e-10</span>,
- map_output <span class='op'>=</span> <span class='cn'>TRUE</span>,
- <span class='va'>...</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>x</th>
- <td><p>A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>, or a kinetic
-fit as fitted by <code><a href='mkinfit.html'>mkinfit</a></code>. In the latter case, the fitted
-parameters are used for the prediction.</p></td>
- </tr>
- <tr>
- <th>odeparms</th>
- <td><p>A numeric vector specifying the parameters used in the
-kinetic model, which is generally defined as a set of ordinary
-differential equations.</p></td>
- </tr>
- <tr>
- <th>odeini</th>
- <td><p>A numeric vector containing the initial values of the state
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">x</span>, <span class="va">odeparms</span>, <span class="va">odeini</span>, <span class="va">outtimes</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mkinmod</span></span>
+<span><span class="fu">mkinpredict</span><span class="op">(</span></span>
+<span> <span class="va">x</span>,</span>
+<span> odeparms <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>k_parent_sink <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span>
+<span> odeini <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>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span>
+<span> outtimes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">120</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span>
+<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span>
+<span> use_compiled <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span> method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,</span>
+<span> atol <span class="op">=</span> <span class="fl">1e-08</span>,</span>
+<span> rtol <span class="op">=</span> <span class="fl">1e-10</span>,</span>
+<span> maxsteps <span class="op">=</span> <span class="fl">20000</span>,</span>
+<span> map_output <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span> na_stop <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span> <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mkinfit</span></span>
+<span><span class="fu">mkinpredict</span><span class="op">(</span></span>
+<span> <span class="va">x</span>,</span>
+<span> odeparms <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.ode</span>,</span>
+<span> odeini <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.state</span>,</span>
+<span> outtimes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">120</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span>
+<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span>
+<span> use_compiled <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span> method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,</span>
+<span> atol <span class="op">=</span> <span class="fl">1e-08</span>,</span>
+<span> rtol <span class="op">=</span> <span class="fl">1e-10</span>,</span>
+<span> map_output <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span> <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>x</dt>
+<dd><p>A kinetic model as produced by <a href="mkinmod.html">mkinmod</a>, or a kinetic fit as
+fitted by <a href="mkinfit.html">mkinfit</a>. In the latter case, the fitted parameters are used for
+the prediction.</p></dd>
+
+
+<dt>odeparms</dt>
+<dd><p>A numeric vector specifying the parameters used in the
+kinetic model, which is generally defined as a set of ordinary differential
+equations.</p></dd>
+
+
+<dt>odeini</dt>
+<dd><p>A numeric vector containing the initial values of the state
variables of the model. Note that the state variables can differ from the
-observed variables, for example in the case of the SFORB model.</p></td>
- </tr>
- <tr>
- <th>outtimes</th>
- <td><p>A numeric vector specifying the time points for which model
-predictions should be generated.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Further arguments passed to the ode solver in case such a
-solver is used.</p></td>
- </tr>
- <tr>
- <th>solution_type</th>
- <td><p>The method that should be used for producing the
+observed variables, for example in the case of the SFORB model.</p></dd>
+
+
+<dt>outtimes</dt>
+<dd><p>A numeric vector specifying the time points for which model
+predictions should be generated.</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Further arguments passed to the ode solver in case such a
+solver is used.</p></dd>
+
+
+<dt>solution_type</dt>
+<dd><p>The method that should be used for producing the
predictions. This should generally be "analytical" if there is only one
observed variable, and usually "deSolve" in the case of several observed
variables. The third possibility "eigen" is faster but not applicable to
-some models e.g. using FOMC for the parent compound.</p></td>
- </tr>
- <tr>
- <th>use_compiled</th>
- <td><p>If set to <code>FALSE</code>, no compiled version of the
-<code><a href='mkinmod.html'>mkinmod</a></code> model is used, even if is present.</p></td>
- </tr>
- <tr>
- <th>method.ode</th>
- <td><p>The solution method passed via <code>mkinpredict</code>
-to <code>ode</code> in case the solution type is "deSolve". The default
-"lsoda" is performant, but sometimes fails to converge.</p></td>
- </tr>
- <tr>
- <th>atol</th>
- <td><p>Absolute error tolerance, passed to <code>ode</code>. Default
-is 1e-8, lower than in <code>lsoda</code>.</p></td>
- </tr>
- <tr>
- <th>rtol</th>
- <td><p>Absolute error tolerance, passed to <code>ode</code>. Default
-is 1e-10, much lower than in <code>lsoda</code>.</p></td>
- </tr>
- <tr>
- <th>map_output</th>
- <td><p>Boolean to specify if the output should list values for
+some models e.g. using FOMC for the parent compound.</p></dd>
+
+
+<dt>use_compiled</dt>
+<dd><p>If set to <code>FALSE</code>, no compiled version of the
+<a href="mkinmod.html">mkinmod</a> model is used, even if is present.</p></dd>
+
+
+<dt>method.ode</dt>
+<dd><p>The solution method passed via mkinpredict to ode] in
+case the solution type is "deSolve". The default "lsoda" is performant, but
+sometimes fails to converge.</p></dd>
+
+
+<dt>atol</dt>
+<dd><p>Absolute error tolerance, passed to ode. Default is 1e-8,
+lower than in lsoda.</p></dd>
+
+
+<dt>rtol</dt>
+<dd><p>Absolute error tolerance, passed to ode. Default is 1e-10,
+much lower than in lsoda.</p></dd>
+
+
+<dt>maxsteps</dt>
+<dd><p>Maximum number of steps, passed to ode.</p></dd>
+
+
+<dt>map_output</dt>
+<dd><p>Boolean to specify if the output should list values for
the observed variables (default) or for all state variables (if set to
FALSE). Setting this to FALSE has no effect for analytical solutions,
-as these always return mapped output.</p></td>
- </tr>
- <tr>
- <th>na_stop</th>
- <td><p>Should it be an error if deSolve::ode returns NaN values</p></td>
- </tr>
- </table>
+as these always return mapped output.</p></dd>
+
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+<dt>na_stop</dt>
+<dd><p>Should it be an error if ode returns NaN values</p></dd>
- <p>A matrix with the numeric solution in wide format</p>
- <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+<p>A matrix with the numeric solution in wide format</p>
+ </div>
+ <div id="author">
+ <h2>Author</h2>
<p>Johannes Ranke</p>
+ </div>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
-<span class='va'>SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-<span class='co'># Compare solution types</span>
-<span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
- solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 0 0 100.0000000
-#&gt; 1 1 74.0818221
-#&gt; 2 2 54.8811636
-#&gt; 3 3 40.6569660
-#&gt; 4 4 30.1194212
-#&gt; 5 5 22.3130160
-#&gt; 6 6 16.5298888
-#&gt; 7 7 12.2456428
-#&gt; 8 8 9.0717953
-#&gt; 9 9 6.7205513
-#&gt; 10 10 4.9787068
-#&gt; 11 11 3.6883167
-#&gt; 12 12 2.7323722
-#&gt; 13 13 2.0241911
-#&gt; 14 14 1.4995577
-#&gt; 15 15 1.1108997
-#&gt; 16 16 0.8229747
-#&gt; 17 17 0.6096747
-#&gt; 18 18 0.4516581
-#&gt; 19 19 0.3345965
-#&gt; 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
- solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 0 0 100.0000000
-#&gt; 1 1 74.0818221
-#&gt; 2 2 54.8811636
-#&gt; 3 3 40.6569660
-#&gt; 4 4 30.1194212
-#&gt; 5 5 22.3130160
-#&gt; 6 6 16.5298888
-#&gt; 7 7 12.2456428
-#&gt; 8 8 9.0717953
-#&gt; 9 9 6.7205513
-#&gt; 10 10 4.9787068
-#&gt; 11 11 3.6883167
-#&gt; 12 12 2.7323722
-#&gt; 13 13 2.0241911
-#&gt; 14 14 1.4995577
-#&gt; 15 15 1.1108996
-#&gt; 16 16 0.8229747
-#&gt; 17 17 0.6096747
-#&gt; 18 18 0.4516581
-#&gt; 19 19 0.3345965
-#&gt; 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
- solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 0 0 100.0000000
-#&gt; 1 1 74.0818221
-#&gt; 2 2 54.8811636
-#&gt; 3 3 40.6569660
-#&gt; 4 4 30.1194212
-#&gt; 5 5 22.3130160
-#&gt; 6 6 16.5298888
-#&gt; 7 7 12.2456428
-#&gt; 8 8 9.0717953
-#&gt; 9 9 6.7205513
-#&gt; 10 10 4.9787068
-#&gt; 11 11 3.6883167
-#&gt; 12 12 2.7323722
-#&gt; 13 13 2.0241911
-#&gt; 14 14 1.4995577
-#&gt; 15 15 1.1108996
-#&gt; 16 16 0.8229747
-#&gt; 17 17 0.6096747
-#&gt; 18 18 0.4516581
-#&gt; 19 19 0.3345965
-#&gt; 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
- solution_type <span class='op'>=</span> <span class='st'>"eigen"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 0 0 100.0000000
-#&gt; 1 1 74.0818221
-#&gt; 2 2 54.8811636
-#&gt; 3 3 40.6569660
-#&gt; 4 4 30.1194212
-#&gt; 5 5 22.3130160
-#&gt; 6 6 16.5298888
-#&gt; 7 7 12.2456428
-#&gt; 8 8 9.0717953
-#&gt; 9 9 6.7205513
-#&gt; 10 10 4.9787068
-#&gt; 11 11 3.6883167
-#&gt; 12 12 2.7323722
-#&gt; 13 13 2.0241911
-#&gt; 14 14 1.4995577
-#&gt; 15 15 1.1108997
-#&gt; 16 16 0.8229747
-#&gt; 17 17 0.6096747
-#&gt; 18 18 0.4516581
-#&gt; 19 19 0.3345965
-#&gt; 20 20 0.2478752</div><div class='input'>
-<span class='co'># Compare integration methods to analytical solution</span>
-<span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
- solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>21</span>,<span class='op'>]</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
- method <span class='op'>=</span> <span class='st'>"lsoda"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>21</span>,<span class='op'>]</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
- method <span class='op'>=</span> <span class='st'>"ode45"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>21</span>,<span class='op'>]</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>,
- method <span class='op'>=</span> <span class='st'>"rk4"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>21</span>,<span class='op'>]</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 20.0000000 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='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>2001</span>,<span class='op'>]</span>
-</div><div class='output co'>#&gt; time degradinol
-#&gt; 20.0000000 0.2478752 </div><div class='input'>
-<span class='co'># Comparison of the performance of solution types</span>
-<span class='va'>SFO_SFO</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
- m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='kw'>if</span><span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
- <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span>replications <span class='op'>=</span> <span class='fl'>10</span>, order <span class='op'>=</span> <span class='st'>"relative"</span>, columns <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='st'>"test"</span>, <span class='st'>"relative"</span>, <span class='st'>"elapsed"</span><span class='op'>)</span>,
- eigen <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>,
- solution_type <span class='op'>=</span> <span class='st'>"eigen"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span>,
- deSolve_compiled <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>,
- solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span>,
- deSolve <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>,
- solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span>,
- analytical <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>,
- solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span><span class='op'>)</span>
-<span class='op'>}</span>
-</div><div class='output co'>#&gt; test relative elapsed
-#&gt; 2 deSolve_compiled 1.0 0.005
-#&gt; 4 analytical 1.0 0.005
-#&gt; 1 eigen 4.4 0.022
-#&gt; 3 deSolve 46.8 0.234</div><div class='input'>
-<span class='co'># \dontrun{</span>
- <span class='co'># Predict from a fitted model</span>
- <span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
- <span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span>
- <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; time parent m1
-#&gt; 0 0.0 82.49216 0.000000
-#&gt; 0.1 0.1 80.00562 1.236394
-#&gt; 0.2 0.2 77.59404 2.423201
-#&gt; 0.3 0.3 75.25514 3.562040
-#&gt; 0.4 0.4 72.98675 4.654478
-#&gt; 0.5 0.5 70.78673 5.702033</div><div class='input'><span class='co'># }</span>
-
-</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># Compare solution types</span></span></span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
+<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0 0 100.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 74.0818221</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 2 54.8811636</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 3 40.6569660</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 4 30.1194212</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5 5 22.3130160</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6 6 16.5298888</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7 7 12.2456428</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8 8 9.0717953</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9 9 6.7205513</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 10 4.9787068</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 11 11 3.6883167</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 12 12 2.7323722</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 13 13 2.0241911</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 14 14 1.4995577</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 15 15 1.1108997</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 16 16 0.8229747</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 17 17 0.6096747</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 18 18 0.4516581</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 19 19 0.3345965</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20 20 0.2478752</span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
+<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0 0 100.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 74.0818221</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 2 54.8811636</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 3 40.6569660</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 4 30.1194212</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5 5 22.3130160</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6 6 16.5298888</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7 7 12.2456428</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8 8 9.0717953</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9 9 6.7205513</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 10 4.9787068</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 11 11 3.6883167</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 12 12 2.7323722</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 13 13 2.0241911</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 14 14 1.4995577</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 15 15 1.1108996</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 16 16 0.8229747</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 17 17 0.6096747</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 18 18 0.4516581</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 19 19 0.3345965</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20 20 0.2478752</span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
+<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0 0 100.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 74.0818221</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 2 54.8811636</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 3 40.6569660</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 4 30.1194212</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5 5 22.3130160</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6 6 16.5298888</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7 7 12.2456428</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8 8 9.0717953</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9 9 6.7205513</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 10 4.9787068</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 11 11 3.6883167</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 12 12 2.7323722</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 13 13 2.0241911</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 14 14 1.4995577</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 15 15 1.1108996</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 16 16 0.8229747</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 17 17 0.6096747</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 18 18 0.4516581</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 19 19 0.3345965</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20 20 0.2478752</span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
+<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0 0 100.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 74.0818221</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 2 54.8811636</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 3 40.6569660</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 4 30.1194212</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5 5 22.3130160</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6 6 16.5298888</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7 7 12.2456428</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8 8 9.0717953</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9 9 6.7205513</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 10 4.9787068</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 11 11 3.6883167</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 12 12 2.7323722</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 13 13 2.0241911</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 14 14 1.4995577</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 15 15 1.1108997</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 16 16 0.8229747</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 17 17 0.6096747</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 18 18 0.4516581</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 19 19 0.3345965</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20 20 0.2478752</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Compare integration methods to analytical solution</span></span></span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
+<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000 0.2478752 </span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
+<span class="r-in"><span> method <span class="op">=</span> <span class="st">"lsoda"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000 0.2478752 </span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
+<span class="r-in"><span> method <span class="op">=</span> <span class="st">"ode45"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000 0.2478752 </span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span></span>
+<span class="r-in"><span> method <span class="op">=</span> <span class="st">"rk4"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000 0.2480043 </span>
+<span class="r-in"><span><span class="co"># rk4 is not as precise here</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># The number of output times used to make a lot of difference until the</span></span></span>
+<span class="r-in"><span><span class="co"># default for atol was adjusted</span></span></span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000 0.2478752 </span>
+<span class="r-in"><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</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>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">2001</span>,<span class="op">]</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> time degradinol </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 20.0000000 0.2478752 </span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Comparison of the performance of solution types</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">10</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <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 class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> eigen <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span></span>
+<span class="r-in"><span> deSolve_compiled <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span></span>
+<span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span></span>
+<span class="r-in"><span> analytical <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> test relative elapsed</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled 1.00 0.004</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 analytical 5.25 0.021</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 eigen 6.00 0.024</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 deSolve 52.50 0.210</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span>
+<span class="r-in"><span> <span class="va">f</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">f</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">f</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DLSODA- At current T (=R1), MXSTEP (=I1) steps </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> taken on this call before reaching TOUT </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, I1 = 1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> In above message, R1 = 9.99904e-07</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>an excessive amount of work (&gt; maxsteps ) was done, but integration was not successful - increase maxsteps</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Returning early. Results are accurate, as far as they go</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in out[available, var]:</span> (subscript) logical subscript too long</span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+ </div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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- <h2 data-toc-skip>Contents</h2>
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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+ <footer><div class="copyright">
+ <p></p><p>Developed by Johannes Ranke.</p>
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+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
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