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</div> - - <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> use_symbols <span class="op">=</span> <span class="cn">FALSE</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">20000L</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></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 fast in comparison to uncompiled -ODE models, but not applicable to 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>use_symbols</dt> -<dd><p>If set to <code>TRUE</code> (default), symbol info present in -the <a href="mkinmod.html">mkinmod</a> object is used if available for accessing compiled code</p></dd> - - -<dt>method.ode</dt> -<dd><p>The solution method passed via mkinpredict to ode] in -case the solution type is "deSolve" and we are not using compiled code. -When using compiled code, only lsoda is supported.</p></dd> - - -<dt>atol</dt> -<dd><p>Absolute error tolerance, passed to the ode solver.</p></dd> - - -<dt>rtol</dt> -<dd><p>Absolute error tolerance, passed to the ode solver.</p></dd> - - -<dt>maxsteps</dt> -<dd><p>Maximum number of steps, passed to the ode solver.</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></dd> - - -<dt>na_stop</dt> -<dd><p>Should it be an error if ode returns NaN values</p></dd> - -</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> - - <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"><-</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">#></span> time degradinol</span> -<span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> -<span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> -<span class="r-out co"><span class="r-pr">#></span> 2 2 54.8811636</span> -<span class="r-out co"><span class="r-pr">#></span> 3 3 40.6569660</span> -<span class="r-out co"><span class="r-pr">#></span> 4 4 30.1194212</span> -<span class="r-out co"><span class="r-pr">#></span> 5 5 22.3130160</span> -<span class="r-out co"><span class="r-pr">#></span> 6 6 16.5298888</span> -<span class="r-out co"><span class="r-pr">#></span> 7 7 12.2456428</span> -<span class="r-out co"><span class="r-pr">#></span> 8 8 9.0717953</span> -<span class="r-out co"><span class="r-pr">#></span> 9 9 6.7205513</span> -<span class="r-out co"><span class="r-pr">#></span> 10 10 4.9787068</span> -<span class="r-out co"><span class="r-pr">#></span> 11 11 3.6883167</span> -<span class="r-out co"><span class="r-pr">#></span> 12 12 2.7323722</span> -<span class="r-out co"><span class="r-pr">#></span> 13 13 2.0241911</span> -<span class="r-out co"><span class="r-pr">#></span> 14 14 1.4995577</span> -<span class="r-out co"><span class="r-pr">#></span> 15 15 1.1108997</span> -<span class="r-out co"><span class="r-pr">#></span> 16 16 0.8229747</span> -<span class="r-out co"><span class="r-pr">#></span> 17 17 0.6096747</span> -<span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> -<span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> -<span class="r-out co"><span class="r-pr">#></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">#></span> time degradinol</span> -<span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> -<span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> -<span class="r-out co"><span class="r-pr">#></span> 2 2 54.8811636</span> -<span class="r-out co"><span class="r-pr">#></span> 3 3 40.6569660</span> -<span class="r-out co"><span class="r-pr">#></span> 4 4 30.1194212</span> -<span class="r-out co"><span class="r-pr">#></span> 5 5 22.3130160</span> -<span class="r-out co"><span class="r-pr">#></span> 6 6 16.5298888</span> -<span class="r-out co"><span class="r-pr">#></span> 7 7 12.2456428</span> -<span class="r-out co"><span class="r-pr">#></span> 8 8 9.0717953</span> -<span class="r-out co"><span class="r-pr">#></span> 9 9 6.7205513</span> -<span class="r-out co"><span class="r-pr">#></span> 10 10 4.9787068</span> -<span class="r-out co"><span class="r-pr">#></span> 11 11 3.6883167</span> -<span class="r-out co"><span class="r-pr">#></span> 12 12 2.7323722</span> -<span class="r-out co"><span class="r-pr">#></span> 13 13 2.0241911</span> -<span class="r-out co"><span class="r-pr">#></span> 14 14 1.4995577</span> -<span class="r-out co"><span class="r-pr">#></span> 15 15 1.1108996</span> -<span class="r-out co"><span class="r-pr">#></span> 16 16 0.8229747</span> -<span class="r-out co"><span class="r-pr">#></span> 17 17 0.6096747</span> -<span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> -<span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> -<span class="r-out co"><span class="r-pr">#></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">#></span> time degradinol</span> -<span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> -<span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> -<span class="r-out co"><span class="r-pr">#></span> 2 2 54.8811636</span> -<span class="r-out co"><span class="r-pr">#></span> 3 3 40.6569660</span> -<span class="r-out co"><span class="r-pr">#></span> 4 4 30.1194212</span> -<span class="r-out co"><span class="r-pr">#></span> 5 5 22.3130160</span> -<span class="r-out co"><span class="r-pr">#></span> 6 6 16.5298888</span> -<span class="r-out co"><span class="r-pr">#></span> 7 7 12.2456428</span> -<span class="r-out co"><span class="r-pr">#></span> 8 8 9.0717953</span> -<span class="r-out co"><span class="r-pr">#></span> 9 9 6.7205513</span> -<span class="r-out co"><span class="r-pr">#></span> 10 10 4.9787068</span> -<span class="r-out co"><span class="r-pr">#></span> 11 11 3.6883167</span> -<span class="r-out co"><span class="r-pr">#></span> 12 12 2.7323722</span> -<span class="r-out co"><span class="r-pr">#></span> 13 13 2.0241911</span> -<span class="r-out co"><span class="r-pr">#></span> 14 14 1.4995577</span> -<span class="r-out co"><span class="r-pr">#></span> 15 15 1.1108996</span> -<span class="r-out co"><span class="r-pr">#></span> 16 16 0.8229747</span> -<span class="r-out co"><span class="r-pr">#></span> 17 17 0.6096747</span> -<span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> -<span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> -<span class="r-out co"><span class="r-pr">#></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">#></span> time degradinol</span> -<span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> -<span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> -<span class="r-out co"><span class="r-pr">#></span> 2 2 54.8811636</span> -<span class="r-out co"><span class="r-pr">#></span> 3 3 40.6569660</span> -<span class="r-out co"><span class="r-pr">#></span> 4 4 30.1194212</span> -<span class="r-out co"><span class="r-pr">#></span> 5 5 22.3130160</span> -<span class="r-out co"><span class="r-pr">#></span> 6 6 16.5298888</span> -<span class="r-out co"><span class="r-pr">#></span> 7 7 12.2456428</span> -<span class="r-out co"><span class="r-pr">#></span> 8 8 9.0717953</span> -<span class="r-out co"><span class="r-pr">#></span> 9 9 6.7205513</span> -<span class="r-out co"><span class="r-pr">#></span> 10 10 4.9787068</span> -<span class="r-out co"><span class="r-pr">#></span> 11 11 3.6883167</span> -<span class="r-out co"><span class="r-pr">#></span> 12 12 2.7323722</span> -<span class="r-out co"><span class="r-pr">#></span> 13 13 2.0241911</span> -<span class="r-out co"><span class="r-pr">#></span> 14 14 1.4995577</span> -<span class="r-out co"><span class="r-pr">#></span> 15 15 1.1108997</span> -<span class="r-out co"><span class="r-pr">#></span> 16 16 0.8229747</span> -<span class="r-out co"><span class="r-pr">#></span> 17 17 0.6096747</span> -<span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> -<span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> -<span class="r-out co"><span class="r-pr">#></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">#></span> time degradinol </span> -<span class="r-out co"><span class="r-pr">#></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>, use_compiled <span class="op">=</span> <span class="cn">FALSE</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">#></span> time degradinol </span> -<span class="r-out co"><span class="r-pr">#></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>, use_compiled <span class="op">=</span> <span class="cn">FALSE</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">#></span> time degradinol </span> -<span class="r-out co"><span class="r-pr">#></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>, use_compiled <span class="op">=</span> <span class="cn">FALSE</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">#></span> time degradinol </span> -<span class="r-out co"><span class="r-pr">#></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">#></span> time degradinol </span> -<span class="r-out co"><span class="r-pr">#></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">#></span> time degradinol </span> -<span class="r-out co"><span class="r-pr">#></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">#></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">#></span> Loading required package: rbenchmark</span> -<span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.00 0.004</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.00 0.016</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 4.25 0.017</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 40.75 0.163</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"><-</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"><-</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-err co"><span class="r-pr">#></span> <span class="error">Error in !is.null(x$symbols) & use_symbols:</span> operations are possible only for numeric, logical or complex types</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"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> - - - <footer><div class="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> -</div> - - </footer></div> - - - - - - - </body></html> - |