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+ <h1>Produce predictions from a kinetic model using specific parameters</h1>
+ <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinpredict.R'><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 parameters and initial values for the state variables.</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>mkinpredict</span>(
+ <span class='no'>x</span>,
+ <span class='no'>odeparms</span>,
+ <span class='no'>odeini</span>,
+ <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>,
+ <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+ <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+ <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='no'>...</span>
+)
+
+<span class='co'># S3 method for mkinmod</span>
+<span class='fu'>mkinpredict</span>(
+ <span class='no'>x</span>,
+ <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+ <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>,
+ <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+ <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+ <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='no'>...</span>
+)
+
+<span class='co'># S3 method for mkinfit</span>
+<span class='fu'>mkinpredict</span>(
+ <span class='no'>x</span>,
+ <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>,
+ <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>,
+ <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>,
+ <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>,
+ <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>,
+ <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>,
+ <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='no'>...</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
+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>solution_type</th>
+ <td><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
+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>...</th>
+ <td><p>Further arguments passed to the ode solver in case such a
+solver is used.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A matrix with the numeric solution in wide format</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'>
+<span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
+<span class='co'># Compare solution types</span>
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt; time degradinol
+#&gt; 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='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#&gt; time degradinol
+#&gt; 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='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; time degradinol
+#&gt; 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='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#&gt; time degradinol
+#&gt; 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='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+ <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 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='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#&gt; time degradinol
+#&gt; 20.0000000 0.2478752 </div><div class='input'>
+<span class='co'># Comparison of the performance of solution types</span>
+<span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) {
+ <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(<span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>order</span> <span class='kw'>=</span> <span class='st'>"relative"</span>, <span class='kw'>columns</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"test"</span>, <span class='st'>"relative"</span>, <span class='st'>"elapsed"</span>),
+ <span class='kw'>eigen</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.15</span>, <span class='kw'>f_parent_to_m1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_m1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,],
+ <span class='kw'>deSolve_compiled</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.15</span>, <span class='kw'>f_parent_to_m1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_m1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,],
+ <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.15</span>, <span class='kw'>f_parent_to_m1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_m1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,],
+ <span class='kw'>analytical</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>,
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.15</span>, <span class='kw'>f_parent_to_m1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_m1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
+ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</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 4.0 0.020
+#&gt; 3 deSolve 45.6 0.228</div><div class='input'>
+<span class='co'># \dontrun{</span>
+ <span class='co'># Predict from a fitted model</span>
+ <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)
+ <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</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 1.236198
+#&gt; 0.2 0.2 77.59404 2.422818
+#&gt; 0.3 0.3 75.25514 3.561476
+#&gt; 0.4 0.4 72.98675 4.653740
+#&gt; 0.5 0.5 70.78673 5.701130</div><div class='input'># }
+
+</div></pre>
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