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<h1>Produce predictions from a kinetic model using specific parameters</h1>
</div>
<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>
<pre><span class='fu'>mkinpredict</span>(<span class='no'>mkinmod</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='no'>outtimes</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>
<dl class="dl-horizontal">
<dt>mkinmod</dt>
<dd>
A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>.
</dd>
<dt>odeparms</dt>
<dd>
A numeric vector specifying the parameters used in the kinetic model, which
is generally defined as a set of ordinary differential equations.
</dd>
<dt>odeini</dt>
<dd>
A numeric vectory 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.
</dd>
<dt>outtimes</dt>
<dd>
A numeric vector specifying the time points for which model predictions
should be generated.
</dd>
<dt>solution_type</dt>
<dd>
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.
</dd>
<dt>method.ode</dt>
<dd>
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.
</dd>
<dt>use_compiled</dt>
<dd>
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.
</dd>
<dt>atol</dt>
<dd>
Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8,
lower than in <code>lsoda</code>.
</dd>
<dt>rtol</dt>
<dd>
Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10,
much lower than in <code>lsoda</code>.
</dd>
<dt>map_output</dt>
<dd>
Boolean to specify if the output should list values for the observed
variables (default) or for all state variables (if set to FALSE).
</dd>
<dt>&#8230;</dt>
<dd>
Further arguments passed to the ode solver in case such a solver is used.
</dd>
</dl>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A matrix in the same format as the output of <code>ode</code>.</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'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</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'>#> time degradinol
#> 1 0 100.0000000
#> 2 1 74.0818221
#> 3 2 54.8811636
#> 4 3 40.6569660
#> 5 4 30.1194212
#> 6 5 22.3130160
#> 7 6 16.5298888
#> 8 7 12.2456428
#> 9 8 9.0717953
#> 10 9 6.7205513
#> 11 10 4.9787068
#> 12 11 3.6883167
#> 13 12 2.7323722
#> 14 13 2.0241911
#> 15 14 1.4995577
#> 16 15 1.1108997
#> 17 16 0.8229747
#> 18 17 0.6096747
#> 19 18 0.4516581
#> 20 19 0.3345965
#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</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'>#> time degradinol
#> 1 0 100.0000000
#> 2 1 74.0818221
#> 3 2 54.8811636
#> 4 3 40.6569660
#> 5 4 30.1194212
#> 6 5 22.3130160
#> 7 6 16.5298888
#> 8 7 12.2456428
#> 9 8 9.0717953
#> 10 9 6.7205513
#> 11 10 4.9787068
#> 12 11 3.6883167
#> 13 12 2.7323722
#> 14 13 2.0241911
#> 15 14 1.4995577
#> 16 15 1.1108996
#> 17 16 0.8229747
#> 18 17 0.6096747
#> 19 18 0.4516581
#> 20 19 0.3345965
#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</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'>#> time degradinol
#> 1 0 100.0000000
#> 2 1 74.0818221
#> 3 2 54.8811636
#> 4 3 40.6569660
#> 5 4 30.1194212
#> 6 5 22.3130160
#> 7 6 16.5298888
#> 8 7 12.2456428
#> 9 8 9.0717953
#> 10 9 6.7205513
#> 11 10 4.9787068
#> 12 11 3.6883167
#> 13 12 2.7323722
#> 14 13 2.0241911
#> 15 14 1.4995577
#> 16 15 1.1108996
#> 17 16 0.8229747
#> 18 17 0.6096747
#> 19 18 0.4516581
#> 20 19 0.3345965
#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</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'>#> time degradinol
#> 1 0 100.0000000
#> 2 1 74.0818221
#> 3 2 54.8811636
#> 4 3 40.6569660
#> 5 4 30.1194212
#> 6 5 22.3130160
#> 7 6 16.5298888
#> 8 7 12.2456428
#> 9 8 9.0717953
#> 10 9 6.7205513
#> 11 10 4.9787068
#> 12 11 3.6883167
#> 13 12 2.7323722
#> 14 13 2.0241911
#> 15 14 1.4995577
#> 16 15 1.1108997
#> 17 16 0.8229747
#> 18 17 0.6096747
#> 19 18 0.4516581
#> 20 19 0.3345965
#> 21 20 0.2478752</div><div class='input'>
<span class='co'># Compare integration methods to analytical solution</span>
<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</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'>#> time degradinol
#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</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'>#> time degradinol
#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</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'>#> time degradinol
#> 21 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</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'>#> time degradinol
#> 21 20 0.2480043</div><div class='input'> <span class='co'># rk4 is not as precise here</span>
<span class='co'># The number of output times used to make a lot of difference until the</span>
<span class='co'># default for atol was adjusted</span>
<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
<span class='fu'>seq</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'>#> time degradinol
#> 201 20 0.2478752</div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
<span class='fu'>seq</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'>#> time degradinol
#> 2001 20 0.2478752</div><div class='input'>
<span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span>
<span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</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'>seq</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>,]))</div><div class='output co'>#> time parent m1
#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed
#> 0.024 0.004 0.004 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</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'>seq</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>,]))</div><div class='output co'>#> time parent m1
#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed
#> 0.016 0.004 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</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'>seq</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>,]))</div><div class='output co'>#> time parent m1
#> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed
#> 0.032 0.000 0.035 </div></pre>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<h2>Author</h2>
Johannes Ranke
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