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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:21:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:55:25 +0200
commita350a16bb2c11986faf5883a2804d46b03bd7c8f (patch)
tree00ca40222b1f4c9bcffca081982e006763e697d8 /docs/mkinpredict.html
parent3b399df5231576880fd9e0ae7253064d82edfe86 (diff)
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+<title>mkinpredict. mkin 0.9.44.9000</title>
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+ Johannes Ranke
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+
+ <h1>
+ Produce predictions from a kinetic model using specific parameters
+</h1>
+
+<div class="row">
+ <div class="span8">
+ <h2>Usage</h2>
+ <pre><span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">mkinmod</span><span class="keyword">,</span> <span class="symbol">odeparms</span><span class="keyword">,</span> <span class="symbol">odeini</span><span class="keyword">,</span> <span class="symbol">outtimes</span><span class="keyword">,</span> <span class="argument">solution_type</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"deSolve"</span><span class="keyword">,</span>
+ <span class="argument">use_compiled</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"auto"</span><span class="keyword">,</span> <span class="argument">method.ode</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"lsoda"</span><span class="keyword">,</span> <span class="argument">atol</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1e-08</span><span class="keyword">,</span> <span class="argument">rtol</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1e-10</span><span class="keyword">,</span>
+ <span class="argument">map_output</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre>
+
+ <h2>Arguments</h2>
+ <dl>
+ <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 &quot;analytical&quot; if there is only one observed variable, and
+ usually &quot;deSolve&quot; in the case of several observed variables. The third
+ possibility &quot;eigen&quot; 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><a href='mkinpredict.html'>mkinpredict</a></code> to
+ <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/ode'>ode</a></code> in case the solution type is &quot;deSolve&quot;. The default
+ &quot;lsoda&quot; 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><a href='http://www.rdocumentation.org/packages/deSolve/topics/ode'>ode</a></code>. Default is 1e-8,
+ lower than in <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/lsoda'>lsoda</a></code>.
+ </dd>
+ <dt>rtol</dt>
+ <dd>
+ Absolute error tolerance, passed to <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/ode'>ode</a></code>. Default is 1e-10,
+ much lower than in <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/lsoda'>lsoda</a></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>...</dt>
+ <dd>
+ Further arguments passed to the ode solver in case such a solver is used.
+ </dd>
+ </dl>
+
+ <div class="Description">
+ <h2>Description</h2>
+
+ <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>
+
+ <div class="Value">
+ <h2>Value</h2>
+
+ <p><dl>
+ A matrix in the same format as the output of <code><a href='http://www.rdocumentation.org/packages/deSolve/topics/ode'>ode</a></code>.
+</dl></p>
+
+ </div>
+
+ <h2 id="examples">Examples</h2>
+ <pre class="examples"><div class='input'> <span class="symbol">SFO</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span>
+ <span class="comment"># Compare solution types</span>
+ <span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span> <span class="number">0</span><span class="keyword">:</span><span class="number">20</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span> <span class="argument">=</span> <span class="string">"analytical"</span><span class="keyword">)</span></div>
+<div class='output'> 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="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span> <span class="number">0</span><span class="keyword">:</span><span class="number">20</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span> <span class="argument">=</span> <span class="string">"deSolve"</span><span class="keyword">)</span></div>
+<div class='output'> 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="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span> <span class="number">0</span><span class="keyword">:</span><span class="number">20</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span> <span class="argument">=</span> <span class="string">"deSolve"</span><span class="keyword">,</span> <span class="argument">use_compiled</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span></div>
+<div class='output'> 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="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span> <span class="number">0</span><span class="keyword">:</span><span class="number">20</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span> <span class="argument">=</span> <span class="string">"eigen"</span><span class="keyword">)</span></div>
+<div class='output'> 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="comment"># Compare integration methods to analytical solution</span>
+ <span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span> <span class="number">0</span><span class="keyword">:</span><span class="number">20</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span> <span class="argument">=</span> <span class="string">"analytical"</span><span class="keyword">)</span><span class="keyword">[</span><span class="number">21</span><span class="keyword">,</span><span class="keyword">]</span></div>
+<div class='output'> time degradinol
+21 20 0.2478752
+</div>
+<div class='input'> <span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span> <span class="number">0</span><span class="keyword">:</span><span class="number">20</span><span class="keyword">,</span>
+ <span class="argument">method</span> <span class="argument">=</span> <span class="string">"lsoda"</span><span class="keyword">)</span><span class="keyword">[</span><span class="number">21</span><span class="keyword">,</span><span class="keyword">]</span></div>
+<div class='output'> time degradinol
+21 20 0.2478752
+</div>
+<div class='input'> <span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span> <span class="number">0</span><span class="keyword">:</span><span class="number">20</span><span class="keyword">,</span>
+ <span class="argument">method</span> <span class="argument">=</span> <span class="string">"ode45"</span><span class="keyword">)</span><span class="keyword">[</span><span class="number">21</span><span class="keyword">,</span><span class="keyword">]</span></div>
+<div class='output'> time degradinol
+21 20 0.2478752
+</div>
+<div class='input'> <span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span> <span class="number">0</span><span class="keyword">:</span><span class="number">20</span><span class="keyword">,</span>
+ <span class="argument">method</span> <span class="argument">=</span> <span class="string">"rk4"</span><span class="keyword">)</span><span class="keyword">[</span><span class="number">21</span><span class="keyword">,</span><span class="keyword">]</span></div>
+<div class='output'> time degradinol
+21 20 0.2480043
+</div>
+<div class='input'> <span class="comment"># rk4 is not as precise here</span>
+
+ <span class="comment"># The number of output times used to make a lot of difference until the</span>
+ <span class="comment"># default for atol was adjusted</span>
+ <span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">20</span><span class="keyword">,</span> <span class="argument">by</span> <span class="argument">=</span> <span class="number">0.1</span><span class="keyword">)</span><span class="keyword">)</span><span class="keyword">[</span><span class="number">201</span><span class="keyword">,</span><span class="keyword">]</span></div>
+<div class='output'> time degradinol
+201 20 0.2478752
+</div>
+<div class='input'> <span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_degradinol_sink</span> <span class="argument">=</span> <span class="number">0.3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">degradinol</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">20</span><span class="keyword">,</span> <span class="argument">by</span> <span class="argument">=</span> <span class="number">0.01</span><span class="keyword">)</span><span class="keyword">)</span><span class="keyword">[</span><span class="number">2001</span><span class="keyword">,</span><span class="keyword">]</span></div>
+<div class='output'> time degradinol
+2001 20 0.2478752
+</div>
+<div class='input'>
+ <span class="comment"># Check compiled model versions - they are faster than the eigenvalue based solutions!</span>
+ <span class="symbol">SFO_SFO</span> <span class="assignement">=</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">to</span> <span class="argument">=</span> <span class="string">"m1"</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span></div>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
+<div class='input'> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span><span class="keyword">(</span>
+ <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_parent_m1</span> <span class="argument">=</span> <span class="number">0.05</span><span class="keyword">,</span> <span class="argument">k_parent_sink</span> <span class="argument">=</span> <span class="number">0.1</span><span class="keyword">,</span> <span class="argument">k_m1_sink</span> <span class="argument">=</span> <span class="number">0.01</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">,</span> <span class="argument">m1</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">20</span><span class="keyword">,</span> <span class="argument">by</span> <span class="argument">=</span> <span class="number">0.1</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span> <span class="argument">=</span> <span class="string">"eigen"</span><span class="keyword">)</span><span class="keyword">[</span><span class="number">201</span><span class="keyword">,</span><span class="keyword">]</span><span class="keyword">)</span><span class="keyword">)</span></div>
+<div class='output'> time parent m1
+201 20 4.978707 27.46227
+</div>
+<div class='output'> user system elapsed
+ 0.008 0.020 0.005
+</div>
+<div class='input'> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span><span class="keyword">(</span>
+ <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_parent_m1</span> <span class="argument">=</span> <span class="number">0.05</span><span class="keyword">,</span> <span class="argument">k_parent_sink</span> <span class="argument">=</span> <span class="number">0.1</span><span class="keyword">,</span> <span class="argument">k_m1_sink</span> <span class="argument">=</span> <span class="number">0.01</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">,</span> <span class="argument">m1</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">20</span><span class="keyword">,</span> <span class="argument">by</span> <span class="argument">=</span> <span class="number">0.1</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span> <span class="argument">=</span> <span class="string">"deSolve"</span><span class="keyword">)</span><span class="keyword">[</span><span class="number">201</span><span class="keyword">,</span><span class="keyword">]</span><span class="keyword">)</span><span class="keyword">)</span></div>
+<div class='output'> time parent m1
+201 20 4.978707 27.46227
+</div>
+<div class='output'> user system elapsed
+ 0.012 0.004 0.002
+</div>
+<div class='input'> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span><span class="keyword">(</span>
+ <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="functioncall"><a href='mkinpredict.html'>mkinpredict</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_parent_m1</span> <span class="argument">=</span> <span class="number">0.05</span><span class="keyword">,</span> <span class="argument">k_parent_sink</span> <span class="argument">=</span> <span class="number">0.1</span><span class="keyword">,</span> <span class="argument">k_m1_sink</span> <span class="argument">=</span> <span class="number">0.01</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">,</span> <span class="argument">m1</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">20</span><span class="keyword">,</span> <span class="argument">by</span> <span class="argument">=</span> <span class="number">0.1</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="argument">solution_type</span> <span class="argument">=</span> <span class="string">"deSolve"</span><span class="keyword">,</span> <span class="argument">use_compiled</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span><span class="keyword">[</span><span class="number">201</span><span class="keyword">,</span><span class="keyword">]</span><span class="keyword">)</span><span class="keyword">)</span></div>
+<div class='output'> time parent m1
+201 20 4.978707 27.46227
+</div>
+<div class='output'> user system elapsed
+ 0.036 0.000 0.036
+</div></pre>
+ </div>
+ <div class="span4 sidebar">
+ <!-- <ul>
+ <li>mkinpredict</li>
+ </ul>
+ <ul>
+ <li> manip </li>
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+
+
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+
+ </div>
+</div>
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+ <p class="pull-right"><a href="#">Back to top</a></p>
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