Rebuild vignettes and static documentation

author: Johannes Ranke <jranke@uni-bremen.de> 2015-11-09 09:05:15 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2015-11-09 09:05:15 +0100
commit: 3151647526f299686b68420a83ae38cd7f3d08f5 (patch)
tree: c061b5a23ac6cc5644c6851012105b185715ef5e /inst/web/mkinpredict.html
parent: 415ca2bea5d5c3815bd9f8fa1566cec5bb3fc775 (diff)
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+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8">
+<title>mkinpredict. mkin 0.9-41</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<meta name="author" content="
+  Johannes Ranke
+">
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+  </head>
+
+  <body>
+    <div class="navbar">
+  <div class="navbar-inner">
+    <div class="container">
+      <a class="brand" href="#">mkin 0.9-41</a>
+      <div class="nav">
+        <ul class="nav">
+          <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
+        </ul>
+      </div>
+    </div>
+  </div>
+</div>
+
+    <div class="container">
+      <header>
+        
+      </header>
+      
+      <h1>
+  Produce predictions from a kinetic model using specifc parameters
+</h1>
+
+<div class="row">
+  <div class="span8">
+    <h2>Usage</h2>
+    <pre><div>mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type&nbsp;=&nbsp;"deSolve",
+	      use_compiled&nbsp;=&nbsp;"auto", method.ode&nbsp;=&nbsp;"lsoda", atol&nbsp;=&nbsp;1e-08, rtol&nbsp;=&nbsp;1e-10, map_output&nbsp;=&nbsp;TRUE, ...)</div></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 "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><a href='mkinpredict.html'>mkinpredict</a></code> to
+    <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/ode'>ode</a></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><a href='http://www.inside-r.org/packages/cran/deSolve/docs/ode'>ode</a></code>. Default is 1e-8,
+    lower than in <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/lsoda'>lsoda</a></code>.
+  </dd>
+      <dt>rtol</dt>
+      <dd>
+    Absolute error tolerance, passed to <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/ode'>ode</a></code>. Default is 1e-10,
+    much lower than in <code><a href='http://www.inside-r.org/packages/cran/deSolve/docs/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.inside-r.org/packages/cran/deSolve/docs/ode'>ode</a></code>.
+</dl></p>
+  
+    </div>
+    
+    <h2 id="examples">Examples</h2>
+    <pre class="examples"><div class='input'>  SFO &lt;- mkinmod(degradinol = list(type = &quot;SFO&quot;))
+  # Compare solution types
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
+	      solution_type = &quot;analytical&quot;)
+</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'>  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
+	      solution_type = &quot;deSolve&quot;)
+</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'>  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
+	      solution_type = &quot;deSolve&quot;, use_compiled = FALSE)
+</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'>  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
+	      solution_type = &quot;eigen&quot;)
+</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'>
+
+  # Compare integration methods to analytical solution
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
+	      solution_type = &quot;analytical&quot;)[21,]
+</div>
+<div class='output'>   time degradinol
+21   20  0.2478752
+</div>
+<div class='input'>  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
+	      method = &quot;lsoda&quot;)[21,]
+</div>
+<div class='output'>   time degradinol
+21   20  0.2478752
+</div>
+<div class='input'>  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+	      method = &quot;ode45&quot;)[21,]
+</div>
+<div class='output'>   time degradinol
+21   20  0.2478752
+</div>
+<div class='input'>  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+	      method = &quot;rk4&quot;)[21,]
+</div>
+<div class='output'>   time degradinol
+21   20  0.2480043
+</div>
+<div class='input'> # rk4 is not as precise here
+
+  # The number of output times used to make a lot of difference until the
+  # default for atol was adjusted
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 
+	      seq(0, 20, by = 0.1))[201,]
+</div>
+<div class='output'>    time degradinol
+201   20  0.2478752
+</div>
+<div class='input'>  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 
+	      seq(0, 20, by = 0.01))[2001,]
+</div>
+<div class='output'>     time degradinol
+2001   20  0.2478752
+</div>
+<div class='input'>
+  # Check compiled model versions - they are faster than the eigenvalue based solutions!
+  SFO_SFO = mkinmod(parent = list(type = &quot;SFO&quot;, to = &quot;m1&quot;),
+                    m1 = list(type = &quot;SFO&quot;))
+</div>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
+<div class='input'>  system.time(
+    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
+                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
+                solution_type = &quot;eigen&quot;)[201,]))
+</div>
+<div class='output'>    time   parent       m1
+201   20 4.978707 27.46227
+</div>
+<div class='output'>   user  system elapsed 
+  0.000   0.028   0.004 
+</div>
+<div class='input'>  system.time(
+    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
+                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), 
+                solution_type = &quot;deSolve&quot;)[201,]))
+</div>
+<div class='output'>    time   parent       m1
+201   20 4.978707 27.46227
+</div>
+<div class='output'>   user  system elapsed 
+  0.000   0.020   0.003 
+</div>
+<div class='input'>  system.time(
+    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
+                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), 
+                solution_type = &quot;deSolve&quot;, use_compiled = FALSE)[201,]))
+</div>
+<div class='output'>    time   parent       m1
+201   20 4.978707 27.46227
+</div>
+<div class='output'>   user  system elapsed 
+  0.052   0.000   0.054 
+</div></pre>
+  </div>
+  <div class="span4">
+    <!-- <ul>
+      <li>mkinpredict</li>
+    </ul>
+    <ul>
+      <li> manip </li>
+    </ul> -->
+      
+    
+    <h2>Author</h2>
+    
+  Johannes Ranke
+
+    
+  </div>
+</div>
+      
+      <footer>
+      <p class="pull-right"><a href="#">Back to top</a></p>
+<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p>
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+\ No newline at end of file
author	Johannes Ranke <jranke@uni-bremen.de>	2015-11-09 09:05:15 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2015-11-09 09:05:15 +0100
commit	3151647526f299686b68420a83ae38cd7f3d08f5 (patch)
tree	c061b5a23ac6cc5644c6851012105b185715ef5e /inst/web/mkinpredict.html
parent	415ca2bea5d5c3815bd9f8fa1566cec5bb3fc775 (diff)