Remove staticdocs from old location

author: Johannes Ranke <jranke@uni-bremen.de> 2016-10-06 08:56:45 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2016-10-06 08:56:45 +0200
commit: ec1487f0f2cef32d44b0c6ce94a6f1b4f65a79d3 (patch)
tree: 10820a2fa5ae6b51115c2d2f40e40bcc8f0b8d5e /inst/web/mkinpredict.html
parent: 6b7c2049d4feb9dd76dd532830adba23b8a5007f (diff)
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-<!DOCTYPE html>
-<html lang="en">
-  <head>
-    <meta charset="utf-8">
-<title>mkinpredict. mkin 0.9.44.9000</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-  Johannes Ranke
-">
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-  MathJax.Hub.Config({
-    tex2jax: {
-      inlineMath: [ ['$','$'], ["\\(","\\)"] ],
-      processEscapes: true
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-</script>
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-  src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
-  </head>
-
-  <body>
-    <div class="navbar">
-  <div class="navbar-inner">
-    <div class="container">
-      <a class="brand" href="#">mkin 0.9.44.9000</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 specific 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 
-  0.004   0.028   0.005 
-</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 
-  0.016   0.004   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 
-  0.032   0.000   0.035 
-</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>
-      </footer>
-    </div>
-  </body>
-</html>
-\ No newline at end of file
author	Johannes Ranke <jranke@uni-bremen.de>	2016-10-06 08:56:45 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2016-10-06 08:56:45 +0200
commit	ec1487f0f2cef32d44b0c6ce94a6f1b4f65a79d3 (patch)
tree	10820a2fa5ae6b51115c2d2f40e40bcc8f0b8d5e /inst/web/mkinpredict.html
parent	6b7c2049d4feb9dd76dd532830adba23b8a5007f (diff)