<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>mkinpredict. mkin 0.9.43</title> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="author" content=" Johannes Ranke "> <link href="css/bootstrap.css" rel="stylesheet"> <link href="css/bootstrap-responsive.css" rel="stylesheet"> <link href="css/highlight.css" rel="stylesheet"> <link href="css/staticdocs.css" rel="stylesheet"> <!--[if lt IE 9]> <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> <![endif]--> <script type="text/x-mathjax-config"> MathJax.Hub.Config({ tex2jax: { inlineMath: [ ['$','$'], ["\\(","\\)"] ], processEscapes: true } }); </script> <script type="text/javascript" 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 0.9.43</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 = "deSolve", use_compiled = "auto", method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, map_output = 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 <- mkinmod(degradinol = list(type = "SFO")) # Compare solution types mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "analytical") </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 = "deSolve") </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 = "deSolve", 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 = "eigen") </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 = "analytical")[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 = "lsoda")[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 = "ode45")[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 = "rk4")[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 = "SFO", to = "m1"), m1 = list(type = "SFO")) </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 = "eigen")[201,])) </div> <div class='output'> time parent m1 201 20 4.978707 27.46227 </div> <div class='output'> user system elapsed 0.028 0.044 0.011 </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 = "deSolve")[201,])) </div> <div class='output'> time parent m1 201 20 4.978707 27.46227 </div> <div class='output'> user system elapsed 0.024 0.000 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 = "deSolve", use_compiled = FALSE)[201,])) </div> <div class='output'> time parent m1 201 20 4.978707 27.46227 </div> <div class='output'> user system elapsed 0.140 0.000 0.139 </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>. 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