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diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html new file mode 100644 index 00000000..9f229fd5 --- /dev/null +++ b/inst/web/mkinpredict.html @@ -0,0 +1,355 @@ +<!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 +"> + +<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 0.9-41</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 = "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 + 0.000 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 = "deSolve")[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 = "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 + 0.052 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> + </footer> + </div> + </body> +</html>
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