diff options
Diffstat (limited to 'inst/web/mkinpredict.html')
| -rw-r--r-- | inst/web/mkinpredict.html | 355 |
1 files changed, 0 insertions, 355 deletions
diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html deleted file mode 100644 index d8edeb23..00000000 --- a/inst/web/mkinpredict.html +++ /dev/null @@ -1,355 +0,0 @@ -<!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 -"> - -<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 0.9.44.9000</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 = "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 - 0.004 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 = "deSolve")[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 = "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 - 0.032 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 |