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| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
| commit | 2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch) | |
| tree | f286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/mkinpredict.html | |
| parent | 351248d07f810ccb6c497633a02cd48ee35526e6 (diff) | |
Make tests more platform independent, update docs
Diffstat (limited to 'docs/reference/mkinpredict.html')
| -rw-r--r-- | docs/reference/mkinpredict.html | 636 |
1 files changed, 282 insertions, 354 deletions
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5775ba62..b52d9ece 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - 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- - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +kinetic parameters and initial values for the state variables."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,13 +19,12 @@ kinetic parameters and initial values for the state variables." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> @@ -89,8 +33,7 @@ kinetic parameters and initial values for the state variables." /> <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,6 +43,9 @@ kinetic parameters and initial values for the state variables." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -114,343 +60,325 @@ kinetic parameters and initial values for the state variables." /> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Produce predictions from a kinetic model using specific parameters</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinpredict.R'><code>R/mkinpredict.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinpredict.R" class="external-link"><code>R/mkinpredict.R</code></a></small> <div class="hidden name"><code>mkinpredict.Rd</code></div> </div> <div class="ref-description"> <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 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> - <pre class="usage"><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>odeparms</span>, <span class='va'>odeini</span>, <span class='va'>outtimes</span>, <span class='va'>...</span><span class='op'>)</span> - -<span class='co'># S3 method for mkinmod</span> -<span class='fu'>mkinpredict</span><span class='op'>(</span> - <span class='va'>x</span>, - odeparms <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent_sink <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, - odeini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, - outtimes <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>120</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, - solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, - use_compiled <span class='op'>=</span> <span class='st'>"auto"</span>, - method.ode <span class='op'>=</span> <span class='st'>"lsoda"</span>, - atol <span class='op'>=</span> <span class='fl'>1e-08</span>, - rtol <span class='op'>=</span> <span class='fl'>1e-10</span>, - map_output <span class='op'>=</span> <span class='cn'>TRUE</span>, - na_stop <span class='op'>=</span> <span class='cn'>TRUE</span>, - <span class='va'>...</span> -<span class='op'>)</span> - -<span class='co'># S3 method for mkinfit</span> -<span class='fu'>mkinpredict</span><span class='op'>(</span> - <span class='va'>x</span>, - odeparms <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>bparms.ode</span>, - odeini <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>bparms.state</span>, - outtimes <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>120</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, - solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, - use_compiled <span class='op'>=</span> <span class='st'>"auto"</span>, - method.ode <span class='op'>=</span> <span class='st'>"lsoda"</span>, - atol <span class='op'>=</span> <span class='fl'>1e-08</span>, - rtol <span class='op'>=</span> <span class='fl'>1e-10</span>, - map_output <span class='op'>=</span> <span class='cn'>TRUE</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">x</span>, <span class="va">odeparms</span>, <span class="va">odeini</span>, <span class="va">outtimes</span>, <span class="va">...</span><span class="op">)</span> + +<span class="co"># S3 method for mkinmod</span> +<span class="fu">mkinpredict</span><span class="op">(</span> + <span class="va">x</span>, + odeparms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent_sink <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>, + odeini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, + outtimes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">120</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>, + solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, + use_compiled <span class="op">=</span> <span class="st">"auto"</span>, + method.ode <span class="op">=</span> <span class="st">"lsoda"</span>, + atol <span class="op">=</span> <span class="fl">1e-08</span>, + rtol <span class="op">=</span> <span class="fl">1e-10</span>, + map_output <span class="op">=</span> <span class="cn">TRUE</span>, + na_stop <span class="op">=</span> <span class="cn">TRUE</span>, + <span class="va">...</span> +<span class="op">)</span> + +<span class="co"># S3 method for mkinfit</span> +<span class="fu">mkinpredict</span><span class="op">(</span> + <span class="va">x</span>, + odeparms <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.ode</span>, + odeini <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.state</span>, + outtimes <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">120</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>, + solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, + use_compiled <span class="op">=</span> <span class="st">"auto"</span>, + method.ode <span class="op">=</span> <span class="st">"lsoda"</span>, + atol <span class="op">=</span> <span class="fl">1e-08</span>, + rtol <span class="op">=</span> <span class="fl">1e-10</span>, + map_output <span class="op">=</span> <span class="cn">TRUE</span>, + <span class="va">...</span> +<span class="op">)</span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>, or a kinetic -fit as fitted by <code><a href='mkinfit.html'>mkinfit</a></code>. In the latter case, the fitted -parameters are used for the prediction.</p></td> - </tr> - <tr> - <th>odeparms</th> - <td><p>A numeric vector specifying the parameters used in the + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>A kinetic model as produced by <code><a href="mkinmod.html">mkinmod</a></code>, or a kinetic +fit as fitted by <code><a href="mkinfit.html">mkinfit</a></code>. In the latter case, the fitted +parameters are used for the prediction.</p></dd> +<dt>odeparms</dt> +<dd><p>A numeric vector specifying the parameters used in the kinetic model, which is generally defined as a set of ordinary -differential equations.</p></td> - </tr> - <tr> - <th>odeini</th> - <td><p>A numeric vector containing the initial values of the state +differential equations.</p></dd> +<dt>odeini</dt> +<dd><p>A numeric vector 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.</p></td> - </tr> - <tr> - <th>outtimes</th> - <td><p>A numeric vector specifying the time points for which model -predictions should be generated.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to the ode solver in case such a -solver is used.</p></td> - </tr> - <tr> - <th>solution_type</th> - <td><p>The method that should be used for producing the +observed variables, for example in the case of the SFORB model.</p></dd> +<dt>outtimes</dt> +<dd><p>A numeric vector specifying the time points for which model +predictions should be generated.</p></dd> +<dt>...</dt> +<dd><p>Further arguments passed to the ode solver in case such a +solver is used.</p></dd> +<dt>solution_type</dt> +<dd><p>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.</p></td> - </tr> - <tr> - <th>use_compiled</th> - <td><p>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.</p></td> - </tr> - <tr> - <th>method.ode</th> - <td><p>The solution method passed via <code>mkinpredict</code> +some models e.g. using FOMC for the parent compound.</p></dd> +<dt>use_compiled</dt> +<dd><p>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.</p></dd> +<dt>method.ode</dt> +<dd><p>The solution method passed via <code>mkinpredict</code> to <code>ode</code> in case the solution type is "deSolve". The default -"lsoda" is performant, but sometimes fails to converge.</p></td> - </tr> - <tr> - <th>atol</th> - <td><p>Absolute error tolerance, passed to <code>ode</code>. Default -is 1e-8, lower than in <code>lsoda</code>.</p></td> - </tr> - <tr> - <th>rtol</th> - <td><p>Absolute error tolerance, passed to <code>ode</code>. Default -is 1e-10, much lower than in <code>lsoda</code>.</p></td> - </tr> - <tr> - <th>map_output</th> - <td><p>Boolean to specify if the output should list values for +"lsoda" is performant, but sometimes fails to converge.</p></dd> +<dt>atol</dt> +<dd><p>Absolute error tolerance, passed to <code>ode</code>. Default +is 1e-8, lower than in <code>lsoda</code>.</p></dd> +<dt>rtol</dt> +<dd><p>Absolute error tolerance, passed to <code>ode</code>. Default +is 1e-10, much lower than in <code>lsoda</code>.</p></dd> +<dt>map_output</dt> +<dd><p>Boolean to specify if the output should list values for the observed variables (default) or for all state variables (if set to FALSE). Setting this to FALSE has no effect for analytical solutions, -as these always return mapped output.</p></td> - </tr> - <tr> - <th>na_stop</th> - <td><p>Should it be an error if deSolve::ode returns NaN values</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - +as these always return mapped output.</p></dd> +<dt>na_stop</dt> +<dd><p>Should it be an error if deSolve::ode returns NaN values</p></dd> +</dl></div> + <div id="value"> + <h2>Value</h2> <p>A matrix with the numeric solution in wide format</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -<span class='co'># Compare solution types</span> -<span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>, - solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span> -</div><div class='output co'>#> time degradinol -#> 0 0 100.0000000 -#> 1 1 74.0818221 -#> 2 2 54.8811636 -#> 3 3 40.6569660 -#> 4 4 30.1194212 -#> 5 5 22.3130160 -#> 6 6 16.5298888 -#> 7 7 12.2456428 -#> 8 8 9.0717953 -#> 9 9 6.7205513 -#> 10 10 4.9787068 -#> 11 11 3.6883167 -#> 12 12 2.7323722 -#> 13 13 2.0241911 -#> 14 14 1.4995577 -#> 15 15 1.1108997 -#> 16 16 0.8229747 -#> 17 17 0.6096747 -#> 18 18 0.4516581 -#> 19 19 0.3345965 -#> 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>, - solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span> -</div><div class='output co'>#> time degradinol -#> 0 0 100.0000000 -#> 1 1 74.0818221 -#> 2 2 54.8811636 -#> 3 3 40.6569660 -#> 4 4 30.1194212 -#> 5 5 22.3130160 -#> 6 6 16.5298888 -#> 7 7 12.2456428 -#> 8 8 9.0717953 -#> 9 9 6.7205513 -#> 10 10 4.9787068 -#> 11 11 3.6883167 -#> 12 12 2.7323722 -#> 13 13 2.0241911 -#> 14 14 1.4995577 -#> 15 15 1.1108996 -#> 16 16 0.8229747 -#> 17 17 0.6096747 -#> 18 18 0.4516581 -#> 19 19 0.3345965 -#> 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>, - solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -</div><div class='output co'>#> time degradinol -#> 0 0 100.0000000 -#> 1 1 74.0818221 -#> 2 2 54.8811636 -#> 3 3 40.6569660 -#> 4 4 30.1194212 -#> 5 5 22.3130160 -#> 6 6 16.5298888 -#> 7 7 12.2456428 -#> 8 8 9.0717953 -#> 9 9 6.7205513 -#> 10 10 4.9787068 -#> 11 11 3.6883167 -#> 12 12 2.7323722 -#> 13 13 2.0241911 -#> 14 14 1.4995577 -#> 15 15 1.1108996 -#> 16 16 0.8229747 -#> 17 17 0.6096747 -#> 18 18 0.4516581 -#> 19 19 0.3345965 -#> 20 20 0.2478752</div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>, - solution_type <span class='op'>=</span> <span class='st'>"eigen"</span><span class='op'>)</span> -</div><div class='output co'>#> time degradinol -#> 0 0 100.0000000 -#> 1 1 74.0818221 -#> 2 2 54.8811636 -#> 3 3 40.6569660 -#> 4 4 30.1194212 -#> 5 5 22.3130160 -#> 6 6 16.5298888 -#> 7 7 12.2456428 -#> 8 8 9.0717953 -#> 9 9 6.7205513 -#> 10 10 4.9787068 -#> 11 11 3.6883167 -#> 12 12 2.7323722 -#> 13 13 2.0241911 -#> 14 14 1.4995577 -#> 15 15 1.1108997 -#> 16 16 0.8229747 -#> 17 17 0.6096747 -#> 18 18 0.4516581 -#> 19 19 0.3345965 -#> 20 20 0.2478752</div><div class='input'> -<span class='co'># Compare integration methods to analytical solution</span> -<span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>, - solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>21</span>,<span class='op'>]</span> -</div><div class='output co'>#> time degradinol -#> 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>, - method <span class='op'>=</span> <span class='st'>"lsoda"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>21</span>,<span class='op'>]</span> -</div><div class='output co'>#> time degradinol -#> 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>, - method <span class='op'>=</span> <span class='st'>"ode45"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>21</span>,<span class='op'>]</span> -</div><div class='output co'>#> time degradinol -#> 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, <span class='fl'>0</span><span class='op'>:</span><span class='fl'>20</span>, - method <span class='op'>=</span> <span class='st'>"rk4"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>21</span>,<span class='op'>]</span> -</div><div class='output co'>#> time degradinol -#> 20.0000000 0.2480043 </div><div class='input'><span class='co'># rk4 is not as precise here</span> - -<span class='co'># The number of output times used to make a lot of difference until the</span> -<span class='co'># default for atol was adjusted</span> -<span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span> -</div><div class='output co'>#> time degradinol -#> 20.0000000 0.2478752 </div><div class='input'><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_degradinol <span class='op'>=</span> <span class='fl'>0.3</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>degradinol <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>2001</span>,<span class='op'>]</span> -</div><div class='output co'>#> time degradinol -#> 20.0000000 0.2478752 </div><div class='input'> -<span class='co'># Comparison of the performance of solution types</span> -<span class='va'>SFO_SFO</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='kw'>if</span><span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='va'><a href='http://rbenchmark.googlecode.com'>rbenchmark</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span><span class='op'>(</span>replications <span class='op'>=</span> <span class='fl'>10</span>, order <span class='op'>=</span> <span class='st'>"relative"</span>, columns <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"test"</span>, <span class='st'>"relative"</span>, <span class='st'>"elapsed"</span><span class='op'>)</span>, - eigen <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, - solution_type <span class='op'>=</span> <span class='st'>"eigen"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span>, - deSolve_compiled <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, - solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span>, - deSolve <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, - solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span>, - analytical <span class='op'>=</span> <span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.15</span>, f_parent_to_m1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_m1 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>20</span>, by <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span>, - solution_type <span class='op'>=</span> <span class='st'>"analytical"</span>, use_compiled <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>201</span>,<span class='op'>]</span><span class='op'>)</span> -<span class='op'>}</span> -</div><div class='output co'>#> test relative elapsed -#> 2 deSolve_compiled 1.0 0.005 -#> 4 analytical 1.0 0.005 -#> 1 eigen 4.0 0.020 -#> 3 deSolve 46.2 0.231</div><div class='input'> -<span class='co'># \dontrun{</span> - <span class='co'># Predict from a fitted model</span> - <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span><span class='fu'>mkinpredict</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> time parent m1 -#> 0 0.0 82.49216 0.000000 -#> 0.1 0.1 80.00562 1.236394 -#> 0.2 0.2 77.59404 2.423201 -#> 0.3 0.3 75.25514 3.562040 -#> 0.4 0.4 72.98675 4.654478 -#> 0.5 0.5 70.78673 5.702033</div><div class='input'><span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> +<span class="r-in"><span class="va">SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span class="co"># Compare solution types</span></span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> +<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> +<span class="r-out co"><span class="r-pr">#></span> 2 2 54.8811636</span> +<span class="r-out co"><span class="r-pr">#></span> 3 3 40.6569660</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4 30.1194212</span> +<span class="r-out co"><span class="r-pr">#></span> 5 5 22.3130160</span> +<span class="r-out co"><span class="r-pr">#></span> 6 6 16.5298888</span> +<span class="r-out co"><span class="r-pr">#></span> 7 7 12.2456428</span> +<span class="r-out co"><span class="r-pr">#></span> 8 8 9.0717953</span> +<span class="r-out co"><span class="r-pr">#></span> 9 9 6.7205513</span> +<span class="r-out co"><span class="r-pr">#></span> 10 10 4.9787068</span> +<span class="r-out co"><span class="r-pr">#></span> 11 11 3.6883167</span> +<span class="r-out co"><span class="r-pr">#></span> 12 12 2.7323722</span> +<span class="r-out co"><span class="r-pr">#></span> 13 13 2.0241911</span> +<span class="r-out co"><span class="r-pr">#></span> 14 14 1.4995577</span> +<span class="r-out co"><span class="r-pr">#></span> 15 15 1.1108997</span> +<span class="r-out co"><span class="r-pr">#></span> 16 16 0.8229747</span> +<span class="r-out co"><span class="r-pr">#></span> 17 17 0.6096747</span> +<span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> +<span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> +<span class="r-out co"><span class="r-pr">#></span> 20 20 0.2478752</span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> +<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> +<span class="r-out co"><span class="r-pr">#></span> 2 2 54.8811636</span> +<span class="r-out co"><span class="r-pr">#></span> 3 3 40.6569660</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4 30.1194212</span> +<span class="r-out co"><span class="r-pr">#></span> 5 5 22.3130160</span> +<span class="r-out co"><span class="r-pr">#></span> 6 6 16.5298888</span> +<span class="r-out co"><span class="r-pr">#></span> 7 7 12.2456428</span> +<span class="r-out co"><span class="r-pr">#></span> 8 8 9.0717953</span> +<span class="r-out co"><span class="r-pr">#></span> 9 9 6.7205513</span> +<span class="r-out co"><span class="r-pr">#></span> 10 10 4.9787068</span> +<span class="r-out co"><span class="r-pr">#></span> 11 11 3.6883167</span> +<span class="r-out co"><span class="r-pr">#></span> 12 12 2.7323722</span> +<span class="r-out co"><span class="r-pr">#></span> 13 13 2.0241911</span> +<span class="r-out co"><span class="r-pr">#></span> 14 14 1.4995577</span> +<span class="r-out co"><span class="r-pr">#></span> 15 15 1.1108996</span> +<span class="r-out co"><span class="r-pr">#></span> 16 16 0.8229747</span> +<span class="r-out co"><span class="r-pr">#></span> 17 17 0.6096747</span> +<span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> +<span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> +<span class="r-out co"><span class="r-pr">#></span> 20 20 0.2478752</span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> +<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> +<span class="r-out co"><span class="r-pr">#></span> 2 2 54.8811636</span> +<span class="r-out co"><span class="r-pr">#></span> 3 3 40.6569660</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4 30.1194212</span> +<span class="r-out co"><span class="r-pr">#></span> 5 5 22.3130160</span> +<span class="r-out co"><span class="r-pr">#></span> 6 6 16.5298888</span> +<span class="r-out co"><span class="r-pr">#></span> 7 7 12.2456428</span> +<span class="r-out co"><span class="r-pr">#></span> 8 8 9.0717953</span> +<span class="r-out co"><span class="r-pr">#></span> 9 9 6.7205513</span> +<span class="r-out co"><span class="r-pr">#></span> 10 10 4.9787068</span> +<span class="r-out co"><span class="r-pr">#></span> 11 11 3.6883167</span> +<span class="r-out co"><span class="r-pr">#></span> 12 12 2.7323722</span> +<span class="r-out co"><span class="r-pr">#></span> 13 13 2.0241911</span> +<span class="r-out co"><span class="r-pr">#></span> 14 14 1.4995577</span> +<span class="r-out co"><span class="r-pr">#></span> 15 15 1.1108996</span> +<span class="r-out co"><span class="r-pr">#></span> 16 16 0.8229747</span> +<span class="r-out co"><span class="r-pr">#></span> 17 17 0.6096747</span> +<span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> +<span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> +<span class="r-out co"><span class="r-pr">#></span> 20 20 0.2478752</span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> +<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0 100.0000000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 74.0818221</span> +<span class="r-out co"><span class="r-pr">#></span> 2 2 54.8811636</span> +<span class="r-out co"><span class="r-pr">#></span> 3 3 40.6569660</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4 30.1194212</span> +<span class="r-out co"><span class="r-pr">#></span> 5 5 22.3130160</span> +<span class="r-out co"><span class="r-pr">#></span> 6 6 16.5298888</span> +<span class="r-out co"><span class="r-pr">#></span> 7 7 12.2456428</span> +<span class="r-out co"><span class="r-pr">#></span> 8 8 9.0717953</span> +<span class="r-out co"><span class="r-pr">#></span> 9 9 6.7205513</span> +<span class="r-out co"><span class="r-pr">#></span> 10 10 4.9787068</span> +<span class="r-out co"><span class="r-pr">#></span> 11 11 3.6883167</span> +<span class="r-out co"><span class="r-pr">#></span> 12 12 2.7323722</span> +<span class="r-out co"><span class="r-pr">#></span> 13 13 2.0241911</span> +<span class="r-out co"><span class="r-pr">#></span> 14 14 1.4995577</span> +<span class="r-out co"><span class="r-pr">#></span> 15 15 1.1108997</span> +<span class="r-out co"><span class="r-pr">#></span> 16 16 0.8229747</span> +<span class="r-out co"><span class="r-pr">#></span> 17 17 0.6096747</span> +<span class="r-out co"><span class="r-pr">#></span> 18 18 0.4516581</span> +<span class="r-out co"><span class="r-pr">#></span> 19 19 0.3345965</span> +<span class="r-out co"><span class="r-pr">#></span> 20 20 0.2478752</span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># Compare integration methods to analytical solution</span></span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> +<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol </span> +<span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> +<span class="r-in"> method <span class="op">=</span> <span class="st">"lsoda"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol </span> +<span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> +<span class="r-in"> method <span class="op">=</span> <span class="st">"ode45"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol </span> +<span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="fl">0</span><span class="op">:</span><span class="fl">20</span>,</span> +<span class="r-in"> method <span class="op">=</span> <span class="st">"rk4"</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol </span> +<span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2480043 </span> +<span class="r-in"><span class="co"># rk4 is not as precise here</span></span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># The number of output times used to make a lot of difference until the</span></span> +<span class="r-in"><span class="co"># default for atol was adjusted</span></span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol </span> +<span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> +<span class="r-in"><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_degradinol <span class="op">=</span> <span class="fl">0.3</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">2001</span>,<span class="op">]</span></span> +<span class="r-out co"><span class="r-pr">#></span> time degradinol </span> +<span class="r-out co"><span class="r-pr">#></span> 20.0000000 0.2478752 </span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># Comparison of the performance of solution types</span></span> +<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span> +<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">10</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> +<span class="r-in"> eigen <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> +<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span> +<span class="r-in"> deSolve_compiled <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> +<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span> +<span class="r-in"> deSolve <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> +<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span>,</span> +<span class="r-in"> analytical <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> +<span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span class="op">}</span></span> +<span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.005</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.2 0.006</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.2 0.021</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 40.8 0.204</span> +<span class="r-in"></span> +<span class="r-in"><span class="co"># \dontrun{</span></span> +<span class="r-in"> <span class="co"># Predict from a fitted model</span></span> +<span class="r-in"> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-in"> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">f</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> time parent m1</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.0 82.49216 0.000000</span> +<span class="r-out co"><span class="r-pr">#></span> 0.1 0.1 80.00562 1.236394</span> +<span class="r-out co"><span class="r-pr">#></span> 0.2 0.2 77.59404 2.423201</span> +<span class="r-out co"><span class="r-pr">#></span> 0.3 0.3 75.25514 3.562040</span> +<span class="r-out co"><span class="r-pr">#></span> 0.4 0.4 72.98675 4.654478</span> +<span class="r-out co"><span class="r-pr">#></span> 0.5 0.5 70.78673 5.702033</span> +<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |