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diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html new file mode 100644 index 00000000..e11dacdf --- /dev/null +++ b/docs/dev/reference/mkinpredict.html @@ -0,0 +1,390 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link 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time series for all the observed variables in a +kinetic model as specified by mkinmod, using a specific set of +kinetic parameters and initial values for the state variables."><meta name="robots" content="noindex"></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">mkin</a> + + <small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active 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of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a class="dropdown-item" 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parameters</h1> + <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="d-none name"><code>mkinpredict.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <p>This function produces a time series for all the observed variables in a +kinetic model as specified by <a href="mkinmod.html">mkinmod</a>, using a specific set of +kinetic parameters and initial values for the state variables.</p> + </div> + + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><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> +<span></span> +<span><span class="co"># S3 method for class 'mkinmod'</span></span> +<span><span class="fu">mkinpredict</span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<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>,</span> +<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>,</span> +<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>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> use_symbols <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,</span> +<span> atol <span class="op">=</span> <span class="fl">1e-08</span>,</span> +<span> rtol <span class="op">=</span> <span class="fl">1e-10</span>,</span> +<span> maxsteps <span class="op">=</span> <span class="fl">20000L</span>,</span> +<span> map_output <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> na_stop <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for class 'mkinfit'</span></span> +<span><span class="fu">mkinpredict</span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> odeparms <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> odeini <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">bparms.state</span>,</span> +<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>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> method.ode <span class="op">=</span> <span class="st">"lsoda"</span>,</span> +<span> atol <span class="op">=</span> <span class="fl">1e-08</span>,</span> +<span> rtol <span class="op">=</span> <span class="fl">1e-10</span>,</span> +<span> map_output <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> +<dd><p>A kinetic model as produced by <a href="mkinmod.html">mkinmod</a>, or a kinetic fit as +fitted by <a href="mkinfit.html">mkinfit</a>. In the latter case, the fitted parameters are used for +the prediction.</p></dd> + + +<dt id="arg-odeparms">odeparms<a class="anchor" aria-label="anchor" href="#arg-odeparms"></a></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></dd> + + +<dt id="arg-odeini">odeini<a class="anchor" aria-label="anchor" href="#arg-odeini"></a></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></dd> + + +<dt id="arg-outtimes">outtimes<a class="anchor" aria-label="anchor" href="#arg-outtimes"></a></dt> +<dd><p>A numeric vector specifying the time points for which model +predictions should be generated.</p></dd> + + +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> +<dd><p>Further arguments passed to the ode solver in case such a +solver is used.</p></dd> + + +<dt id="arg-solution-type">solution_type<a class="anchor" aria-label="anchor" href="#arg-solution-type"></a></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 fast in comparison to uncompiled +ODE models, but not applicable to some models, e.g. using FOMC for the +parent compound.</p></dd> + + +<dt id="arg-use-compiled">use_compiled<a class="anchor" aria-label="anchor" href="#arg-use-compiled"></a></dt> +<dd><p>If set to <code>FALSE</code>, no compiled version of the +<a href="mkinmod.html">mkinmod</a> model is used, even if is present.</p></dd> + + +<dt id="arg-use-symbols">use_symbols<a class="anchor" aria-label="anchor" href="#arg-use-symbols"></a></dt> +<dd><p>If set to <code>TRUE</code> (default), symbol info present in +the <a href="mkinmod.html">mkinmod</a> object is used if available for accessing compiled code</p></dd> + + +<dt id="arg-method-ode">method.ode<a class="anchor" aria-label="anchor" href="#arg-method-ode"></a></dt> +<dd><p>The solution method passed via mkinpredict to <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode()</a></code> in +case the solution type is "deSolve" and we are not using compiled code. +When using compiled code, only lsoda is supported.</p></dd> + + +<dt id="arg-atol">atol<a class="anchor" aria-label="anchor" href="#arg-atol"></a></dt> +<dd><p>Absolute error tolerance, passed to the ode solver.</p></dd> + + +<dt id="arg-rtol">rtol<a class="anchor" aria-label="anchor" href="#arg-rtol"></a></dt> +<dd><p>Absolute error tolerance, passed to the ode solver.</p></dd> + + +<dt id="arg-maxsteps">maxsteps<a class="anchor" aria-label="anchor" href="#arg-maxsteps"></a></dt> +<dd><p>Maximum number of steps, passed to the ode solver.</p></dd> + + +<dt id="arg-map-output">map_output<a class="anchor" aria-label="anchor" href="#arg-map-output"></a></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></dd> + + +<dt id="arg-na-stop">na_stop<a class="anchor" aria-label="anchor" href="#arg-na-stop"></a></dt> +<dd><p>Should it be an error if <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode()</a></code> returns NaN values</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + <p>A matrix with the numeric solution in wide format</p> + </div> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> + <p>Johannes Ranke</p> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><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> +<span class="r-in"><span><span class="co"># Compare solution types</span></span></span> +<span class="r-in"><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" 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> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span></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="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> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></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><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> +<span class="r-in"><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></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><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> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"eigen"</span><span class="op">)</span></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></span> +<span class="r-in"><span><span class="co"># Compare integration methods to analytical solution</span></span></span> +<span class="r-in"><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" 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> +<span class="r-in"><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></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="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> +<span class="r-in"><span> method <span class="op">=</span> <span class="st">"lsoda"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></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="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> +<span class="r-in"><span> method <span class="op">=</span> <span class="st">"ode45"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></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="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> +<span class="r-in"><span> method <span class="op">=</span> <span class="st">"rk4"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">21</span>,<span class="op">]</span></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><span class="co"># rk4 is not as precise here</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The number of output times used to make a lot of difference until the</span></span></span> +<span class="r-in"><span><span class="co"># default for atol was adjusted</span></span></span> +<span class="r-in"><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" 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> +<span class="r-in"><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 class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span></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="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> +<span class="r-in"><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">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">2001</span>,<span class="op">]</span></span></span> +<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></span> +<span class="r-in"><span><span class="co"># Comparison of the performance of solution types</span></span></span> +<span class="r-in"><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" 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> +<span class="r-in"><span> 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> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><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> +<span class="r-in"><span> <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> +<span class="r-in"><span> eigen <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span> +<span class="r-in"><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 <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> +<span class="r-in"><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>, 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> +<span class="r-in"><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>,</span></span> +<span class="r-in"><span> deSolve_compiled <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span> +<span class="r-in"><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 <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> +<span class="r-in"><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>, 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> +<span class="r-in"><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>,</span></span> +<span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span> +<span class="r-in"><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 <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> +<span class="r-in"><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>, 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> +<span class="r-in"><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>,</span></span> +<span class="r-in"><span> analytical <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span></span> +<span class="r-in"><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 <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> +<span class="r-in"><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>, 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> +<span class="r-in"><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></span> +<span class="r-in"><span><span class="op">}</span></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> 2 deSolve_compiled 1.0 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.0 0.008</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 30.5 0.061</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> +<span class="r-in"><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></span> +<span class="r-in"><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></span> +<span class="r-in"><span> <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> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in !is.null(x$symbols) & use_symbols:</span> operations are possible only for numeric, logical or complex types</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> +</div> + + </footer></div> + + + + + + </body></html> + |