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</ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </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/HEAD/R/mkinpredict.R" class="external-link"><code>R/mkinpredict.R</code></a></small> - <div class="hidden name"><code>mkinpredict.Rd</code></div> +<li class="nav-item"><a class="nav-link" href="../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">News</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><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/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"> + <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 id="ref-usage"> + <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 mkinmod</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> @@ -137,7 +92,7 @@ kinetic parameters and initial values for the state variables.</p> <span> <span class="va">...</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for mkinfit</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> @@ -153,37 +108,39 @@ kinetic parameters and initial values for the state variables.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>x</dt> + <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>odeparms</dt> +<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>odeini</dt> +<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>outtimes</dt> +<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>...</dt> +<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>solution_type</dt> +<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 @@ -192,58 +149,56 @@ ODE models, but not applicable to some models, e.g. using FOMC for the parent compound.</p></dd> -<dt>use_compiled</dt> +<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>use_symbols</dt> +<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>method.ode</dt> -<dd><p>The solution method passed via mkinpredict to ode] in +<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>atol</dt> +<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>rtol</dt> +<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>maxsteps</dt> +<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>map_output</dt> +<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>na_stop</dt> -<dd><p>Should it be an error if ode returns NaN values</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 id="value"> - <h2>Value</h2> - - -<p>A matrix with the numeric solution in wide format</p> + <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 id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <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> @@ -398,10 +353,10 @@ as these always return mapped output.</p></dd> <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 0.005</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> 1 eigen 3.2 0.016</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 24.4 0.122</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4 0.008</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 32 0.064</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> @@ -413,27 +368,23 @@ as these always return mapped output.</p></dd> <span class="r-in"><span></span></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> -</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="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<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> + </footer></div> + - - </body></html> |