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diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 2348d40e..327a7d8d 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinpredict • mkin</title> +<title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -26,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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]--> + + </head> <body> @@ -71,6 +72,9 @@ <li> <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> </ul> </li> <li> @@ -96,8 +100,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Produce predictions from a kinetic model using specific parameters</h1> </div> @@ -106,71 +109,72 @@ kinetic parameters and initial values for the state variables.</p> - <pre><span class='fu'>mkinpredict</span>(<span class='no'>mkinmod</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='no'>outtimes</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, + <pre class="usage"><span class='fu'>mkinpredict</span>(<span class='no'>mkinmod</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='no'>outtimes</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>mkinmod</dt> - <dd> - A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>. - </dd> - <dt>odeparms</dt> - <dd> - A numeric vector specifying the parameters used in the kinetic model, which - is generally defined as a set of ordinary differential equations. - </dd> - <dt>odeini</dt> - <dd> - A numeric vectory containing the initial values of the state variables of + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>mkinmod</th> + <td><p>A kinetic model as produced by <code><a href='mkinmod.html'>mkinmod</a></code>.</p></td> + </tr> + <tr> + <th>odeparms</th> + <td><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 vectory containing the initial values of the state variables of the model. Note that the state variables can differ from the observed - variables, for example in the case of the SFORB model. - </dd> - <dt>outtimes</dt> - <dd> - A numeric vector specifying the time points for which model predictions - should be generated. - </dd> - <dt>solution_type</dt> - <dd> - The method that should be used for producing the predictions. This should - generally be "analytical" if there is only one observed variable, and - usually "deSolve" in the case of several observed variables. The third - possibility "eigen" is faster but not applicable to some models e.g. - using FOMC for the parent compound. - </dd> - <dt>method.ode</dt> - <dd> - The solution method passed via <code>mkinpredict</code> to - <code>ode</code> in case the solution type is "deSolve". The default - "lsoda" is performant, but sometimes fails to converge. - </dd> - <dt>use_compiled</dt> - <dd> - If set to <code>FALSE</code>, no compiled version of the <code><a href='mkinmod.html'>mkinmod</a></code> - model is used, even if is present. - </dd> - <dt>atol</dt> - <dd> - Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8, - lower than in <code>lsoda</code>. - </dd> - <dt>rtol</dt> - <dd> - Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10, - much lower than in <code>lsoda</code>. - </dd> - <dt>map_output</dt> - <dd> - Boolean to specify if the output should list values for the observed - variables (default) or for all state variables (if set to FALSE). - </dd> - <dt>…</dt> - <dd> - Further arguments passed to the ode solver in case such a solver is used. - </dd> - </dl> + 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>solution_type</th> + <td><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>method.ode</th> + <td><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>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>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 the observed + variables (default) or for all state variables (if set to FALSE).</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> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -295,17 +299,17 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.016 0.016 0.004 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.004 0.000 0.004 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.016 0.004 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.004 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.032 0.000 0.034 </div></pre> +#> 0.032 0.000 0.033 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |