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diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5faff3c7..f7d543ad 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -8,11 +8,13 @@ <title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,15 +34,16 @@ -<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" /> +<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" /> <meta property="og:description" content="This function produces a 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." /> +kinetic model as specified by mkinmod, using a specific set of +kinetic parameters and initial values for the state variables." /> <meta name="twitter:card" content="summary" /> + <!-- 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> @@ -111,7 +114,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -133,89 +135,105 @@ </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 parameters and initial values for the state variables.</p> - +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='no'>x</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='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> - + <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>) + +<span class='co'># S3 method for mkinmod</span> +<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='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>) + +<span class='co'># S3 method for mkinfit</span> +<span class='fu'>mkinpredict</span>(<span class='no'>x</span>, <span class='kw'>odeparms</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.ode</span>, + <span class='kw'>odeini</span> <span class='kw'>=</span> <span class='no'>x</span>$<span class='no'>bparms.state</span>, <span class='kw'>outtimes</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>120</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='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> <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> +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 kinetic model, which - is generally defined as a set of ordinary differential equations.</p></td> + <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.</p></td> + <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.</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> + <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> + <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> + <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>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> + <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>atol</th> - <td><p>Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8, - lower than in <code>lsoda</code>.</p></td> + <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> + <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> + <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> + <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> <p>A matrix in the same format as the output of <code>ode</code>.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)) + <pre class="examples"><div class='input'> + <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)) <span class='co'># Compare solution types</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#> time degradinol @@ -342,7 +360,7 @@ <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/seq.html'>seq</a></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 verstrichen -#> 0.022 0.000 0.021 </div><div class='input'> +#> 0.021 0.000 0.021 </div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Predict from a fitted model</span> <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 552.5739 @@ -380,15 +398,14 @@ #> 4 0.3 75.25515 3.399419 #> 5 0.4 72.98675 4.441969 #> 6 0.5 70.78673 5.441679</div><div class='input'> # } + </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> |