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diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 0f384062..8312c17c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,13 +6,16 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title> +<title>Fit one or more kinetic models with one or more state variables to one or +more datasets — mmkin • 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 --> @@ -32,14 +35,16 @@ -<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" /> -<meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets - specified in its first two arguments." /> +<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or +more datasets — mmkin" /> +<meta property="og:description" content="This function calls mkinfit on all combinations of models and +datasets specified in its first two arguments." /> <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> @@ -110,7 +115,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -126,65 +130,64 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1> + <h1>Fit one or more kinetic models with one or more state variables to one or +more datasets</h1> <div class="hidden name"><code>mmkin.Rd</code></div> </div> <div class="ref-description"> - - <p>This function calls <code><a href='mkinfit.html'>mkinfit</a></code> on all combinations of models and datasets - specified in its first two arguments.</p> - + <p>This function calls <code><a href='mkinfit.html'>mkinfit</a></code> on all combinations of models and +datasets specified in its first two arguments.</p> </div> - <pre class="usage"><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre> - + <pre class="usage"><span class='fu'>mmkin</span>(<span class='kw'>models</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='no'>datasets</span>, + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</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>models</th> - <td><p>Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", - "HS", "SFORB"), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code> - objects.</p></td> + <td><p>Either a character vector of shorthand names like +<code><a href='https://rdrr.io/r/base/c.html'>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</a></code>, or an optionally named +list of <code><a href='mkinmod.html'>mkinmod</a></code> objects.</p></td> </tr> <tr> <th>datasets</th> - <td><p>An optionally named list of datasets suitable as observed data for - <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> + <td><p>An optionally named list of datasets suitable as observed +data for <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> </tr> <tr> <th>cores</th> - <td><p>The number of cores to be used for multicore processing. This is only - used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines, - cores > 1 is not supported, you need to use the <code>cluster</code> argument - to use multiple logical processors.</p></td> + <td><p>The number of cores to be used for multicore processing. This +is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows +machines, cores > 1 is not supported, you need to use the <code>cluster</code> +argument to use multiple logical processors.</p></td> </tr> <tr> <th>cluster</th> - <td><p>A cluster as returned by <code>makeCluster</code> to be used for parallel - execution.</p></td> + <td><p>A cluster as returned by <code>makeCluster</code> to be used +for parallel execution.</p></td> </tr> <tr> <th>...</th> <td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using the model - and dataset names as row and column indices.</p> - + <p>A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using + the model and dataset names as row and column indices.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <div class='dont-index'><p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p></div> - + <div class='dont-index'><p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for + plotting.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> + <pre class="examples"><div class='input'> +<span class='co'># \dontrun{</span> <span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>), <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> @@ -199,8 +202,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 0.016 0.029 4.960 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 19.084 0.004 19.099 </div><div class='input'> +#> 0.011 0.032 4.774 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 18.676 0.000 18.687 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505684 0.2494316 @@ -221,17 +224,15 @@ <span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> <span class='co'># allow to plot the observed variables separately</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></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="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> |