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diff --git a/docs/plot.mkinfit.html b/docs/plot.mkinfit.html new file mode 100644 index 00000000..76ae3c4d --- /dev/null +++ b/docs/plot.mkinfit.html @@ -0,0 +1,238 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>plot.mkinfit. mkin 0.9.44.9000</title> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="author" content=" + Johannes Ranke +"> + +<link href="css/bootstrap.css" rel="stylesheet"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<![endif]--> + +<script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + processEscapes: true + } + }); +</script> +<script type="text/javascript" + src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + </head> + + <body> + <div class="navbar"> + <div class="navbar-inner"> + <div class="container"> + <a class="brand" href="index.html">mkin 0.9.44.9000</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html">Home</a></li> + <li><a href="reference.html">Reference</a></li> + </ul> + </div> + </div> + </div> +</div> + + + <div class="container"> + <header> + + </header> + + <h1> + Plot the observed data and the fitted model of an mkinfit object +</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><span class="comment"># S3 method for mkinfit</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="argument">fit</span> <span class="argument">=</span> <span class="symbol">x</span><span class="keyword">,</span> + <span class="argument">obs_vars</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/names'>names</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">mkinmod</span><span class="keyword">$</span><span class="symbol">map</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">xlab</span> <span class="argument">=</span> <span class="string">"Time"</span><span class="keyword">,</span> <span class="argument">ylab</span> <span class="argument">=</span> <span class="string">"Observed"</span><span class="keyword">,</span> + <span class="argument">xlim</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/range'>range</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">data</span><span class="keyword">$</span><span class="symbol">time</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">ylim</span> <span class="argument">=</span> <span class="string">"default"</span><span class="keyword">,</span> + <span class="argument">col_obs</span> <span class="argument">=</span> <span class="number">1</span><span class="keyword">:</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/length'>length</a></span><span class="keyword">(</span><span class="symbol">obs_vars</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">pch_obs</span> <span class="argument">=</span> <span class="symbol">col_obs</span><span class="keyword">,</span> + <span class="argument">lty_obs</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span><span class="keyword">(</span><span class="number">1</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/length'>length</a></span><span class="keyword">(</span><span class="symbol">obs_vars</span><span class="keyword">)</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">add</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">legend</span> <span class="argument">=</span> <span class="keyword">!</span><span class="symbol">add</span><span class="keyword">,</span> + <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">maxabs</span> <span class="argument">=</span> <span class="string">"auto"</span><span class="keyword">,</span> + <span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">rel.height.middle</span> <span class="argument">=</span> <span class="number">0.9</span><span class="keyword">,</span> + <span class="argument">lpos</span> <span class="argument">=</span> <span class="string">"topright"</span><span class="keyword">,</span> <span class="argument">inset</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0.05</span><span class="keyword">,</span> <span class="number">0.05</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">show_errmin</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">errmin_digits</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span> +<span class="functioncall"><a href='plot.mkinfit.html'>plot_sep</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">show_errmin</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre> + + <h2>Arguments</h2> + <dl> + <dt>x</dt> + <dd> + Alias for fit introduced for compatibility with the generic S3 method. + </dd> + <dt>fit</dt> + <dd> + An object of class <code><a href='mkinfit.html'>mkinfit</a></code>. + </dd> + <dt>obs_vars</dt> + <dd> + A character vector of names of the observed variables for which the + data and the model should be plotted. Defauls to all observed variables + in the model. + </dd> + <dt>xlab</dt> + <dd> + Label for the x axis. + </dd> + <dt>ylab</dt> + <dd> + Label for the y axis. + </dd> + <dt>xlim</dt> + <dd> + Plot range in x direction. + </dd> + <dt>ylim</dt> + <dd> + Plot range in y direction. + </dd> + <dt>col_obs</dt> + <dd> + Colors used for plotting the observed data and the corresponding model prediction lines. + </dd> + <dt>pch_obs</dt> + <dd> + Symbols to be used for plotting the data. + </dd> + <dt>lty_obs</dt> + <dd> + Line types to be used for the model predictions. + </dd> + <dt>add</dt> + <dd> + Should the plot be added to an existing plot? + </dd> + <dt>legend</dt> + <dd> + Should a legend be added to the plot? + </dd> + <dt>show_residuals</dt> + <dd> + Should residuals be shown? If only one plot of the fits is shown, the + residual plot is in the lower third of the plot? Otherwise, i.e. if + "sep_obs" is given, the residual plots will be located to the right of + the plots of the fitted curves. + </dd> + <dt>maxabs</dt> + <dd> + Maximum absolute value of the residuals. This is used for the scaling of + the y axis and defaults to "auto". + </dd> + <dt>sep_obs</dt> + <dd> + Should the observed variables be shown in separate subplots? If yes, residual plots + requested by "show_residuals" will be shown next to, not below the plot of the fits. + </dd> + <dt>rel.height.middle</dt> + <dd> + The relative height of the middle plot, if more than two rows of plots are shown. + </dd> + <dt>lpos</dt> + <dd> + Position(s) of the legend(s). Passed to <code><a href='http://www.rdocumentation.org/packages/graphics/topics/legend'>legend</a></code> as the first argument. + If not length one, this should be of the same length as the obs_var argument. + </dd> + <dt>inset</dt> + <dd> + Passed to <code><a href='http://www.rdocumentation.org/packages/graphics/topics/legend'>legend</a></code> if applicable. + </dd> + <dt>show_errmin</dt> + <dd> + Should the FOCUS chi2 error value be shown in the upper margin of the plot? + </dd> + <dt>errmin_digits</dt> + <dd> + The number of significant digits for rounding the FOCUS chi2 error percentage. + </dd> + <dt>...</dt> + <dd> + Further arguments passed to <code><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></code>. + </dd> + </dl> + + <div class="Description"> + <h2>Description</h2> + + <p>Solves the differential equations with the optimised and fixed parameters + from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots + the observed data together with the solution of the fitted model.</p> + + </div> + + <div class="Value"> + <h2>Value</h2> + + <p><dl> + The function is called for its side effect. +</dl></p> + + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class="comment"># One parent compound, one metabolite, both single first order, path from</span> +<span class="comment"># parent to sink included, use Levenberg-Marquardt for speed</span> +<span class="symbol">SFO_SFO</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"m1"</span><span class="keyword">,</span> <span class="argument">full</span> <span class="argument">=</span> <span class="string">"Parent"</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">full</span> <span class="argument">=</span> <span class="string">"Metabolite M1"</span> <span class="keyword">)</span><span class="keyword">)</span></div> +<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> +<div class='input'><span class="symbol">fit</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO</span><span class="keyword">,</span> <span class="symbol">FOCUS_2006_D</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">method.modFit</span> <span class="argument">=</span> <span class="string">"Marq"</span><span class="keyword">)</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">)</span></div> +<p><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /></p> +<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div> +<p><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /></p> +<div class='input'> +<span class="comment"># Show the observed variables separately</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">lpos</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"topright"</span><span class="keyword">,</span> <span class="string">"bottomright"</span><span class="keyword">)</span><span class="keyword">)</span></div> +<p><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /></p> +<div class='input'> +<span class="comment"># Show the observed variables separately, with residuals</span> +<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">lpos</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"topright"</span><span class="keyword">,</span> <span class="string">"bottomright"</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">show_errmin</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div> +<p><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /></p> +<div class='input'> +<span class="comment"># The same can be obtained with less typing, using the convenience function plot_sep</span> +<span class="functioncall"><a href='plot.mkinfit.html'>plot_sep</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">lpos</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"topright"</span><span class="keyword">,</span> <span class="string">"bottomright"</span><span class="keyword">)</span><span class="keyword">)</span></div></pre> + </div> + <div class="span4 sidebar"> + <!-- <ul> + <li>plot.mkinfit</li><li>plot_sep</li> + </ul> + <ul> + + </ul> --> + + + + <h2>Author</h2> + + Johannes Ranke + + + </div> +</div> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> + </footer> + </div> + </body> +</html>
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