diff options
Diffstat (limited to 'docs/plot.mkinfit.html')
| -rw-r--r-- | docs/plot.mkinfit.html | 238 |
1 files changed, 0 insertions, 238 deletions
diff --git a/docs/plot.mkinfit.html b/docs/plot.mkinfit.html deleted file mode 100644 index 76ae3c4d..00000000 --- a/docs/plot.mkinfit.html +++ /dev/null @@ -1,238 +0,0 @@ -<!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>
\ No newline at end of file |