<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> <html> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> <!-- Bootstrap --> <link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> <!-- mathjax --> <script src='https://cdn.mathjax.org/mathjax/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> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a class="navbar-brand" href="../index.html">mkin</a> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> Articles <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"> <li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> <li> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> </ul> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> </a> </li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> </header> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot the observed data and the fitted model of an mkinfit object</h1> </div> <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> <p>If the current plot device is a <code><a href='http://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device, then latex is being used for the formatting of the chi2 error level, if <code>show_errmin = TRUE</code>.</p> <pre># S3 method for mkinfit plot(x, fit = x, obs_vars = names(fit$mkinmod$map), xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = "default", col_obs = 1:length(obs_vars), pch_obs = col_obs, lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add, show_residuals = FALSE, maxabs = "auto", sep_obs = FALSE, rel.height.middle = 0.9, lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE, errmin_digits = 3, …) plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <dl class="dl-horizontal"> <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>legend</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>legend</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>plot</code>. </dd> </dl> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The function is called for its side effect.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span> <span class='co'># parent to sink included, use Levenberg-Marquardt for speed</span> <span class='no'>SFO_SFO</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'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</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='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</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_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) <span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># Show the observed variables separately</span> <span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># Show the observed variables separately, with residuals</span> <span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>), <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /><div class='input'> <span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span> <span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</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> <h2>Author</h2> Johannes Ranke </div> </div> <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> </div> </footer> </div> </body> </html>