<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>plot.mkinfit. mkin 0.9.43.9000</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="#">mkin 0.9.43.9000</a>
<div class="nav">
<ul class="nav">
<li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>"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, ...)</div></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.inside-r.org/r-doc/graphics/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.inside-r.org/r-doc/graphics/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.inside-r.org/r-doc/graphics/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'># One parent compound, one metabolite, both single first order, path from
# parent to sink included, use Levenberg-Marquardt for speed
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
m1 = mkinsub("SFO", full = "Metabolite M1" ))
</div>
<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
<div class='input'>fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq")
plot(fit)
</div>
<p><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /></p>
<div class='input'>plot(fit, show_residuals = TRUE)
</div>
<p><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /></p>
<div class='input'>
# Show the observed variables separately
plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))
</div>
<p><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /></p>
<div class='input'>
# Show the observed variables separately, with residuals
plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
show_errmin = TRUE)
</div>
<p><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /></p>
<div class='input'>
# The same can be obtained with less typing, using the convenience function plot_sep
plot_sep(fit, lpos = c("topright", "bottomright"))
</div></pre>
</div>
<div class="span4">
<!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p>
</footer>
</div>
</body>
</html>
