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diff --git a/inst/web/plot.mkinfit.html b/inst/web/plot.mkinfit.html new file mode 100644 index 00000000..5308ecec --- /dev/null +++ b/inst/web/plot.mkinfit.html @@ -0,0 +1,189 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>plot.mkinfit. mkin 0.9-41</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 0.9-41</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(fit$mkinmod$map), pch_obs = col_obs, lty_obs = rep(1, length(fit$mkinmod$map)), add = FALSE, legend = !add, show_residuals = FALSE, maxabs = "auto", lpos = "topright", inset = c(0.05, 0.05), ...)</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 in the lower third of the plot? + </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>lpos</dt> + <dd> + position of the legend. Passed to <code><a href='http://www.inside-r.org/r-doc/graphics/legend'>legend</a></code> as the first 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>...</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 +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) +plot(fit) +</div> +<p><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /></p></pre> + </div> + <div class="span4"> + <!-- <ul> + <li>plot.mkinfit</li> + </ul> + <ul> + <li> hplot </li> + </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>
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