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diff --git a/inst/web/plot.mkinfit.html b/inst/web/plot.mkinfit.html deleted file mode 100644 index d253de45..00000000 --- a/inst/web/plot.mkinfit.html +++ /dev/null @@ -1,229 +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="#">mkin 0.9.44.9000</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>
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