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diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html new file mode 100644 index 00000000..94aebf63 --- /dev/null +++ b/docs/reference/plot.mkinfit.html @@ -0,0 +1,231 @@ +<!-- 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.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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" 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="../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"> + <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="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://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="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Solves the differential equations with the optimised and fixed parameters + from a previous successful call to <code>mkinfit</code> and plots + the observed data together with the solution of the fitted model.</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>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>mkinfit</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>&#8230;</dt> + <dd> + Further arguments passed to <code>plot</code>. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The function is called for its side effect.</p> + </div> + + <h2 id="examples">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'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</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'>mkinsub</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</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='unknown-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='unknown-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='unknown-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='unknown-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"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> |