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diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html new file mode 100644 index 00000000..45d5f53a --- /dev/null +++ b/docs/reference/synthetic_data_for_UBA.html @@ -0,0 +1,174 @@ +<!-- 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> + — synthetic_data_for_UBA_2014 • 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">Reference</a> +</li> +<li> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1> +</h1> + </div> + + + <p>The 12 datasets were generated using four different models and three different + variance components. The four models are either the SFO or the DFOP model with either + two sequential or two parallel metabolites.</p> + + <p>Variance component 'a' is based on a normal distribution with standard deviation of 3, + Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. + Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the + minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 + for the increase of the standard deviation with y.</p> + + <p>Initial concentrations for metabolites and all values where adding the variance component resulted + in a value below the assumed limit of detection of 0.1 were set to <code>NA</code>.</p> + + <p>As an example, the first dataset has the title <code>SFO_lin_a</code> and is based on the SFO model + with two sequential metabolites (linear pathway), with added variance component 'a'.</p> + + <p>Compare also the code in the example section to see the degradation models.</p> + + + <pre><span class='no'>synthetic_data_for_UBA_2014</span></pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A list containing datasets in the form internally used by the 'gmkin' package. + The list has twelfe components. Each of the components is one dataset that has, + among others, the following components + <dl class='dl-horizontal'> + <dt><code>title</code></dt><dd>The name of the dataset, e.g. <code>SFO_lin_a</code></dd> + <dt><code>data</code></dt><dd>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></dd> + </dl></p> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> + <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for + measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> + + + <h2 class="hasAnchor" id="examples"> + <a class="anchor" href="#examples"></a> + Examples + </h2> + <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> +<span class='co'># m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),</span> +<span class='co'># M1 = list(type = "SFO", to = "M2"),</span> +<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># </span> +<span class='co'># m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),</span> +<span class='co'># sink = FALSE),</span> +<span class='co'># M1 = list(type = "SFO"),</span> +<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"),</span> +<span class='co'># M1 = list(type = "SFO", to = "M2"),</span> +<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),</span> +<span class='co'># sink = FALSE),</span> +<span class='co'># M1 = list(type = "SFO"),</span> +<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)</span> +<span class='co'>## ---------------------------------------------</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="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> |