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diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014.html b/docs/dev/reference/synthetic_data_for_UBA_2014.html new file mode 100644 index 00000000..da4af114 --- /dev/null +++ b/docs/dev/reference/synthetic_data_for_UBA_2014.html @@ -0,0 +1,470 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <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 datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> + +<!-- bootstrap-toc --> +<link rel="stylesheet" href="../bootstrap-toc.css"> +<script src="../bootstrap-toc.js"></script> + +<!-- Font Awesome icons --> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> + +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + + + + +<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" /> +<meta property="og:description" content="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. +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. Note that this is a simplified version + of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the + measured values approximates lognormal distribution for high values, whereas we are using + normally distributed error components all along. +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 NA. +As an example, the first dataset has the title SFO_lin_a and is based on the SFO model + with two sequential metabolites (linear pathway), with added variance component 'a'. +Compare also the code in the example section to see the degradation models." /> + + +<meta name="robots" content="noindex"> + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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 data-spy="scroll" data-target="#toc"> + <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" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Synthetic datasets for one parent compound with two metabolites</h1> + + <div class="hidden name"><code>synthetic_data_for_UBA_2014.Rd</code></div> + </div> + + <div class="ref-description"> + <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. Note that this is a simplified version + of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the + measured values approximates lognormal distribution for high values, whereas we are using + normally distributed error components all along.</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> + </div> + + <pre class="usage"><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 twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, + each containing, among others, the following components</p><dl'> + <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> + <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> + +</dl> + + <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'># \dontrun{</span> +<span class='co'># The data have been generated using the following kinetic models</span> +<span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>), + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + +<span class='no'>m_synth_SFO_par</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), + <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>m_synth_DFOP_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>), + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>m_synth_DFOP_par</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>), + <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='co'># The model predictions without intentional error were generated as follows</span> +<span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>) + +<span class='no'>d_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_SFO_lin</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.8</span>, + <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.3</span>, <span class='kw'>f_M1_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, + <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>), + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>), + <span class='no'>sampling_times</span>) + +<span class='no'>d_synth_DFOP_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_DFOP_lin</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, + <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.3</span>, + <span class='kw'>f_M1_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>), + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>), + <span class='no'>sampling_times</span>) + +<span class='no'>d_synth_SFO_par</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_SFO_par</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, + <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.8</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, + <span class='kw'>f_parent_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>), + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>), + <span class='no'>sampling_times</span>) + +<span class='no'>d_synth_DFOP_par</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_synth_DFOP_par</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.3</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, + <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.6</span>, <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fl'>0.04</span>, + <span class='kw'>f_parent_to_M2</span> <span class='kw'>=</span> <span class='fl'>0.4</span>, <span class='kw'>k_M2</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fl'>0</span>), + <span class='no'>sampling_times</span>) + +<span class='co'># Construct names for datasets with errors</span> +<span class='no'>d_synth_names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"d_synth_"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO_lin"</span>, <span class='st'>"SFO_par"</span>, + <span class='st'>"DFOP_lin"</span>, <span class='st'>"DFOP_par"</span>)) + +<span class='co'># Original function used or adding errors. The add_err function now published</span> +<span class='co'># with this package is a slightly generalised version where the names of</span> +<span class='co'># secondary compartments that should have an initial value of zero (M1 and M2</span> +<span class='co'># in this case) are not hardcoded any more.</span> +<span class='co'># add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)</span> +<span class='co'># {</span> +<span class='co'># set.seed(seed)</span> +<span class='co'># d_long = mkin_wide_to_long(d, time = "time")</span> +<span class='co'># d_rep = data.frame(lapply(d_long, rep, each = 2))</span> +<span class='co'># d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</span> +<span class='co'>#</span> +<span class='co'># d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0</span> +<span class='co'># d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))</span> +<span class='co'># d_NA$value <- round(d_NA$value, 1)</span> +<span class='co'># return(d_NA)</span> +<span class='co'># }</span> + +<span class='co'># The following is the simplified version of the two-component model of Rocke</span> +<span class='co'># and Lorenzato (1995)</span> +<span class='no'>sdfunc_twocomp</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>value</span>, <span class='no'>sd_low</span>, <span class='no'>rsd_high</span>) { + <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span>(<span class='no'>sd_low</span>^<span class='fl'>2</span> + <span class='no'>value</span>^<span class='fl'>2</span> * <span class='no'>rsd_high</span>^<span class='fl'>2</span>) +} + +<span class='co'># Add the errors.</span> +<span class='kw'>for</span> (<span class='no'>d_synth_name</span> <span class='kw'>in</span> <span class='no'>d_synth_names</span>) +{ + <span class='no'>d_synth</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/get.html'>get</a></span>(<span class='no'>d_synth_name</span>) + <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='no'>d_synth_name</span>, <span class='st'>"_a"</span>), <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_synth</span>, <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fl'>3</span>)) + <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='no'>d_synth_name</span>, <span class='st'>"_b"</span>), <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_synth</span>, <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fl'>7</span>)) + <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='no'>d_synth_name</span>, <span class='st'>"_c"</span>), <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_synth</span>, + <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fu'>sdfunc_twocomp</span>(<span class='no'>value</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>))) + +} + +<span class='no'>d_synth_err_names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( + <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='no'>d_synth_names</span>, <span class='kw'>each</span> <span class='kw'>=</span> <span class='fl'>3</span>), <span class='no'>letters</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"_"</span>) +) + +<span class='co'># This is just one example of an evaluation using the kinetic model used for</span> +<span class='co'># the generation of the data</span> + <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.3 +#> R version used for fitting: 4.0.0 +#> Date of fit: Wed May 27 06:02:14 2020 +#> Date of summary: Wed May 27 06:02:14 2020 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1 +#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted using 817 model solutions performed in 0.623 s +#> +#> Error model: Constant variance +#> +#> Error model algorithm: OLS +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 101.3500 state +#> k_parent 0.1000 deparm +#> k_M1 0.1001 deparm +#> k_M2 0.1002 deparm +#> f_parent_to_M1 0.5000 deparm +#> f_M1_to_M2 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 101.350000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_M1 -2.301586 -Inf Inf +#> log_k_M2 -2.300587 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> f_M1_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> M1_0 0 state +#> M2_0 0 state +#> +#> Results: +#> +#> AIC BIC logLik +#> 188.7274 200.3723 -87.36368 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 102.1000 1.57000 98.8600 105.3000 +#> log_k_parent -0.3020 0.03885 -0.3812 -0.2229 +#> log_k_M1 -1.2070 0.07123 -1.3520 -1.0620 +#> log_k_M2 -3.9010 0.06571 -4.0350 -3.7670 +#> f_parent_ilr_1 0.8492 0.16640 0.5103 1.1880 +#> f_M1_ilr_1 0.6780 0.17600 0.3196 1.0360 +#> sigma 2.2730 0.25740 1.7490 2.7970 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1 +#> parent_0 1.000e+00 3.933e-01 -1.605e-01 2.819e-02 -4.624e-01 +#> log_k_parent 3.933e-01 1.000e+00 -4.082e-01 7.166e-02 -5.682e-01 +#> log_k_M1 -1.605e-01 -4.082e-01 1.000e+00 -3.929e-01 7.478e-01 +#> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01 +#> f_parent_ilr_1 -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00 +#> f_M1_ilr_1 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01 +#> sigma -1.384e-07 -2.581e-07 9.499e-08 1.518e-07 1.236e-07 +#> f_M1_ilr_1 sigma +#> parent_0 1.614e-01 -1.384e-07 +#> log_k_parent 4.102e-01 -2.581e-07 +#> log_k_M1 -8.109e-01 9.499e-08 +#> log_k_M2 5.419e-01 1.518e-07 +#> f_parent_ilr_1 -8.605e-01 1.236e-07 +#> f_M1_ilr_1 1.000e+00 8.795e-09 +#> sigma 8.795e-09 1.000e+00 +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 102.10000 65.000 7.281e-36 98.86000 105.30000 +#> k_parent 0.73930 25.740 2.948e-23 0.68310 0.80020 +#> k_M1 0.29920 14.040 1.577e-15 0.25880 0.34590 +#> k_M2 0.02023 15.220 1.653e-16 0.01769 0.02312 +#> f_parent_to_M1 0.76870 18.370 7.295e-19 0.67300 0.84290 +#> f_M1_to_M2 0.72290 14.500 6.418e-16 0.61110 0.81240 +#> sigma 2.27300 8.832 2.161e-10 1.74900 2.79700 +#> +#> FOCUS Chi2 error levels in percent: +#> err.min n.optim df +#> All data 8.454 6 17 +#> parent 8.660 2 6 +#> M1 10.583 2 5 +#> M2 3.586 2 6 +#> +#> Resulting formation fractions: +#> ff +#> parent_M1 0.7687 +#> parent_sink 0.2313 +#> M1_M2 0.7229 +#> M1_sink 0.2771 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 0.9376 3.114 +#> M1 2.3170 7.697 +#> M2 34.2689 113.839 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 101.5 1.021e+02 -0.56248 +#> 0 parent 101.2 1.021e+02 -0.86248 +#> 1 parent 53.9 4.873e+01 5.17118 +#> 1 parent 47.5 4.873e+01 -1.22882 +#> 3 parent 10.4 1.111e+01 -0.70773 +#> 3 parent 7.6 1.111e+01 -3.50773 +#> 7 parent 1.1 5.772e-01 0.52283 +#> 7 parent 0.3 5.772e-01 -0.27717 +#> 14 parent 3.5 3.264e-03 3.49674 +#> 28 parent 3.2 1.045e-07 3.20000 +#> 90 parent 0.6 9.535e-10 0.60000 +#> 120 parent 3.5 -5.941e-10 3.50000 +#> 1 M1 36.4 3.479e+01 1.61088 +#> 1 M1 37.4 3.479e+01 2.61088 +#> 3 M1 34.3 3.937e+01 -5.07027 +#> 3 M1 39.8 3.937e+01 0.42973 +#> 7 M1 15.1 1.549e+01 -0.38715 +#> 7 M1 17.8 1.549e+01 2.31285 +#> 14 M1 5.8 1.995e+00 3.80469 +#> 14 M1 1.2 1.995e+00 -0.79531 +#> 60 M1 0.5 2.111e-06 0.50000 +#> 90 M1 3.2 -9.676e-10 3.20000 +#> 120 M1 1.5 7.671e-10 1.50000 +#> 120 M1 0.6 7.671e-10 0.60000 +#> 1 M2 4.8 4.455e+00 0.34517 +#> 3 M2 20.9 2.153e+01 -0.62527 +#> 3 M2 19.3 2.153e+01 -2.22527 +#> 7 M2 42.0 4.192e+01 0.07941 +#> 7 M2 43.1 4.192e+01 1.17941 +#> 14 M2 49.4 4.557e+01 3.83353 +#> 14 M2 44.3 4.557e+01 -1.26647 +#> 28 M2 34.6 3.547e+01 -0.87275 +#> 28 M2 33.0 3.547e+01 -2.47275 +#> 60 M2 18.8 1.858e+01 0.21837 +#> 60 M2 17.6 1.858e+01 -0.98163 +#> 90 M2 10.6 1.013e+01 0.47130 +#> 90 M2 10.8 1.013e+01 0.67130 +#> 120 M2 9.8 5.521e+00 4.27893 +#> 120 M2 3.3 5.521e+00 -2.22107</div><div class='input'># } +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + |