1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
|
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function finds the smallest relative error still resulting in passing
the chi-squared test as defined in the FOCUS kinetics report from 2006."><title>Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin"><meta property="og:description" content="This function finds the smallest relative error still resulting in passing
the chi-squared test as defined in the FOCUS kinetics report from 2006."><!-- 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>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
<nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container">
<a class="navbar-brand me-2" href="../index.html">mkin</a>
<small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.6</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto"><li class="active nav-item">
<a class="nav-link" href="../reference/index.html">Reference</a>
</li>
<li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
<div class="dropdown-menu" aria-labelledby="dropdown-articles">
<a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a>
<div class="dropdown-divider"></div>
<h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6>
<a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
<a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
<a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
<div class="dropdown-divider"></div>
<h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6>
<a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
<a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
<a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
<a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
<a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
<a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
<div class="dropdown-divider"></div>
<h6 class="dropdown-header" data-toc-skip>Performance</h6>
<a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
<a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
<a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
<div class="dropdown-divider"></div>
<h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6>
<a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
<a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</div>
</li>
<li class="nav-item">
<a class="nav-link" href="../news/index.html">News</a>
</li>
</ul><form class="form-inline my-2 my-lg-0" role="search">
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
<ul class="navbar-nav"><li class="nav-item">
<a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github">
<span class="fab fa fab fa-github fa-lg"></span>
</a>
</li>
</ul></div>
</div>
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="" class="logo" alt=""><h1>Calculate the minimum error to assume in order to pass the variance test</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinerrmin.R" class="external-link"><code>R/mkinerrmin.R</code></a></small>
<div class="d-none name"><code>mkinerrmin.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>This function finds the smallest relative error still resulting in passing
the chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit</span>, alpha <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>fit</dt>
<dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd>
<dt>alpha</dt>
<dd><p>The confidence level chosen for the chi-squared test.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>A dataframe with the following components:</p>
<dl><dt>err.min</dt>
<dd><p>The
relative error, expressed as a fraction.</p></dd>
<dt>n.optim</dt>
<dd><p>The number of
optimised parameters attributed to the data series.</p></dd>
<dt>df</dt>
<dd><p>The number of
remaining degrees of freedom for the chi2 error level calculations. Note
that mean values are used for the chi2 statistic and therefore every time
point with observed values in the series only counts one time.</p></dd>
</dl><p>The
dataframe has one row for the total dataset and one further row for each
observed state variable in the model.</p>
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>This function is used internally by <code><a href="summary.mkinfit.html">summary.mkinfit</a></code>.</p>
</div>
<div class="section level2">
<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
<p>FOCUS (2006) “Guidance Document on Estimating Persistence
and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC
Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">fit_FOCUS_D</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_D</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span>
<span class="r-out co"><span class="r-pr">#></span> All data 0.0640 4 15</span>
<span class="r-out co"><span class="r-pr">#></span> parent 0.0646 2 7</span>
<span class="r-out co"><span class="r-pr">#></span> m1 0.0469 2 8</span>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span> <span class="va">fit_FOCUS_E</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_E</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_E</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span>
<span class="r-out co"><span class="r-pr">#></span> All data 0.1544 4 13</span>
<span class="r-out co"><span class="r-pr">#></span> parent 0.1659 2 7</span>
<span class="r-out co"><span class="r-pr">#></span> m1 0.1095 2 6</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</nav></aside></div>
<footer><div class="pkgdown-footer-left">
<p></p><p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown-footer-right">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
</body></html>
|
