blob: 3b176eed90d0575ec5a55107200aca08b9f8635c (
plain) (
blame)
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
|
<!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"><title>Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015 • 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-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015"><meta name="description" content="Data taken from US EPA (2015), p. 19 and 23."><meta property="og:description" content="Data taken from US EPA (2015), p. 19 and 23."><meta name="robots" content="noindex"></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
<nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container">
<a class="navbar-brand me-2" href="../index.html">mkin</a>
<small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</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">
<button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
<ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a></li>
<li><hr class="dropdown-divider"></li>
<li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li>
<li><a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li>
<li><a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li>
<li><a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li>
<li><hr class="dropdown-divider"></li>
<li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li>
<li><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></li>
<li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
<li><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></li>
<li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li>
<li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li>
<li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li>
<li><hr class="dropdown-divider"></li>
<li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li>
<li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li>
<li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li>
<li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li>
<li><hr class="dropdown-divider"></li>
<li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li>
<li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li>
<li><a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li>
</ul></li>
<li class="nav-item"><a class="nav-link" href="../coverage/coverage.html">Test coverage</a></li>
<li class="nav-item"><a class="nav-link" href="../news/index.html">News</a></li>
</ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
<input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="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">
<h1>Example datasets from the NAFTA SOP published 2015</h1>
<div class="d-none name"><code>NAFTA_SOP_2015.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Data taken from US EPA (2015), p. 19 and 23.</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="va">NAFTA_SOP_Appendix_B</span></span>
<span> <span class="va">NAFTA_SOP_Appendix_D</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>2 datasets with observations on the following variables.</p><dl><dt><code>name</code></dt>
<dd><p>a factor containing the name of the observed variable</p></dd>
<dt><code>time</code></dt>
<dd><p>a numeric vector containing time points</p></dd>
<dt><code>value</code></dt>
<dd><p>a numeric vector containing concentrations</p></dd>
</dl></div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
<p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics
in environmental media. NAFTA Technical Working Group on Pesticides
<a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a>
accessed 2019-02-22</p>
<p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
Calculate Representative Half-life Values and Characterizing Pesticide
Degradation
<a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</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 class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span>
<span class="r-msg co"><span class="r-pr">#></span> The representative half-life of the IORE model is longer than the one corresponding</span>
<span class="r-msg co"><span class="r-pr">#></span> to the terminal degradation rate found with the DFOP model.</span>
<span class="r-msg co"><span class="r-pr">#></span> The representative half-life obtained from the DFOP model may be used</span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span>
<span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span>
<span class="r-out co"><span class="r-pr">#></span> 1378.6832 615.7730 517.8836 </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Critical sum of squares for checking the SFO model:</span>
<span class="r-out co"><span class="r-pr">#></span> [1] 717.4598</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Parameters:</span>
<span class="r-out co"><span class="r-pr">#></span> $SFO</span>
<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 83.7558 1.80e-14 77.18268 90.3288</span>
<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0017 7.43e-05 0.00112 0.0026</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 8.7518 1.22e-05 5.64278 11.8608</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $IORE</span>
<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 9.69e+01 NA 8.88e+01 1.05e+02</span>
<span class="r-out co"><span class="r-pr">#></span> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09</span>
<span class="r-out co"><span class="r-pr">#></span> N_parent 6.68e+00 NA 4.19e+00 9.17e+00</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 5.85e+00 NA 3.76e+00 7.94e+00</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $DFOP</span>
<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02</span>
<span class="r-out co"><span class="r-pr">#></span> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02</span>
<span class="r-out co"><span class="r-pr">#></span> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03</span>
<span class="r-out co"><span class="r-pr">#></span> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> DTx values:</span>
<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span>
<span class="r-out co"><span class="r-pr">#></span> SFO 407 1350 407</span>
<span class="r-out co"><span class="r-pr">#></span> IORE 541 5190000 1560000</span>
<span class="r-out co"><span class="r-pr">#></span> DFOP 429 2380 841</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span>
<span class="r-out co"><span class="r-pr">#></span> [1] 841.41</span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="NAFTA_SOP_2015-1.png" alt="" width="700" height="433"></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside></div>
<footer><div class="pkgdown-footer-left">
<p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown-footer-right">
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
</div>
</footer></div>
</body></html>
|
