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
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
|
<!-- 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>summary.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>Lists model equations, the summary as returned by <code>summary.modFit</code>,
the chi2 error levels calculated according to FOCUS guidance (2006) as far
as defined therein, and optionally the data, consisting of observed, predicted
and residual values.</p>
<pre><span class='co'># S3 method for mkinfit</span>
<span class='fu'>summary</span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>)
<span class='co'># S3 method for summary.mkinfit</span>
<span class='fu'>print</span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'>max</span>(<span class='fl'>3</span>, <span class='fu'>getOption</span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre>
<h2>Arguments</h2>
<dl class="dl-horizontal">
<dt>object</dt>
<dd>
an object of class <code>mkinfit</code>.
</dd>
<dt>x</dt>
<dd>
an object of class <code>summary.mkinfit</code>.
</dd>
<dt>data</dt>
<dd>
logical, indicating whether the data should be included in the summary.
</dd>
<dt>distimes</dt>
<dd>
logical, indicating whether DT50 and DT90 values should be included.
</dd>
<dt>alpha</dt>
<dd>
error level for confidence interval estimation from t distribution
</dd>
<dt>digits</dt>
<dd>
Number of digits to use for printing
</dd>
<dt>&#8230;</dt>
<dd>
optional arguments passed to methods like <code>print</code>.
</dd>
</dl>
<div class="Value">
<h2>Value</h2>
<p>The summary function returns a list derived from
<code>summary.modFit</code>, with components, among others</p>
<p>The print method is called for its side effect, i.e. printing the summary.</p>
</div>
<div class="References">
<h2>References</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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
</div>
<h2 id="examples">Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'>mkinfit</span>(<span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000
#> R version: 3.3.1
#> Date of fit: Thu Oct 6 09:18:07 2016
#> Date of summary: Thu Oct 6 09:18:07 2016
#>
#> Equations:
#> d_parent = - k_parent_sink * parent
#>
#> Model predictions using solution type analytical
#>
#> Fitted with method Port using 35 model solutions performed in 0.079 s
#>
#> Weighting: none
#>
#> Starting values for parameters to be optimised:
#> value type
#> parent_0 101.24 state
#> k_parent_sink 0.10 deparm
#>
#> Starting values for the transformed parameters actually optimised:
#> value lower upper
#> parent_0 101.240000 -Inf Inf
#> log_k_parent_sink -2.302585 -Inf Inf
#>
#> Fixed parameter values:
#> None
#>
#> Optimised, transformed parameters with symmetric confidence intervals:
#> Estimate Std. Error Lower Upper
#> parent_0 109.200 4.3910 98.410 119.900
#> log_k_parent_sink -3.291 0.1152 -3.573 -3.009
#>
#> Parameter correlation:
#> parent_0 log_k_parent_sink
#> parent_0 1.000 0.575
#> log_k_parent_sink 0.575 1.000
#>
#> Residual standard error: 6.08 on 6 degrees of freedom
#>
#> 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_0 109.20000 24.860 1.394e-07 98.41000 119.90000
#> k_parent_sink 0.03722 8.679 6.457e-05 0.02807 0.04934
#>
#> Chi2 error levels in percent:
#> err.min n.optim df
#> All data 8.385 2 6
#> parent 8.385 2 6
#>
#> Resulting formation fractions:
#> ff
#> parent_sink 1
#>
#> Estimated disappearance times:
#> DT50 DT90
#> parent 18.62 61.87
#>
#> Data:
#> time variable observed predicted residual
#> 0 parent 101.24 109.153 -7.9132
#> 3 parent 99.27 97.622 1.6484
#> 7 parent 90.11 84.119 5.9913
#> 14 parent 72.19 64.826 7.3641
#> 30 parent 29.71 35.738 -6.0283
#> 62 parent 5.98 10.862 -4.8818
#> 90 parent 1.54 3.831 -2.2911
#> 118 parent 0.39 1.351 -0.9613
#> </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>
|
