aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/mccall81_245T.html
blob: 74b9c088a992d2e42ab2aaa9f973f4c135dcb334 (plain) (tree) 
38f9e15f








8f38147e


38f9e15f



38f9e15f

38f9e15f

8f38147e

38f9e15f








8f38147e

38f9e15f












8f38147e

38f9e15f

8f38147e

38f9e15f












2409369d

38f9e15f


2409369d




38f9e15f


8f38147e

38f9e15f

2409369d

38f9e15f




8f38147e

38f9e15f



8f38147e




38f9e15f

8f38147e

38f9e15f

38f9e15f








8f38147e

38f9e15f

8f38147e

38f9e15f




8f38147e

38f9e15f





8f38147e


38f9e15f

8f38147e

38f9e15f

38f9e15f

8f38147e






38f9e15f







8f38147e

38f9e15f




2409369d


38f9e15f









2409369d

38f9e15f


















































































8f38147e











38f9e15f




8f38147e








38f9e15f





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

230
231
232
233

234
235
236
237
238
239
240
241

242
243
244
245
246








                                                                      

                                   


                                                                                                                                                                               
                  
 
                                                                                                                                                                                                                







                                                                                                                                                                                                                      
                                                   











                                                                                                      
                                                    
              
                                                                            











                                                                                                         
                                                 

     



                                               

           
      
                                              
        



                                
 


               



                                 
     
          
 







                                                                              
                                                                                      
 
                                                      



                                                                                               
                                                                             




                                                                                                                      

                                                                                      
 
                                                                                                                                                                                   
                                                                                                 
    





                                                                                                                                                                                                                                                                                                                                                                                                                                             






                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                



                                                                                                                                                                                                                      

                                                








                                                                        
                                                                           

















































































                                                                                










                                                         



              







                                                                                




               
<!-- 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>
 — mccall81_245T • 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>Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
 extracts.</p>
    

    <pre><span class='no'>mccall81_245T</span></pre>
        
    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>

    <p>A dataframe containing the following variables.
  <dl class='dl-horizontal'>
    <dt><code>name</code></dt><dd>the name of the compound observed. Note that T245 is used as 
                       an acronym for 2,4,5-T. T245 is a legitimate object name
                       in R, which is necessary for specifying models using
                       <code><a href='mkinmod.html'>mkinmod</a></code>.</dd> 
    <dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after
                       treatment</dd>
    <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd>
    <dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd>
  </dl></p>
    
    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

    <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
  <a href = 'http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p>
    

    <h2 class="hasAnchor" id="examples">
      <a class="anchor" href="#examples"></a>
      Examples
    </h2>
    <pre class="examples"><div class='input'>  <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>),
                         <span class='kw'>phenol</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>),
                         <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'>  <span class='co'>## Not run: ------------------------------------</span>
<span class='co'>#     fit.1 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span>
<span class='co'>#     summary(fit.1, data = FALSE)</span>
<span class='co'>#   </span>
<span class='co'>## ---------------------------------------------</span>
  <span class='co'># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span>
  <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
                 <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
                 <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
  <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version:    0.9.44.9000 
#&gt; R version:       3.3.1 
#&gt; Date of fit:     Wed Oct 26 23:50:40 2016 
#&gt; Date of summary: Wed Oct 26 23:50:40 2016 
#&gt; 
#&gt; Equations:
#&gt; d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
#&gt; d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol -
#&gt;            k_phenol_anisole * phenol
#&gt; d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole
#&gt; 
#&gt; Model predictions using solution type deSolve 
#&gt; 
#&gt; Fitted with method Port using 246 model solutions performed in 1.43 s
#&gt; 
#&gt; Weighting: none
#&gt; 
#&gt; Starting values for parameters to be optimised:
#&gt;                     value   type
#&gt; T245_0           100.9000  state
#&gt; k_T245_sink        0.1000 deparm
#&gt; k_T245_phenol      0.1001 deparm
#&gt; k_phenol_anisole   0.1002 deparm
#&gt; k_anisole_sink     0.1003 deparm
#&gt; 
#&gt; Starting values for the transformed parameters actually optimised:
#&gt;                           value lower upper
#&gt; T245_0               100.900000  -Inf   Inf
#&gt; log_k_T245_sink       -2.302585  -Inf   Inf
#&gt; log_k_T245_phenol     -2.301586  -Inf   Inf
#&gt; log_k_phenol_anisole  -2.300587  -Inf   Inf
#&gt; log_k_anisole_sink    -2.299590  -Inf   Inf
#&gt; 
#&gt; Fixed parameter values:
#&gt;               value   type
#&gt; phenol_0          0  state
#&gt; anisole_0         0  state
#&gt; k_phenol_sink     0 deparm
#&gt; 
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
#&gt;                      Estimate Std. Error  Lower    Upper
#&gt; T245_0               103.9000    2.35200 98.930 108.8000
#&gt; log_k_T245_sink       -4.1130    0.13250 -4.390  -3.8350
#&gt; log_k_T245_phenol     -3.6120    0.05002 -3.716  -3.5070
#&gt; log_k_phenol_anisole  -0.9037    0.30580 -1.544  -0.2637
#&gt; log_k_anisole_sink    -5.0090    0.11180 -5.243  -4.7750
#&gt; 
#&gt; Parameter correlation:
#&gt;                        T245_0 log_k_T245_sink log_k_T245_phenol
#&gt; T245_0                1.00000         0.63761           -0.1742
#&gt; log_k_T245_sink       0.63761         1.00000           -0.3831
#&gt; log_k_T245_phenol    -0.17416        -0.38313            1.0000
#&gt; log_k_phenol_anisole -0.05948         0.08745           -0.3047
#&gt; log_k_anisole_sink   -0.16208        -0.60469            0.5227
#&gt;                      log_k_phenol_anisole log_k_anisole_sink
#&gt; T245_0                           -0.05948            -0.1621
#&gt; log_k_T245_sink                   0.08745            -0.6047
#&gt; log_k_T245_phenol                -0.30470             0.5227
#&gt; log_k_phenol_anisole              1.00000            -0.1774
#&gt; log_k_anisole_sink               -0.17744             1.0000
#&gt; 
#&gt; Residual standard error: 2.706 on 19 degrees of freedom
#&gt; 
#&gt; Backtransformed parameters:
#&gt; Confidence intervals for internally transformed parameters are asymmetric.
#&gt; t-test (unrealistically) based on the assumption of normal distribution
#&gt; for estimators of untransformed parameters.
#&gt;                   Estimate t value    Pr(&gt;t)     Lower     Upper
#&gt; T245_0           1.039e+02  44.160 6.462e-21 98.930000 108.80000
#&gt; k_T245_sink      1.636e-02   7.545 1.978e-07  0.012400   0.02159
#&gt; k_T245_phenol    2.701e-02  19.990 1.607e-14  0.024320   0.02999
#&gt; k_phenol_anisole 4.051e-01   3.270 2.014e-03  0.213600   0.76820
#&gt; k_anisole_sink   6.679e-03   8.942 1.544e-08  0.005285   0.00844
#&gt; 
#&gt; Chi2 error levels in percent:
#&gt;          err.min n.optim df
#&gt; All data   9.831       5 17
#&gt; T245       7.908       3  5
#&gt; phenol    99.808       1  6
#&gt; anisole    5.379       1  6
#&gt; 
#&gt; Resulting formation fractions:
#&gt;                    ff
#&gt; T245_sink      0.3772
#&gt; T245_phenol    0.6228
#&gt; phenol_anisole 1.0000
#&gt; phenol_sink    0.0000
#&gt; anisole_sink   1.0000
#&gt; 
#&gt; Estimated disappearance times:
#&gt;            DT50    DT90
#&gt; T245     15.982  53.091
#&gt; phenol    1.711   5.685
#&gt; anisole 103.784 344.763
#&gt; </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>

Contact - Imprint