aboutsummaryrefslogtreecommitdiff
path: root/inst/web/mccall81_245T.html
blob: f7a454ca92baa043ed8f8db3b65d27c9a7a81a1a (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
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
<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">
<title>mccall81_245T. mkin 0.9-41</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="">

<link href="css/bootstrap.css" rel="stylesheet">
<link href="css/bootstrap-responsive.css" rel="stylesheet">
<link href="css/highlight.css" rel="stylesheet">
<link href="css/staticdocs.css" rel="stylesheet">

<!--[if lt IE 9]>
  <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->

<script type="text/x-mathjax-config">
  MathJax.Hub.Config({
    tex2jax: {
      inlineMath: [ ['$','$'], ["\\(","\\)"] ],
      processEscapes: true
    }
  });
</script>
<script type="text/javascript"
  src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
  </head>

  <body>
    <div class="navbar">
  <div class="navbar-inner">
    <div class="container">
      <a class="brand" href="#">mkin 0.9-41</a>
      <div class="nav">
        <ul class="nav">
          <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
        </ul>
      </div>
    </div>
  </div>
</div>

    <div class="container">
      <header>
        
      </header>
      
      <h1>
  Datasets on aerobic soil metabolism of 2,4,5-T in six soils
</h1>

<div class="row">
  <div class="span8">
    <h2>Usage</h2>
    <pre><div>mccall81_245T</div></pre>
        
    <div class="Description">
      <h2>Description</h2>

      <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>
  
    </div>

    <div class="Format">
      <h2>Format</h2>

      <p>A dataframe containing the following variables.
  <dl>
    <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></p>
  
      <p><dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after
                       treatment</dd></p>
  
      <p><dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd></p>
  
      <p><dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd></p>
  
      <p></dl></p>
  
      <p></p>
  
    </div>

    <div class="Source">
      <h2>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>
  
    </div>
    
    <h2 id="examples">Examples</h2>
    <pre class="examples"><div class='input'>  SFO_SFO_SFO &lt;- mkinmod(T245 = list(type = &quot;SFO&quot;, to = &quot;phenol&quot;),
                         phenol = list(type = &quot;SFO&quot;, to = &quot;anisole&quot;),
                         anisole = list(type = &quot;SFO&quot;))
</div>
<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
<div class='input'>  ## Not run: 
#     fit.1 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == &quot;Commerce&quot;))
#     summary(fit.1, data = FALSE)
#   ## End(Not run)
  # No covariance matrix and k_phenol_sink is really small, therefore fix it to zero
  fit.2 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == &quot;Commerce&quot;),
                 parms.ini = c(k_phenol_sink = 0),
                 fixed_parms = &quot;k_phenol_sink&quot;, quiet = TRUE)
  summary(fit.2, data = FALSE)
</div>
<div class='output'>mkin version:    0.9.41 
R version:       3.2.2 
Date of fit:     Mon Nov  9 09:06:00 2015 
Date of summary: Mon Nov  9 09:06:00 2015 

Equations:
d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol - k_phenol_anisole * phenol
d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole

Model predictions using solution type deSolve 

Fitted with method Port using 246 model solutions performed in 1.372 s

Weighting: none

Starting values for parameters to be optimised:
                    value   type
T245_0           100.9000  state
k_T245_sink        0.1000 deparm
k_T245_phenol      0.1001 deparm
k_phenol_anisole   0.1002 deparm
k_anisole_sink     0.1003 deparm

Starting values for the transformed parameters actually optimised:
                          value lower upper
T245_0               100.900000  -Inf   Inf
log_k_T245_sink       -2.302585  -Inf   Inf
log_k_T245_phenol     -2.301586  -Inf   Inf
log_k_phenol_anisole  -2.300587  -Inf   Inf
log_k_anisole_sink    -2.299590  -Inf   Inf

Fixed parameter values:
              value   type
phenol_0          0  state
anisole_0         0  state
k_phenol_sink     0 deparm

Optimised, transformed parameters with symmetric confidence intervals:
                     Estimate Std. Error  Lower    Upper
T245_0               103.9000    2.35200 98.930 108.8000
log_k_T245_sink       -4.1130    0.13250 -4.390  -3.8350
log_k_T245_phenol     -3.6120    0.05002 -3.716  -3.5070
log_k_phenol_anisole  -0.9037    0.30580 -1.544  -0.2637
log_k_anisole_sink    -5.0090    0.11180 -5.243  -4.7750

Parameter correlation:
                       T245_0 log_k_T245_sink log_k_T245_phenol log_k_phenol_anisole log_k_anisole_sink
T245_0                1.00000         0.63761           -0.1742             -0.05948            -0.1621
log_k_T245_sink       0.63761         1.00000           -0.3831              0.08745            -0.6047
log_k_T245_phenol    -0.17416        -0.38313            1.0000             -0.30470             0.5227
log_k_phenol_anisole -0.05948         0.08745           -0.3047              1.00000            -0.1774
log_k_anisole_sink   -0.16208        -0.60469            0.5227             -0.17744             1.0000

Residual standard error: 2.706 on 19 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(&gt;t)     Lower     Upper
T245_0           1.039e+02  44.160 6.462e-21 98.930000 108.80000
k_T245_sink      1.636e-02   7.545 1.978e-07  0.012400   0.02159
k_T245_phenol    2.701e-02  19.990 1.607e-14  0.024320   0.02999
k_phenol_anisole 4.051e-01   3.270 2.014e-03  0.213600   0.76820
k_anisole_sink   6.679e-03   8.942 1.544e-08  0.005285   0.00844

Chi2 error levels in percent:
         err.min n.optim df
All data   9.831       5 17
T245       7.908       3  5
phenol    99.808       1  6
anisole    5.379       1  6

Resulting formation fractions:
                   ff
T245_sink      0.3772
T245_phenol    0.6228
phenol_anisole 1.0000
phenol_sink    0.0000
anisole_sink   1.0000

Estimated disappearance times:
           DT50    DT90
T245     15.982  53.091
phenol    1.711   5.685
anisole 103.784 344.763
</div></pre>
  </div>
  <div class="span4">
    <!-- <ul>
      <li>mccall81_245T</li>
    </ul>
    <ul>
      <li>datasets</li>
    </ul> -->
      
        
  </div>
</div>
      
      <footer>
      <p class="pull-right"><a href="#">Back to top</a></p>
<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p>
      </footer>
    </div>
  </body>
</html>

Contact - Imprint