aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/synthetic_data_for_UBA.html
blob: bc2bb02b8589596d043b9f73a3832be50c464647 (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
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
<!-- 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>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • 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">Functions and data</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
    Articles
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/mkin.html">Introduction to mkin</a>
    </li>
    <li>
      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
    </li>
    <li>
      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
    </li>
    <li>
      <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
    </li>
  </ul>
</li>
      </ul>
      
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="http://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="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Synthetic datasets for one parent compound with two metabolites</h1>
    </div>

    
    <p>The 12 datasets were generated using four different models and three different
 variance components. The four models are either the SFO or the DFOP model with either
 two sequential or two parallel metabolites.</p>

    <p>Variance component &#39;a&#39; is based on a normal distribution with standard deviation of 3,
 Variance component &#39;b&#39; is also based on a normal distribution, but with a standard deviation of 7.
 Variance component &#39;c&#39; is based on the error model from Rocke and Lorenzato (1995), with the 
 minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07
 for the increase of the standard deviation with y.</p>

    <p>Initial concentrations for metabolites and all values where adding the variance component resulted
 in a value below the assumed limit of detection of 0.1 were set to <code>NA</code>.</p>

    <p>As an example, the first dataset has the title <code>SFO_lin_a</code> and is based on the SFO model
 with two sequential metabolites (linear pathway), with added variance component &#39;a&#39;.</p>

    <p>Compare also the code in the example section to see the degradation models.</p>
    

    <pre><span class='no'>synthetic_data_for_UBA_2014</span></pre>
        
    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>

    <p>A list containing datasets in the form internally used by the &#39;gmkin&#39; package.
  The list has twelfe components. Each of the components is one dataset that has,
  among others, the following components
  <dl class='dl-horizontal'>
    <dt><code>title</code></dt><dd>The name of the dataset, e.g. <code>SFO_lin_a</code></dd>
    <dt><code>data</code></dt><dd>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></dd>
  </dl></p>
    
    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

    <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
  zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p>
    <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for
  measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p>
    

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'>
<span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
                           <span class='kw'>M1</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'>"M2"</span>),
                           <span class='kw'>M2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>

<span class='no'>m_synth_SFO_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>),
                                         <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
                           <span class='kw'>M1</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'>M2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>m_synth_DFOP_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
                            <span class='kw'>M1</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'>"M2"</span>),
                            <span class='kw'>M2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>m_synth_DFOP_par</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>),
                                          <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
                            <span class='kw'>M1</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'>M2</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'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><img src='synthetic_data_for_UBA_2014-10.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version:    0.9.44.9000 
#&gt; R version:       3.3.2 
#&gt; Date of fit:     Thu Dec  8 07:57:58 2016 
#&gt; Date of summary: Thu Dec  8 07:57:58 2016 
#&gt; 
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
#&gt; d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
#&gt; d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2
#&gt; 
#&gt; Model predictions using solution type deSolve 
#&gt; 
#&gt; Fitted with method Port using 351 model solutions performed in 2.152 s
#&gt; 
#&gt; Weighting: none
#&gt; 
#&gt; Starting values for parameters to be optimised:
#&gt;                   value   type
#&gt; parent_0       101.3500  state
#&gt; k_parent         0.1000 deparm
#&gt; k_M1             0.1001 deparm
#&gt; k_M2             0.1002 deparm
#&gt; f_parent_to_M1   0.5000 deparm
#&gt; f_M1_to_M2       0.5000 deparm
#&gt; 
#&gt; Starting values for the transformed parameters actually optimised:
#&gt;                     value lower upper
#&gt; parent_0       101.350000  -Inf   Inf
#&gt; log_k_parent    -2.302585  -Inf   Inf
#&gt; log_k_M1        -2.301586  -Inf   Inf
#&gt; log_k_M2        -2.300587  -Inf   Inf
#&gt; f_parent_ilr_1   0.000000  -Inf   Inf
#&gt; f_M1_ilr_1       0.000000  -Inf   Inf
#&gt; 
#&gt; Fixed parameter values:
#&gt;      value  type
#&gt; M1_0     0 state
#&gt; M2_0     0 state
#&gt; 
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
#&gt;                Estimate Std. Error   Lower    Upper
#&gt; parent_0       102.1000    1.71400 98.5800 105.5000
#&gt; log_k_parent    -0.3020    0.04294 -0.3894  -0.2147
#&gt; log_k_M1        -1.2070    0.07599 -1.3610  -1.0520
#&gt; log_k_M2        -3.9010    0.06952 -4.0420  -3.7590
#&gt; f_parent_ilr_1   0.8492    0.18090  0.4812   1.2170
#&gt; f_M1_ilr_1       0.6780    0.18860  0.2943   1.0620
#&gt; 
#&gt; Parameter correlation:
#&gt;                parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1
#&gt; parent_0        1.00000      0.40213  -0.1693  0.02912        -0.4726
#&gt; log_k_parent    0.40213      1.00000  -0.4210  0.07241        -0.5837
#&gt; log_k_M1       -0.16931     -0.42102   1.0000 -0.37657         0.7438
#&gt; log_k_M2        0.02912      0.07241  -0.3766  1.00000        -0.2518
#&gt; f_parent_ilr_1 -0.47263     -0.58367   0.7438 -0.25177         1.0000
#&gt; f_M1_ilr_1      0.17148      0.42642  -0.8054  0.52648        -0.8602
#&gt;                f_M1_ilr_1
#&gt; parent_0           0.1715
#&gt; log_k_parent       0.4264
#&gt; log_k_M1          -0.8054
#&gt; log_k_M2           0.5265
#&gt; f_parent_ilr_1    -0.8602
#&gt; f_M1_ilr_1         1.0000
#&gt; 
#&gt; Residual standard error: 2.471 on 33 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; parent_0       102.10000   59.55 1.815e-35 98.58000 105.5000
#&gt; k_parent         0.73930   23.29 2.337e-22  0.67750   0.8068
#&gt; k_M1             0.29920   13.16 5.552e-15  0.25630   0.3492
#&gt; k_M2             0.02023   14.38 4.497e-16  0.01756   0.0233
#&gt; f_parent_to_M1   0.76870   16.90 4.093e-18  0.66380   0.8483
#&gt; f_M1_to_M2       0.72290   13.53 2.557e-15  0.60260   0.8178
#&gt; 
#&gt; Chi2 error levels in percent:
#&gt;          err.min n.optim df
#&gt; All data   8.454       6 17
#&gt; parent     8.660       2  6
#&gt; M1        10.583       2  5
#&gt; M2         3.586       2  6
#&gt; 
#&gt; Resulting formation fractions:
#&gt;                 ff
#&gt; parent_M1   0.7687
#&gt; parent_sink 0.2313
#&gt; M1_M2       0.7229
#&gt; M1_sink     0.2771
#&gt; 
#&gt; Estimated disappearance times:
#&gt;           DT50    DT90
#&gt; parent  0.9376   3.114
#&gt; M1      2.3170   7.697
#&gt; M2     34.2689 113.839
#&gt; 
#&gt; Data:
#&gt;  time variable observed  predicted residual
#&gt;     0   parent    101.5  1.021e+02 -0.56248
#&gt;     0   parent    101.2  1.021e+02 -0.86248
#&gt;     1   parent     53.9  4.873e+01  5.17119
#&gt;     1   parent     47.5  4.873e+01 -1.22881
#&gt;     3   parent     10.4  1.111e+01 -0.70773
#&gt;     3   parent      7.6  1.111e+01 -3.50773
#&gt;     7   parent      1.1  5.772e-01  0.52283
#&gt;     7   parent      0.3  5.772e-01 -0.27717
#&gt;    14   parent       NA  3.264e-03       NA
#&gt;    14   parent      3.5  3.264e-03  3.49674
#&gt;    28   parent       NA  1.045e-07       NA
#&gt;    28   parent      3.2  1.045e-07  3.20000
#&gt;    60   parent       NA -1.054e-10       NA
#&gt;    60   parent       NA -1.054e-10       NA
#&gt;    90   parent      0.6 -1.875e-11  0.60000
#&gt;    90   parent       NA -1.875e-11       NA
#&gt;   120   parent       NA -2.805e-11       NA
#&gt;   120   parent      3.5 -2.805e-11  3.50000
#&gt;     0       M1       NA  0.000e+00       NA
#&gt;     0       M1       NA  0.000e+00       NA
#&gt;     1       M1     36.4  3.479e+01  1.61089
#&gt;     1       M1     37.4  3.479e+01  2.61089
#&gt;     3       M1     34.3  3.937e+01 -5.07027
#&gt;     3       M1     39.8  3.937e+01  0.42973
#&gt;     7       M1     15.1  1.549e+01 -0.38714
#&gt;     7       M1     17.8  1.549e+01  2.31286
#&gt;    14       M1      5.8  1.995e+00  3.80469
#&gt;    14       M1      1.2  1.995e+00 -0.79531
#&gt;    28       M1       NA  3.034e-02       NA
#&gt;    28       M1       NA  3.034e-02       NA
#&gt;    60       M1      0.5  2.111e-06  0.50000
#&gt;    60       M1       NA  2.111e-06       NA
#&gt;    90       M1       NA  2.913e-10       NA
#&gt;    90       M1      3.2  2.913e-10  3.20000
#&gt;   120       M1      1.5  3.625e-11  1.50000
#&gt;   120       M1      0.6  3.625e-11  0.60000
#&gt;     0       M2       NA  0.000e+00       NA
#&gt;     0       M2       NA  0.000e+00       NA
#&gt;     1       M2       NA  4.455e+00       NA
#&gt;     1       M2      4.8  4.455e+00  0.34517
#&gt;     3       M2     20.9  2.153e+01 -0.62527
#&gt;     3       M2     19.3  2.153e+01 -2.22527
#&gt;     7       M2     42.0  4.192e+01  0.07942
#&gt;     7       M2     43.1  4.192e+01  1.17942
#&gt;    14       M2     49.4  4.557e+01  3.83354
#&gt;    14       M2     44.3  4.557e+01 -1.26646
#&gt;    28       M2     34.6  3.547e+01 -0.87275
#&gt;    28       M2     33.0  3.547e+01 -2.47275
#&gt;    60       M2     18.8  1.858e+01  0.21837
#&gt;    60       M2     17.6  1.858e+01 -0.98163
#&gt;    90       M2     10.6  1.013e+01  0.47131
#&gt;    90       M2     10.8  1.013e+01  0.67131
#&gt;   120       M2      9.8  5.521e+00  4.27893
#&gt;   120       M2      3.3  5.521e+00 -2.22107</div><div class='input'>
</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.</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