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
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
|
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<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 method for class "saem.mmkin" — summary.saem.mmkin • mkin</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<meta property="og:title" content="Summary method for class "saem.mmkin" — summary.saem.mmkin" />
<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters
for fixed effects (population), random effects (deviations from the
population mean) and residual error model, as well as the resulting
endpoints such as formation fractions and DT50 values. Optionally
(default is FALSE), the data are listed in full." />
<meta name="robots" content="noindex">
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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 data-spy="scroll" data-target="#toc">
<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" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
<span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.5</span>
</span>
</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</li>
<li>
<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
<li>
<a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
<span class="fab 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>Summary method for class "saem.mmkin"</h1>
<small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/summary.saem.mmkin.R'><code>R/summary.saem.mmkin.R</code></a></small>
<div class="hidden name"><code>summary.saem.mmkin.Rd</code></div>
</div>
<div class="ref-description">
<p>Lists model equations, initial parameter values, optimised parameters
for fixed effects (population), random effects (deviations from the
population mean) and residual error model, as well as the resulting
endpoints such as formation fractions and DT50 values. Optionally
(default is FALSE), the data are listed in full.</p>
</div>
<pre class="usage"><span class='co'># S3 method for saem.mmkin</span>
<span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='cn'>FALSE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for summary.saem.mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>verbose</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>object</th>
<td><p>an object of class <a href='saem.html'>saem.mmkin</a></p></td>
</tr>
<tr>
<th>data</th>
<td><p>logical, indicating whether the full data should be included in
the summary.</p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>Should the summary be verbose?</p></td>
</tr>
<tr>
<th>distimes</th>
<td><p>logical, indicating whether DT50 and DT90 values should be
included.</p></td>
</tr>
<tr>
<th>...</th>
<td><p>optional arguments passed to methods like <code>print</code>.</p></td>
</tr>
<tr>
<th>x</th>
<td><p>an object of class summary.saem.mmkin</p></td>
</tr>
<tr>
<th>digits</th>
<td><p>Number of digits to use for printing</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The summary function returns a list based on the <a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a>
obtained in the fit, with at least the following additional components</p>
<dt>saemixversion, mkinversion, Rversion</dt><dd><p>The saemix, mkin and R versions used</p></dd>
<dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were
produced</p></dd>
<dt>diffs</dt><dd><p>The differential equations used in the degradation model</p></dd>
<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd>
<dt>data</dt><dd><p>The data</p></dd>
<dt>confint_trans</dt><dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd>
<dt>confint_back</dt><dd><p>Backtransformed parameters, with confidence intervals if available</p></dd>
<dt>confint_errmod</dt><dd><p>Error model parameters with confidence intervals</p></dd>
<dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted
model.</p></dd>
<dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>
The print method is called for its side effect, i.e. printing the summary.
<h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
<p>Johannes Ranke for the mkin specific parts
saemix authors for the parts inherited from saemix.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Generate five datasets following DFOP-SFO kinetics</span>
<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
<span class='va'>dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>1234</span><span class='op'>)</span>
<span class='va'>k1_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.1</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span>
<span class='va'>k2_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.02</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span>
<span class='va'>g_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>qlogis</a></span><span class='op'>(</span><span class='fl'>0.5</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>f_parent_to_m1_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/stats/Normal.html'>rnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/stats/Logistic.html'>qlogis</a></span><span class='op'>(</span><span class='fl'>0.3</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>k_m1_in</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/Lognormal.html'>rlnorm</a></span><span class='op'>(</span><span class='fl'>5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0.02</span><span class='op'>)</span>, <span class='fl'>0.3</span><span class='op'>)</span>
<span class='va'>pred_dfop_sfo</span> <span class='op'><-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>g</span>, <span class='va'>f_parent_to_m1</span>, <span class='va'>k_m1</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>,
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='va'>k1</span>, k2 <span class='op'>=</span> <span class='va'>k2</span>, g <span class='op'>=</span> <span class='va'>g</span>, f_parent_to_m1 <span class='op'>=</span> <span class='va'>f_parent_to_m1</span>, k_m1 <span class='op'>=</span> <span class='va'>k_m1</span><span class='op'>)</span>,
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
<span class='va'>sampling_times</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='va'>ds_mean_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>,
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='va'>k1_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>, k2 <span class='op'>=</span> <span class='va'>k2_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>, g <span class='op'>=</span> <span class='va'>g_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>,
f_parent_to_m1 <span class='op'>=</span> <span class='va'>f_parent_to_m1_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>, k_m1 <span class='op'>=</span> <span class='va'>k_m1_in</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span><span class='op'>)</span>,
<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, m1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
<span class='va'>sampling_times</span><span class='op'>)</span>
<span class='op'>}</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds_mean_dfop_sfo</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"ds"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>)</span>
<span class='va'>ds_syn_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>ds_mean_dfop_sfo</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>{</span>
<span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>ds</span>,
sdfunc <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='fl'>0.07</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span>,
n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>
<span class='op'>}</span><span class='op'>)</span>
<span class='co'># \dontrun{</span>
<span class='co'># Evaluate using mmkin and saem</span>
<span class='va'>f_mmkin_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_syn_dfop_sfo</span>,
quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span>
<span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#> Running main SAEM algorithm
#> [1] "Fri Jun 11 10:58:28 2021"
#> ....
#> Minimisation finished
#> [1] "Fri Jun 11 10:58:40 2021"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#> saemix version used for fitting: 3.1.9000
#> mkin version used for pre-fitting: 1.0.5
#> R version used for fitting: 4.1.0
#> Date of fit: Fri Jun 11 10:58:41 2021
#> Date of summary: Fri Jun 11 10:58:41 2021
#>
#> Equations:
#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
#> * parent
#> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
#> exp(-k2 * time))) * parent - k_m1 * m1
#>
#> Data:
#> 171 observations of 2 variable(s) grouped in 5 datasets
#>
#> Model predictions using solution type analytical
#>
#> Fitted in 12.75 s using 300, 100 iterations
#>
#> Variance model: Two-component variance function
#>
#> Mean of starting values for individual parameters:
#> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2
#> 101.65645 -4.05368 -0.94311 -2.35943 -4.07006
#> g_qlogis
#> -0.01132
#>
#> Fixed degradation parameter values:
#> None
#>
#> Results:
#>
#> Likelihood computed by importance sampling
#> AIC BIC logLik
#> 825.9 820.4 -398.9
#>
#> Optimised parameters:
#> est. lower upper
#> parent_0 101.118986 97.368 104.8695
#> log_k_m1 -4.057591 -4.177 -3.9379
#> f_parent_qlogis -0.933087 -1.290 -0.5763
#> log_k1 -2.945520 -3.833 -2.0576
#> log_k2 -3.531954 -4.310 -2.7542
#> g_qlogis -0.009584 -1.688 1.6687
#>
#> Correlation:
#> prnt_0 lg_k_1 f_prn_ log_k1 log_k2
#> log_k_m1 -0.198
#> f_parent_qlogis -0.153 0.184
#> log_k1 0.080 -0.077 -0.045
#> log_k2 0.005 0.008 -0.003 -0.019
#> g_qlogis -0.059 0.048 0.041 -0.334 -0.253
#>
#> Random effects:
#> est. lower upper
#> SD.parent_0 2.97797 -0.62927 6.5852
#> SD.log_k_m1 0.09235 -0.02448 0.2092
#> SD.f_parent_qlogis 0.38712 0.13469 0.6396
#> SD.log_k1 0.88671 0.27052 1.5029
#> SD.log_k2 0.80497 0.25587 1.3541
#> SD.g_qlogis 0.36812 -3.56188 4.2981
#>
#> Variance model:
#> est. lower upper
#> a.1 0.85879 0.68143 1.03615
#> b.1 0.07787 0.06288 0.09286
#>
#> Backtransformed parameters:
#> est. lower upper
#> parent_0 101.11899 97.36850 104.86947
#> k_m1 0.01729 0.01534 0.01949
#> f_parent_to_m1 0.28230 0.21587 0.35979
#> k1 0.05257 0.02163 0.12776
#> k2 0.02925 0.01344 0.06366
#> g 0.49760 0.15606 0.84140
#>
#> Resulting formation fractions:
#> ff
#> parent_m1 0.2823
#> parent_sink 0.7177
#>
#> Estimated disappearance times:
#> DT50 DT90 DT50back DT50_k1 DT50_k2
#> parent 17.47 62.31 18.76 13.18 23.7
#> m1 40.09 133.17 NA NA NA
#>
#> Data:
#> ds name time observed predicted residual std standardized
#> ds 1 parent 0 89.8 9.838e+01 -8.584661 7.7094 -1.113536
#> ds 1 parent 0 104.1 9.838e+01 5.715339 7.7094 0.741350
#> ds 1 parent 1 88.7 9.388e+01 -5.182489 7.3611 -0.704041
#> ds 1 parent 1 95.5 9.388e+01 1.617511 7.3611 0.219739
#> ds 1 parent 3 81.8 8.563e+01 -3.825382 6.7229 -0.569010
#> ds 1 parent 3 94.5 8.563e+01 8.874618 6.7229 1.320062
#> ds 1 parent 7 71.5 7.169e+01 -0.188290 5.6482 -0.033336
#> ds 1 parent 7 70.3 7.169e+01 -1.388290 5.6482 -0.245795
#> ds 1 parent 14 54.2 5.361e+01 0.586595 4.2624 0.137621
#> ds 1 parent 14 49.6 5.361e+01 -4.013405 4.2624 -0.941587
#> ds 1 parent 28 31.5 3.219e+01 -0.688936 2.6496 -0.260011
#> ds 1 parent 28 28.8 3.219e+01 -3.388936 2.6496 -1.279016
#> ds 1 parent 60 12.1 1.278e+01 -0.678998 1.3145 -0.516562
#> ds 1 parent 60 13.6 1.278e+01 0.821002 1.3145 0.624595
#> ds 1 parent 90 6.2 6.157e+00 0.043461 0.9835 0.044188
#> ds 1 parent 90 8.3 6.157e+00 2.143461 0.9835 2.179316
#> ds 1 parent 120 2.2 3.076e+00 -0.876218 0.8916 -0.982775
#> ds 1 parent 120 2.4 3.076e+00 -0.676218 0.8916 -0.758453
#> ds 1 m1 1 0.3 1.134e+00 -0.833749 0.8633 -0.965750
#> ds 1 m1 1 0.2 1.134e+00 -0.933749 0.8633 -1.081583
#> ds 1 m1 3 2.2 3.157e+00 -0.957400 0.8933 -1.071763
#> ds 1 m1 3 3.0 3.157e+00 -0.157400 0.8933 -0.176202
#> ds 1 m1 7 6.5 6.369e+00 0.130995 0.9917 0.132090
#> ds 1 m1 7 5.0 6.369e+00 -1.369005 0.9917 -1.380438
#> ds 1 m1 14 10.2 9.971e+00 0.229362 1.1577 0.198112
#> ds 1 m1 14 9.5 9.971e+00 -0.470638 1.1577 -0.406513
#> ds 1 m1 28 12.2 1.265e+01 -0.447735 1.3067 -0.342637
#> ds 1 m1 28 13.4 1.265e+01 0.752265 1.3067 0.575683
#> ds 1 m1 60 11.8 1.097e+01 0.832027 1.2112 0.686945
#> ds 1 m1 60 13.2 1.097e+01 2.232027 1.2112 1.842825
#> ds 1 m1 90 6.6 7.876e+00 -1.275985 1.0553 -1.209109
#> ds 1 m1 90 9.3 7.876e+00 1.424015 1.0553 1.349381
#> ds 1 m1 120 3.5 5.336e+00 -1.835829 0.9540 -1.924292
#> ds 1 m1 120 5.4 5.336e+00 0.064171 0.9540 0.067263
#> ds 2 parent 0 118.0 1.092e+02 8.812058 8.5459 1.031142
#> ds 2 parent 0 99.8 1.092e+02 -9.387942 8.5459 -1.098529
#> ds 2 parent 1 90.2 1.023e+02 -12.114268 8.0135 -1.511724
#> ds 2 parent 1 94.6 1.023e+02 -7.714268 8.0135 -0.962654
#> ds 2 parent 3 96.1 9.066e+01 5.436165 7.1122 0.764344
#> ds 2 parent 3 78.4 9.066e+01 -12.263835 7.1122 -1.724339
#> ds 2 parent 7 77.9 7.365e+01 4.245773 5.7995 0.732090
#> ds 2 parent 7 77.7 7.365e+01 4.045773 5.7995 0.697604
#> ds 2 parent 14 56.0 5.593e+01 0.073803 4.4389 0.016626
#> ds 2 parent 14 54.7 5.593e+01 -1.226197 4.4389 -0.276236
#> ds 2 parent 28 36.6 3.892e+01 -2.320837 3.1502 -0.736737
#> ds 2 parent 28 36.8 3.892e+01 -2.120837 3.1502 -0.673248
#> ds 2 parent 60 22.1 2.136e+01 0.741020 1.8719 0.395868
#> ds 2 parent 60 24.7 2.136e+01 3.341020 1.8719 1.784841
#> ds 2 parent 90 12.4 1.251e+01 -0.113999 1.2989 -0.087765
#> ds 2 parent 90 10.8 1.251e+01 -1.713999 1.2989 -1.319575
#> ds 2 parent 120 6.8 7.338e+00 -0.537708 1.0315 -0.521281
#> ds 2 parent 120 7.9 7.338e+00 0.562292 1.0315 0.545113
#> ds 2 m1 1 1.3 1.576e+00 -0.276176 0.8675 -0.318352
#> ds 2 m1 3 3.7 4.177e+00 -0.476741 0.9183 -0.519146
#> ds 2 m1 3 4.7 4.177e+00 0.523259 0.9183 0.569801
#> ds 2 m1 7 8.1 7.724e+00 0.376365 1.0485 0.358970
#> ds 2 m1 7 7.9 7.724e+00 0.176365 1.0485 0.168214
#> ds 2 m1 14 10.1 1.077e+01 -0.674433 1.2006 -0.561738
#> ds 2 m1 14 10.3 1.077e+01 -0.474433 1.2006 -0.395158
#> ds 2 m1 28 10.7 1.212e+01 -1.416179 1.2758 -1.110010
#> ds 2 m1 28 12.2 1.212e+01 0.083821 1.2758 0.065699
#> ds 2 m1 60 10.7 1.041e+01 0.294930 1.1807 0.249793
#> ds 2 m1 60 12.5 1.041e+01 2.094930 1.1807 1.774316
#> ds 2 m1 90 9.1 8.079e+00 1.020859 1.0646 0.958929
#> ds 2 m1 90 7.4 8.079e+00 -0.679141 1.0646 -0.637941
#> ds 2 m1 120 6.1 5.968e+00 0.131673 0.9765 0.134843
#> ds 2 m1 120 4.5 5.968e+00 -1.468327 0.9765 -1.503683
#> ds 3 parent 0 106.2 1.036e+02 2.638248 8.1101 0.325303
#> ds 3 parent 0 106.9 1.036e+02 3.338248 8.1101 0.411614
#> ds 3 parent 1 107.4 9.580e+01 11.600063 7.5094 1.544743
#> ds 3 parent 1 96.1 9.580e+01 0.300063 7.5094 0.039958
#> ds 3 parent 3 79.4 8.297e+01 -3.574516 6.5182 -0.548391
#> ds 3 parent 3 82.6 8.297e+01 -0.374516 6.5182 -0.057457
#> ds 3 parent 7 63.9 6.517e+01 -1.272397 5.1472 -0.247200
#> ds 3 parent 7 62.4 6.517e+01 -2.772397 5.1472 -0.538618
#> ds 3 parent 14 51.0 4.821e+01 2.790075 3.8512 0.724475
#> ds 3 parent 14 47.1 4.821e+01 -1.109925 3.8512 -0.288205
#> ds 3 parent 28 36.1 3.385e+01 2.250573 2.7723 0.811811
#> ds 3 parent 28 36.6 3.385e+01 2.750573 2.7723 0.992168
#> ds 3 parent 60 20.1 1.964e+01 0.455700 1.7543 0.259760
#> ds 3 parent 60 19.8 1.964e+01 0.155700 1.7543 0.088753
#> ds 3 parent 90 11.3 1.210e+01 -0.795458 1.2746 -0.624068
#> ds 3 parent 90 10.7 1.210e+01 -1.395458 1.2746 -1.094792
#> ds 3 parent 120 8.2 7.451e+00 0.749141 1.0364 0.722816
#> ds 3 parent 120 7.3 7.451e+00 -0.150859 1.0364 -0.145558
#> ds 3 m1 0 0.8 3.695e-13 0.800000 0.8588 0.931542
#> ds 3 m1 1 1.8 1.740e+00 0.059741 0.8694 0.068714
#> ds 3 m1 1 2.3 1.740e+00 0.559741 0.8694 0.643812
#> ds 3 m1 3 4.2 4.531e+00 -0.331379 0.9285 -0.356913
#> ds 3 m1 3 4.1 4.531e+00 -0.431379 0.9285 -0.464618
#> ds 3 m1 7 6.8 8.113e+00 -1.312762 1.0661 -1.231333
#> ds 3 m1 7 10.1 8.113e+00 1.987238 1.0661 1.863971
#> ds 3 m1 14 11.4 1.079e+01 0.613266 1.2013 0.510507
#> ds 3 m1 14 12.8 1.079e+01 2.013266 1.2013 1.675923
#> ds 3 m1 28 11.5 1.133e+01 0.174252 1.2310 0.141553
#> ds 3 m1 28 10.6 1.133e+01 -0.725748 1.2310 -0.589558
#> ds 3 m1 60 7.5 8.948e+00 -1.448281 1.1059 -1.309561
#> ds 3 m1 60 8.6 8.948e+00 -0.348281 1.1059 -0.314922
#> ds 3 m1 90 7.3 6.665e+00 0.634932 1.0034 0.632752
#> ds 3 m1 90 8.1 6.665e+00 1.434932 1.0034 1.430004
#> ds 3 m1 120 5.3 4.795e+00 0.504936 0.9365 0.539199
#> ds 3 m1 120 3.8 4.795e+00 -0.995064 0.9365 -1.062586
#> ds 4 parent 0 104.7 9.985e+01 4.850494 7.8227 0.620050
#> ds 4 parent 0 88.3 9.985e+01 -11.549506 7.8227 -1.476402
#> ds 4 parent 1 94.2 9.676e+01 -2.556304 7.5834 -0.337093
#> ds 4 parent 1 94.6 9.676e+01 -2.156304 7.5834 -0.284346
#> ds 4 parent 3 78.1 9.092e+01 -12.817485 7.1318 -1.797230
#> ds 4 parent 3 96.5 9.092e+01 5.582515 7.1318 0.782764
#> ds 4 parent 7 76.2 8.050e+01 -4.297338 6.3270 -0.679204
#> ds 4 parent 7 77.8 8.050e+01 -2.697338 6.3270 -0.426320
#> ds 4 parent 14 70.8 6.562e+01 5.179989 5.1816 0.999687
#> ds 4 parent 14 67.3 6.562e+01 1.679989 5.1816 0.324222
#> ds 4 parent 28 43.1 4.499e+01 -1.886936 3.6069 -0.523140
#> ds 4 parent 28 45.1 4.499e+01 0.113064 3.6069 0.031346
#> ds 4 parent 60 21.3 2.151e+01 -0.214840 1.8827 -0.114114
#> ds 4 parent 60 23.5 2.151e+01 1.985160 1.8827 1.054433
#> ds 4 parent 90 11.8 1.190e+01 -0.098528 1.2633 -0.077990
#> ds 4 parent 90 12.1 1.190e+01 0.201472 1.2633 0.159475
#> ds 4 parent 120 7.0 6.886e+00 0.113832 1.0125 0.112431
#> ds 4 parent 120 6.2 6.886e+00 -0.686168 1.0125 -0.677724
#> ds 4 m1 0 1.6 4.263e-14 1.600000 0.8588 1.863085
#> ds 4 m1 1 0.9 7.140e-01 0.185984 0.8606 0.216112
#> ds 4 m1 3 3.7 2.022e+00 1.678243 0.8731 1.922160
#> ds 4 m1 3 2.0 2.022e+00 -0.021757 0.8731 -0.024919
#> ds 4 m1 7 3.6 4.207e+00 -0.607229 0.9192 -0.660633
#> ds 4 m1 7 3.8 4.207e+00 -0.407229 0.9192 -0.443044
#> ds 4 m1 14 7.1 6.912e+00 0.188339 1.0135 0.185828
#> ds 4 m1 14 6.6 6.912e+00 -0.311661 1.0135 -0.307506
#> ds 4 m1 28 9.5 9.449e+00 0.050714 1.1309 0.044843
#> ds 4 m1 28 9.3 9.449e+00 -0.149286 1.1309 -0.132004
#> ds 4 m1 60 8.3 8.997e+00 -0.697403 1.1083 -0.629230
#> ds 4 m1 60 9.0 8.997e+00 0.002597 1.1083 0.002343
#> ds 4 m1 90 6.6 6.697e+00 -0.096928 1.0047 -0.096472
#> ds 4 m1 90 7.7 6.697e+00 1.003072 1.0047 0.998348
#> ds 4 m1 120 3.7 4.622e+00 -0.921607 0.9312 -0.989749
#> ds 4 m1 120 3.5 4.622e+00 -1.121607 0.9312 -1.204537
#> ds 5 parent 0 110.4 1.045e+02 5.942426 8.1795 0.726502
#> ds 5 parent 0 112.1 1.045e+02 7.642426 8.1795 0.934338
#> ds 5 parent 1 93.5 9.739e+01 -3.893915 7.6327 -0.510162
#> ds 5 parent 1 91.0 9.739e+01 -6.393915 7.6327 -0.837700
#> ds 5 parent 3 71.0 8.519e+01 -14.188275 6.6891 -2.121098
#> ds 5 parent 3 89.7 8.519e+01 4.511725 6.6891 0.674487
#> ds 5 parent 7 60.4 6.684e+01 -6.439546 5.2753 -1.220701
#> ds 5 parent 7 59.1 6.684e+01 -7.739546 5.2753 -1.467133
#> ds 5 parent 14 56.5 4.736e+01 9.138979 3.7868 2.413407
#> ds 5 parent 14 47.0 4.736e+01 -0.361021 3.7868 -0.095338
#> ds 5 parent 28 30.2 3.033e+01 -0.131178 2.5132 -0.052195
#> ds 5 parent 28 23.9 3.033e+01 -6.431178 2.5132 -2.558936
#> ds 5 parent 60 17.0 1.771e+01 -0.705246 1.6243 -0.434177
#> ds 5 parent 60 18.7 1.771e+01 0.994754 1.6243 0.612409
#> ds 5 parent 90 11.3 1.180e+01 -0.504856 1.2580 -0.401315
#> ds 5 parent 90 11.9 1.180e+01 0.095144 1.2580 0.075631
#> ds 5 parent 120 9.0 7.917e+00 1.083499 1.0571 1.024928
#> ds 5 parent 120 8.1 7.917e+00 0.183499 1.0571 0.173579
#> ds 5 m1 0 0.7 3.553e-15 0.700000 0.8588 0.815100
#> ds 5 m1 1 3.0 3.204e+00 -0.204414 0.8943 -0.228572
#> ds 5 m1 1 2.6 3.204e+00 -0.604414 0.8943 -0.675845
#> ds 5 m1 3 5.1 8.586e+00 -3.485889 1.0884 -3.202858
#> ds 5 m1 3 7.5 8.586e+00 -1.085889 1.0884 -0.997722
#> ds 5 m1 7 16.5 1.612e+01 0.376855 1.5211 0.247743
#> ds 5 m1 7 19.0 1.612e+01 2.876855 1.5211 1.891237
#> ds 5 m1 14 22.9 2.267e+01 0.228264 1.9633 0.116267
#> ds 5 m1 14 23.2 2.267e+01 0.528264 1.9633 0.269072
#> ds 5 m1 28 22.2 2.468e+01 -2.480178 2.1050 -1.178211
#> ds 5 m1 28 24.4 2.468e+01 -0.280178 2.1050 -0.133099
#> ds 5 m1 60 15.5 1.860e+01 -3.099615 1.6838 -1.840794
#> ds 5 m1 60 19.8 1.860e+01 1.200385 1.6838 0.712883
#> ds 5 m1 90 14.9 1.326e+01 1.636345 1.3433 1.218195
#> ds 5 m1 90 14.2 1.326e+01 0.936345 1.3433 0.697072
#> ds 5 m1 120 10.9 9.348e+00 1.551535 1.1258 1.378133
#> ds 5 m1 120 10.4 9.348e+00 1.051535 1.1258 0.934014</div><div class='input'><span class='co'># }</span>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
</div>
</body>
</html>
|
