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
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
|
<!-- 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>Subsetting method for mmkin objects — [.mmkin • 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">
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" />
<meta property="og:description" content="Subsetting method for mmkin objects." />
<meta name="twitter:card" content="summary" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</li>
<li>
<a href="../articles/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>
</ul>
</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>Subsetting method for mmkin objects</h1>
</div>
<p>Subsetting method for mmkin objects.</p>
<pre class="usage"># S3 method for mmkin
[(x, i, j, ..., drop = FALSE)</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>x</th>
<td><p>An <code><a href='mmkin.html'>mmkin</a> object</code></p></td>
</tr>
<tr>
<th>i</th>
<td><p>Row index selecting the fits for specific models</p></td>
</tr>
<tr>
<th>j</th>
<td><p>Column index selecting the fits to specific datasets</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Not used, only there to satisfy the generic method definition</p></td>
</tr>
<tr>
<th>drop</th>
<td><p>If FALSE, the method always returns an mmkin object, otherwise either
a list of mkinfit objects or a single mkinfit object.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='co'># Only use one core, to pass R CMD check --as-cran</span>
<span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'>list</span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>),
<span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#> dataset
#> model B C
#> FOMC List,45 List,45
#> attr(,"class")
#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset
#> model B
#> SFO List,45
#> FOMC List,45
#> attr(,"class")
#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset
#> model B
#> SFO List,45
#> attr(,"class")
#> [1] "mmkin"</div><div class='input'>
<span class='fu'>head</span>(
<span class='co'># This extracts an mkinfit object with lots of components</span>
<span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]]
)</div><div class='output co'>#> $par
#> parent_0 log_alpha log_beta
#> 99.666193 2.549849 5.050586
#>
#> $ssr
#> [1] 28.58291
#>
#> $convergence
#> [1] 0
#>
#> $iterations
#> [1] 21
#>
#> $evaluations
#> function gradient
#> 25 78
#>
#> $counts
#> [1] "relative convergence (4)"
#> </div><div class='input'>
<span class='fu'>head</span>(
<span class='co'># The same can be achieved by</span>
<span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]
)</div><div class='output co'>#> [[1]]
#> $par
#> parent_0 log_k_parent_sink
#> 99.174072 -2.549028
#>
#> $ssr
#> [1] 30.65564
#>
#> $convergence
#> [1] 0
#>
#> $iterations
#> [1] 5
#>
#> $evaluations
#> function gradient
#> 8 15
#>
#> $counts
#> [1] "relative convergence (4)"
#>
#> $hessian
#> parent_0 log_k_parent_sink
#> parent_0 4.163631 -94.09343
#> log_k_parent_sink -94.093431 6311.34610
#>
#> $residuals
#> parent parent parent parent parent parent
#> 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730
#> parent parent
#> -0.24260405 -0.07020339
#>
#> $ms
#> [1] 3.831956
#>
#> $var_ms
#> parent
#> 3.831956
#>
#> $var_ms_unscaled
#> parent
#> 3.831956
#>
#> $var_ms_unweighted
#> parent
#> 3.831956
#>
#> $rank
#> [1] 2
#>
#> $df.residual
#> [1] 6
#>
#> $solution_type
#> [1] "analytical"
#>
#> $transform_rates
#> [1] TRUE
#>
#> $transform_fractions
#> [1] TRUE
#>
#> $method.modFit
#> [1] "Port"
#>
#> $maxit.modFit
#> [1] "auto"
#>
#> $calls
#> [1] 29
#>
#> $time
#> user system elapsed
#> 0.242 0.000 0.244
#>
#> $mkinmod
#> <mkinmod> model generated with
#> Use of formation fractions $use_of_ff: min
#> Specification $spec:
#> $parent
#> $type: SFO; $sink: TRUE
#> Coefficient matrix $coefmat available
#> Differential equations:
#> d_parent/dt = - k_parent_sink * parent
#>
#> $observed
#> name time value
#> 1 parent 0 98.62
#> 2 parent 3 81.43
#> 3 parent 7 53.18
#> 4 parent 14 34.89
#> 5 parent 30 10.09
#> 6 parent 62 1.50
#> 7 parent 90 0.33
#> 8 parent 118 0.08
#>
#> $obs_vars
#> [1] "parent"
#>
#> $predicted
#> name time value
#> 1 parent 0.000000 99.17407218
#> 2 parent 1.191919 90.35253561
#> 3 parent 2.383838 82.31567498
#> 4 parent 3.000000 78.44547872
#> 5 parent 3.575758 74.99369333
#> 6 parent 4.767677 68.32300215
#> 7 parent 5.959596 62.24566915
#> 8 parent 7.000000 57.38445742
#> 9 parent 7.151515 56.70891509
#> 10 parent 8.343434 51.66465547
#> 11 parent 9.535354 47.06908288
#> 12 parent 10.727273 42.88228661
#> 13 parent 11.919192 39.06790599
#> 14 parent 13.111111 35.59281463
#> 15 parent 14.000000 33.20400061
#> 16 parent 14.303030 32.42683275
#> 17 parent 15.494949 29.54246504
#> 18 parent 16.686869 26.91466193
#> 19 parent 17.878788 24.52060198
#> 20 parent 19.070707 22.33949373
#> 21 parent 20.262626 20.35239512
#> 22 parent 21.454545 18.54204899
#> 23 parent 22.646465 16.89273320
#> 24 parent 23.838384 15.39012410
#> 25 parent 25.030303 14.02117212
#> 26 parent 26.222222 12.77398846
#> 27 parent 27.414141 11.63774182
#> 28 parent 28.606061 10.60256435
#> 29 parent 29.797980 9.65946594
#> 30 parent 30.000000 9.50814643
#> 31 parent 30.989899 8.80025617
#> 32 parent 32.181818 8.01747313
#> 33 parent 33.373737 7.30431867
#> 34 parent 34.565657 6.65459931
#> 35 parent 35.757576 6.06267251
#> 36 parent 36.949495 5.52339762
#> 37 parent 38.141414 5.03209124
#> 38 parent 39.333333 4.58448658
#> 39 parent 40.525253 4.17669637
#> 40 parent 41.717172 3.80517911
#> 41 parent 42.909091 3.46670832
#> 42 parent 44.101010 3.15834451
#> 43 parent 45.292929 2.87740968
#> 44 parent 46.484848 2.62146400
#> 45 parent 47.676768 2.38828471
#> 46 parent 48.868687 2.17584671
#> 47 parent 50.060606 1.98230508
#> 48 parent 51.252525 1.80597899
#> 49 parent 52.444444 1.64533711
#> 50 parent 53.636364 1.49898432
#> 51 parent 54.828283 1.36564963
#> 52 parent 56.020202 1.24417505
#> 53 parent 57.212121 1.13350565
#> 54 parent 58.404040 1.03268029
#> 55 parent 59.595960 0.94082335
#> 56 parent 60.787879 0.85713708
#> 57 parent 61.979798 0.78089471
#> 58 parent 62.000000 0.77966270
#> 59 parent 63.171717 0.71143411
#> 60 parent 64.363636 0.64815202
#> 61 parent 65.555556 0.59049888
#> 62 parent 66.747475 0.53797399
#> 63 parent 67.939394 0.49012119
#> 64 parent 69.131313 0.44652489
#> 65 parent 70.323232 0.40680649
#> 66 parent 71.515152 0.37062104
#> 67 parent 72.707071 0.33765429
#> 68 parent 73.898990 0.30761993
#> 69 parent 75.090909 0.28025713
#> 70 parent 76.282828 0.25532825
#> 71 parent 77.474747 0.23261679
#> 72 parent 78.666667 0.21192552
#> 73 parent 79.858586 0.19307474
#> 74 parent 81.050505 0.17590074
#> 75 parent 82.242424 0.16025436
#> 76 parent 83.434343 0.14599973
#> 77 parent 84.626263 0.13301305
#> 78 parent 85.818182 0.12118154
#> 79 parent 87.010101 0.11040244
#> 80 parent 88.202020 0.10058214
#> 81 parent 89.393939 0.09163535
#> 82 parent 90.000000 0.08739595
#> 83 parent 90.585859 0.08348439
#> 84 parent 91.777778 0.07605845
#> 85 parent 92.969697 0.06929305
#> 86 parent 94.161616 0.06312943
#> 87 parent 95.353535 0.05751406
#> 88 parent 96.545455 0.05239819
#> 89 parent 97.737374 0.04773737
#> 90 parent 98.929293 0.04349113
#> 91 parent 100.121212 0.03962259
#> 92 parent 101.313131 0.03609816
#> 93 parent 102.505051 0.03288723
#> 94 parent 103.696970 0.02996191
#> 95 parent 104.888889 0.02729679
#> 96 parent 106.080808 0.02486874
#> 97 parent 107.272727 0.02265667
#> 98 parent 108.464646 0.02064136
#> 99 parent 109.656566 0.01880531
#> 100 parent 110.848485 0.01713257
#> 101 parent 112.040404 0.01560863
#> 102 parent 113.232323 0.01422024
#> 103 parent 114.424242 0.01295535
#> 104 parent 115.616162 0.01180297
#> 105 parent 116.808081 0.01075310
#> 106 parent 118.000000 0.00979661
#>
#> $cost
#> function (P)
#> {
#> assign("calls", calls + 1, inherits = TRUE)
#> if (trace_parms)
#> cat(P, "\n")
#> if (length(state.ini.optim) > 0) {
#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
#> }
#> else {
#> odeini <- state.ini.fixed
#> names(odeini) <- state.ini.fixed.boxnames
#> }
#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)],
#> transparms.fixed)
#> parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
#> transform_fractions = transform_fractions)
#> out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
#> use_compiled = use_compiled, method.ode = method.ode,
#> atol = atol, rtol = rtol, ...)
#> assign("out_predicted", out, inherits = TRUE)
#> mC <- modCost(out, observed, y = "value", err = err, weight = weight,
#> scaleVar = scaleVar)
#> if (mC$model < cost.old) {
#> if (!quiet)
#> cat("Model cost at call ", calls, ": ", mC$model,
#> "\n")
#> if (plot) {
#> outtimes_plot = seq(min(observed$time), max(observed$time),
#> length.out = 100)
#> out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
#> solution_type = solution_type, use_compiled = use_compiled,
#> method.ode = method.ode, atol = atol, rtol = rtol,
#> ...)
#> plot(0, type = "n", xlim = range(observed$time),
#> ylim = c(0, max(observed$value, na.rm = TRUE)),
#> xlab = "Time", ylab = "Observed")
#> col_obs <- pch_obs <- 1:length(obs_vars)
#> lty_obs <- rep(1, length(obs_vars))
#> names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars
#> for (obs_var in obs_vars) {
#> points(subset(observed, name == obs_var, c(time,
#> value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
#> }
#> matlines(out_plot$time, out_plot[-1], col = col_obs,
#> lty = lty_obs)
#> legend("topright", inset = c(0.05, 0.05), legend = obs_vars,
#> col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
#> }
#> assign("cost.old", mC$model, inherits = TRUE)
#> }
#> return(mC)
#> }
#> <bytecode: 0x5555578ff9d0>
#> <environment: 0x555559a0da40>
#>
#> $cost_notrans
#> function (P)
#> {
#> if (length(state.ini.optim) > 0) {
#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
#> }
#> else {
#> odeini <- state.ini.fixed
#> names(odeini) <- state.ini.fixed.boxnames
#> }
#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)],
#> parms.fixed)
#> out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
#> use_compiled = use_compiled, method.ode = method.ode,
#> atol = atol, rtol = rtol, ...)
#> mC <- modCost(out, observed, y = "value", err = err, weight = weight,
#> scaleVar = scaleVar)
#> return(mC)
#> }
#> <bytecode: 0x555559b90d60>
#> <environment: 0x555559a0da40>
#>
#> $hessian_notrans
#> parent_0 k_parent_sink
#> parent_0 4.163631 -1203.894
#> k_parent_sink -1203.893702 1033188.753
#>
#> $start
#> value type
#> parent_0 98.62 state
#> k_parent_sink 0.10 deparm
#>
#> $start_transformed
#> value lower upper
#> parent_0 98.620000 -Inf Inf
#> log_k_parent_sink -2.302585 -Inf Inf
#>
#> $fixed
#> [1] value type
#> <0 rows> (or 0-length row.names)
#>
#> $data
#> time variable observed predicted residual
#> 1 0 parent 98.62 99.17407218 -0.55407218
#> 2 3 parent 81.43 78.44547872 2.98452128
#> 3 7 parent 53.18 57.38445742 -4.20445742
#> 4 14 parent 34.89 33.20400061 1.68599939
#> 5 30 parent 10.09 9.50814643 0.58185357
#> 6 62 parent 1.50 0.77966270 0.72033730
#> 7 90 parent 0.33 0.08739595 0.24260405
#> 8 118 parent 0.08 0.00979661 0.07020339
#>
#> $atol
#> [1] 1e-08
#>
#> $rtol
#> [1] 1e-10
#>
#> $weight.ini
#> [1] "none"
#>
#> $tc.ini
#> sigma_low rsd_high
#> 0.50 0.07
#>
#> $reweight.tol
#> [1] 1e-08
#>
#> $reweight.max.iter
#> [1] 10
#>
#> $bparms.optim
#> parent_0 k_parent_sink
#> 99.17407218 0.07815759
#>
#> $bparms.fixed
#> numeric(0)
#>
#> $bparms.ode
#> k_parent_sink
#> 0.07815759
#>
#> $bparms.state
#> parent
#> 99.17407
#>
#> $date
#> [1] "Wed Mar 21 18:14:20 2018"
#>
#> $version
#> [1] "0.9.47.1"
#>
#> $Rversion
#> [1] "3.4.4"
#>
#> attr(,"class")
#> [1] "mkinfit" "modFit"
#> </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="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<h2>Author</h2>
Johannes Ranke
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
</div>
</body>
</html>
|
