aboutsummaryrefslogtreecommitdiff
path: root/inst/web/Extract.mmkin.html
blob: 6a175a02ccb64390320c9270ffa09d76e0574c5d (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
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
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">
<title>[.mmkin. mkin 0.9-41</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="
  Johannes Ranke
">

<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>Subsetting method for mmkin objects</h1>

<div class="row">
  <div class="span8">
    <h2>Usage</h2>
    <pre><div>"["(x, i, j, ..., drop&nbsp;=&nbsp;FALSE)</div></pre>
    
    <h2>Arguments</h2>
    <dl>
      <dt>x</dt>
      <dd>An <code><a href='mmkin.html'>mmkin</a> object</code></dd>
      <dt>i</dt>
      <dd>Row index selecting the fits for specific models</dd>
      <dt>j</dt>
      <dd>Column index selecting the fits to specific datasets</dd>
      <dt>...</dt>
      <dd>Not used, only there to satisfy the generic method definition</dd>
      <dt>drop</dt>
      <dd>If FALSE, the method always returns an mmkin object, otherwise either 
  a list of mkinfit objects or a single mkinfit object.</dd>
    </dl>
    
    <div class="Description">
      <h2>Description</h2>

      <p>Subsetting method for mmkin objects.</p>
  
    </div>

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

      <p><dl>
  An object of class <code><a href='mmkin.html'>mmkin</a></code>.
</dl></p>
  
    </div>
    
    <h2 id="examples">Examples</h2>
    <pre class="examples"><div class='input'>  # Only use one core, to pass R CMD check --as-cran
  fits &lt;- mmkin(c(&quot;SFO&quot;, &quot;FOMC&quot;), list(B = FOCUS_2006_B, C = FOCUS_2006_C), 
                cores = 1, quiet = TRUE)
  fits[&quot;FOMC&quot;, ]
</div>
<div class='output'>      dataset
model  B       C      
  FOMC List,42 List,42
attr(,&quot;class&quot;)
[1] &quot;mmkin&quot;
</div>
<div class='input'>  fits[, &quot;B&quot;]
</div>
<div class='output'>      dataset
model  B      
  SFO  List,42
  FOMC List,42
attr(,&quot;class&quot;)
[1] &quot;mmkin&quot;
</div>
<div class='input'>  fits[, &quot;B&quot;, drop = TRUE]$FOMC
</div>
<div class='output'>$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] &quot;both X-convergence and relative convergence (5)&quot;

$hessian
            parent_0   log_alpha    log_beta
parent_0    4.123033   -95.69983    93.17699
log_alpha -95.699832  6618.85833 -6352.46648
log_beta   93.176993 -6352.46648  6101.23483

$residuals
      parent       parent       parent       parent       parent       parent       parent       parent 
 1.046192647 -3.322396479  3.655156669 -1.705316770  0.406306255 -0.123734689 -0.036886982 -0.006240458 

$ms
[1] 3.572863

$var_ms
  parent 
3.572863 

$var_ms_unscaled
  parent 
3.572863 

$var_ms_unweighted
  parent 
3.572863 

$rank
[1] 3

$df.residual
[1] 5

$solution_type
[1] &quot;analytical&quot;

$transform_rates
[1] TRUE

$transform_fractions
[1] TRUE

$method.modFit
[1] &quot;Port&quot;

$maxit.modFit
[1] &quot;auto&quot;

$calls
[1] 111

$time
   user  system elapsed 
  0.268   0.000   0.269 

$mkinmod
&lt;mkinmod&gt; model generated with
Use of formation fractions $use_of_ff: min 
Specification $spec:
$parent
$type: FOMC

$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] &quot;parent&quot;

$predicted
      name       time       value
1   parent   0.000000 99.66619265
2   parent   1.191919 90.41690342
3   parent   2.383838 82.08630014
4   parent   3.000000 78.10760352
5   parent   3.575758 74.57722848
6   parent   4.767677 67.80342415
7   parent   5.959596 61.68822425
8   parent   7.000000 56.83515667
9   parent   7.151515 56.16343898
10  parent   8.343434 51.16836285
11  parent   9.535354 46.64890734
12  parent  10.727273 42.55683931
13  parent  11.919192 38.84911158
14  parent  13.111111 35.48727414
15  parent  14.000000 33.18468323
16  parent  14.303030 32.43695565
17  parent  15.494949 29.66740651
18  parent  16.686869 27.15109578
19  parent  17.878788 24.86335532
20  parent  19.070707 22.78206538
21  parent  20.262626 20.88737647
22  parent  21.454545 19.16146324
23  parent  22.646465 17.58830644
24  parent  23.838384 16.15349953
25  parent  25.030303 14.84407724
26  parent  26.222222 13.64836315
27  parent  27.414141 12.55583436
28  parent  28.606061 11.55700107
29  parent  29.797980 10.64329940
30  parent  30.000000 10.49630626
31  parent  30.989899  9.80699593
32  parent  32.181818  9.04110261
33  parent  33.373737  8.33930082
34  parent  34.565657  7.69587362
35  parent  35.757576  7.10564515
36  parent  36.949495  6.56392657
37  parent  38.141414  6.06646759
38  parent  39.333333  5.60941311
39  parent  40.525253  5.18926438
40  parent  41.717172  4.80284421
41  parent  42.909091  4.44726569
42  parent  44.101010  4.11990420
43  parent  45.292929  3.81837216
44  parent  46.484848  3.54049644
45  parent  47.676768  3.28429799
46  parent  48.868687  3.04797350
47  parent  50.060606  2.82987892
48  parent  51.252525  2.62851456
49  parent  52.444444  2.44251172
50  parent  53.636364  2.27062056
51  parent  54.828283  2.11169922
52  parent  56.020202  1.96470393
53  parent  57.212121  1.82868009
54  parent  58.404040  1.70275424
55  parent  59.595960  1.58612677
56  parent  60.787879  1.47806529
57  parent  61.979798  1.37789865
58  parent  62.000000  1.37626531
59  parent  63.171717  1.28501157
60  parent  64.363636  1.19883967
61  parent  65.555556  1.11886504
62  parent  66.747475  1.04461220
63  parent  67.939394  0.97564441
64  parent  69.131313  0.91156031
65  parent  70.323232  0.85199096
66  parent  71.515152  0.79659697
67  parent  72.707071  0.74506609
68  parent  73.898990  0.69711084
69  parent  75.090909  0.65246649
70  parent  76.282828  0.61088912
71  parent  77.474747  0.57215389
72  parent  78.666667  0.53605348
73  parent  79.858586  0.50239663
74  parent  81.050505  0.47100683
75  parent  82.242424  0.44172111
76  parent  83.434343  0.41438896
77  parent  84.626263  0.38887128
78  parent  85.818182  0.36503953
79  parent  87.010101  0.34277481
80  parent  88.202020  0.32196716
81  parent  89.393939  0.30251479
82  parent  90.000000  0.29311302
83  parent  90.585859  0.28432347
84  parent  91.777778  0.26730596
85  parent  92.969697  0.25138141
86  parent  94.161616  0.23647487
87  parent  95.353535  0.22251689
88  parent  96.545455  0.20944302
89  parent  97.737374  0.19719349
90  parent  98.929293  0.18571281
91  parent 100.121212  0.17494947
92  parent 101.313131  0.16485560
93  parent 102.505051  0.15538676
94  parent 103.696970  0.14650163
95  parent 104.888889  0.13816179
96  parent 106.080808  0.13033150
97  parent 107.272727  0.12297753
98  parent 108.464646  0.11606895
99  parent 109.656566  0.10957695
100 parent 110.848485  0.10347470
101 parent 112.040404  0.09773723
102 parent 113.232323  0.09234125
103 parent 114.424242  0.08726506
104 parent 115.616162  0.08248842
105 parent 116.808081  0.07799245
106 parent 118.000000  0.07375954

$cost
function (P) 
{
    assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
    if (trace_parms) 
        cat(P, &quot;\n&quot;)
    if (length(state.ini.optim) &gt; 0) {
        odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
        names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
    }
    else {
        odeini &lt;- state.ini.fixed
        names(odeini) &lt;- state.ini.fixed.boxnames
    }
    odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)], 
        transparms.fixed)
    parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, 
        transform_fractions = transform_fractions)
    out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, 
        use_compiled = use_compiled, method.ode = method.ode, 
        atol = atol, rtol = rtol, ...)
    assign(&quot;out_predicted&quot;, out, inherits = TRUE)
    mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight, 
        scaleVar = scaleVar)
    if (mC$model &lt; cost.old) {
        if (!quiet) 
            cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model, 
                &quot;\n&quot;)
        if (plot) {
            outtimes_plot = seq(min(observed$time), max(observed$time), 
                length.out = 100)
            out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 
                solution_type = solution_type, use_compiled = use_compiled, 
                method.ode = method.ode, atol = atol, rtol = rtol, 
                ...)
            plot(0, type = &quot;n&quot;, xlim = range(observed$time), 
                ylim = c(0, max(observed$value, na.rm = TRUE)), 
                xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
            col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
            lty_obs &lt;- rep(1, length(obs_vars))
            names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
            for (obs_var in obs_vars) {
                points(subset(observed, name == obs_var, c(time, 
                  value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
            }
            matlines(out_plot$time, out_plot[-1], col = col_obs, 
                lty = lty_obs)
            legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars, 
                col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
        }
        assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
    }
    return(mC)
}
&lt;environment: 0x2d96b00&gt;

$cost_notrans
function (P) 
{
    if (length(state.ini.optim) &gt; 0) {
        odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
        names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
    }
    else {
        odeini &lt;- state.ini.fixed
        names(odeini) &lt;- state.ini.fixed.boxnames
    }
    odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)], 
        parms.fixed)
    out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, 
        use_compiled = use_compiled, method.ode = method.ode, 
        atol = atol, rtol = rtol, ...)
    mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight, 
        scaleVar = scaleVar)
    return(mC)
}
&lt;environment: 0x2d96b00&gt;

$hessian_notrans
           parent_0     alpha       beta
parent_0  4.1230329 -7.473531  0.5968527
alpha    -7.4735307 40.365690 -3.1777189
beta      0.5968527 -3.177719  0.2503425

$start
         value   type
parent_0 98.62  state
alpha     1.00 deparm
beta     10.00 deparm

$start_transformed
              value lower upper
parent_0  98.620000  -Inf   Inf
log_alpha  0.000000  -Inf   Inf
log_beta   2.302585  -Inf   Inf

$fixed
[1] value type 
&lt;0 rows&gt; (or 0-length row.names)

$data
  time variable observed   predicted     residual
1    0   parent    98.62 99.66619265 -1.046192647
2    3   parent    81.43 78.10760352  3.322396479
3    7   parent    53.18 56.83515667 -3.655156669
4   14   parent    34.89 33.18468323  1.705316770
5   30   parent    10.09 10.49630626 -0.406306255
6   62   parent     1.50  1.37626531  0.123734689
7   90   parent     0.33  0.29311302  0.036886982
8  118   parent     0.08  0.07375954  0.006240458

$atol
[1] 1e-08

$rtol
[1] 1e-10

$weight.ini
[1] &quot;none&quot;

$reweight.tol
[1] 1e-08

$reweight.max.iter
[1] 10

$bparms.optim
 parent_0     alpha      beta 
 99.66619  12.80517 156.11390 

$bparms.fixed
numeric(0)

$bparms.ode
    alpha      beta 
 12.80517 156.11390 

$bparms.state
  parent 
99.66619 

$date
[1] &quot;Mon Nov  9 10:11:49 2015&quot;

attr(,&quot;class&quot;)
[1] &quot;mkinfit&quot; &quot;modFit&quot; 
</div>
<div class='input'>  fits[&quot;SFO&quot;, &quot;B&quot;]
</div>
<div class='output'>     dataset
model B      
  SFO List,42
attr(,&quot;class&quot;)
[1] &quot;mmkin&quot;
</div>
<div class='input'>  fits[[&quot;SFO&quot;, &quot;B&quot;]] # This is equivalent to
</div>
<div class='output'>$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] &quot;relative convergence (4)&quot;

$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      parent      parent 
 0.55407218 -2.98452128  4.20445742 -1.68599939 -0.58185357 -0.72033730 -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] &quot;analytical&quot;

$transform_rates
[1] TRUE

$transform_fractions
[1] TRUE

$method.modFit
[1] &quot;Port&quot;

$maxit.modFit
[1] &quot;auto&quot;

$calls
[1] 29

$time
   user  system elapsed 
  0.112   0.000   0.112 

$mkinmod
&lt;mkinmod&gt; model generated with
Use of formation fractions $use_of_ff: min 
Specification $spec:
$parent
$type: SFO
Coefficient matrix $coefmat available

$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] &quot;parent&quot;

$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

$cost
function (P) 
{
    assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
    if (trace_parms) 
        cat(P, &quot;\n&quot;)
    if (length(state.ini.optim) &gt; 0) {
        odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
        names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
    }
    else {
        odeini &lt;- state.ini.fixed
        names(odeini) &lt;- state.ini.fixed.boxnames
    }
    odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)], 
        transparms.fixed)
    parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, 
        transform_fractions = transform_fractions)
    out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, 
        use_compiled = use_compiled, method.ode = method.ode, 
        atol = atol, rtol = rtol, ...)
    assign(&quot;out_predicted&quot;, out, inherits = TRUE)
    mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight, 
        scaleVar = scaleVar)
    if (mC$model &lt; cost.old) {
        if (!quiet) 
            cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model, 
                &quot;\n&quot;)
        if (plot) {
            outtimes_plot = seq(min(observed$time), max(observed$time), 
                length.out = 100)
            out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 
                solution_type = solution_type, use_compiled = use_compiled, 
                method.ode = method.ode, atol = atol, rtol = rtol, 
                ...)
            plot(0, type = &quot;n&quot;, xlim = range(observed$time), 
                ylim = c(0, max(observed$value, na.rm = TRUE)), 
                xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
            col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
            lty_obs &lt;- rep(1, length(obs_vars))
            names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
            for (obs_var in obs_vars) {
                points(subset(observed, name == obs_var, c(time, 
                  value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
            }
            matlines(out_plot$time, out_plot[-1], col = col_obs, 
                lty = lty_obs)
            legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars, 
                col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
        }
        assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
    }
    return(mC)
}
&lt;environment: 0x2fa3d28&gt;

$cost_notrans
function (P) 
{
    if (length(state.ini.optim) &gt; 0) {
        odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
        names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
    }
    else {
        odeini &lt;- state.ini.fixed
        names(odeini) &lt;- state.ini.fixed.boxnames
    }
    odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)], 
        parms.fixed)
    out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, 
        use_compiled = use_compiled, method.ode = method.ode, 
        atol = atol, rtol = rtol, ...)
    mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight, 
        scaleVar = scaleVar)
    return(mC)
}
&lt;environment: 0x2fa3d28&gt;

$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 
&lt;0 rows&gt; (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] &quot;none&quot;

$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] &quot;Mon Nov  9 10:11:48 2015&quot;

attr(,&quot;class&quot;)
[1] &quot;mkinfit&quot; &quot;modFit&quot; 
</div>
<div class='input'>  fits[&quot;SFO&quot;, &quot;B&quot;, drop = TRUE]
</div>
<div class='output'>[[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] &quot;relative convergence (4)&quot;

$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      parent      parent 
 0.55407218 -2.98452128  4.20445742 -1.68599939 -0.58185357 -0.72033730 -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] &quot;analytical&quot;

$transform_rates
[1] TRUE

$transform_fractions
[1] TRUE

$method.modFit
[1] &quot;Port&quot;

$maxit.modFit
[1] &quot;auto&quot;

$calls
[1] 29

$time
   user  system elapsed 
  0.112   0.000   0.112 

$mkinmod
&lt;mkinmod&gt; model generated with
Use of formation fractions $use_of_ff: min 
Specification $spec:
$parent
$type: SFO
Coefficient matrix $coefmat available

$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] &quot;parent&quot;

$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

$cost
function (P) 
{
    assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
    if (trace_parms) 
        cat(P, &quot;\n&quot;)
    if (length(state.ini.optim) &gt; 0) {
        odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
        names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
    }
    else {
        odeini &lt;- state.ini.fixed
        names(odeini) &lt;- state.ini.fixed.boxnames
    }
    odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)], 
        transparms.fixed)
    parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, 
        transform_fractions = transform_fractions)
    out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, 
        use_compiled = use_compiled, method.ode = method.ode, 
        atol = atol, rtol = rtol, ...)
    assign(&quot;out_predicted&quot;, out, inherits = TRUE)
    mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight, 
        scaleVar = scaleVar)
    if (mC$model &lt; cost.old) {
        if (!quiet) 
            cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model, 
                &quot;\n&quot;)
        if (plot) {
            outtimes_plot = seq(min(observed$time), max(observed$time), 
                length.out = 100)
            out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 
                solution_type = solution_type, use_compiled = use_compiled, 
                method.ode = method.ode, atol = atol, rtol = rtol, 
                ...)
            plot(0, type = &quot;n&quot;, xlim = range(observed$time), 
                ylim = c(0, max(observed$value, na.rm = TRUE)), 
                xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
            col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
            lty_obs &lt;- rep(1, length(obs_vars))
            names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
            for (obs_var in obs_vars) {
                points(subset(observed, name == obs_var, c(time, 
                  value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
            }
            matlines(out_plot$time, out_plot[-1], col = col_obs, 
                lty = lty_obs)
            legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars, 
                col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
        }
        assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
    }
    return(mC)
}
&lt;environment: 0x2fa3d28&gt;

$cost_notrans
function (P) 
{
    if (length(state.ini.optim) &gt; 0) {
        odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
        names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
    }
    else {
        odeini &lt;- state.ini.fixed
        names(odeini) &lt;- state.ini.fixed.boxnames
    }
    odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)], 
        parms.fixed)
    out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, 
        use_compiled = use_compiled, method.ode = method.ode, 
        atol = atol, rtol = rtol, ...)
    mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight, 
        scaleVar = scaleVar)
    return(mC)
}
&lt;environment: 0x2fa3d28&gt;

$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 
&lt;0 rows&gt; (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] &quot;none&quot;

$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] &quot;Mon Nov  9 10:11:48 2015&quot;

attr(,&quot;class&quot;)
[1] &quot;mkinfit&quot; &quot;modFit&quot; 

</div></pre>
  </div>
  <div class="span4">
    <!-- <ul>
      <li>[.mmkin</li>
    </ul>
    <ul>
      
    </ul> -->
      
    
    <h2>Author</h2>
    
  Johannes Ranke

    
  </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