-
Notifications
You must be signed in to change notification settings - Fork 23
/
Copy pathcha-RCfunctions.html
1789 lines (1751 loc) · 129 KB
/
cha-RCfunctions.html
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
<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>Chapter 11 Writing simple nimbleFunctions | NimbleUserManual.knit</title>
<meta name="description" content="This is the NIMBLE User Manual." />
<meta name="generator" content="bookdown 0.39 and GitBook 2.6.7" />
<meta property="og:title" content="Chapter 11 Writing simple nimbleFunctions | NimbleUserManual.knit" />
<meta property="og:type" content="book" />
<meta property="og:image" content="/nimble-icon.png" />
<meta property="og:description" content="This is the NIMBLE User Manual." />
<meta name="github-repo" content="nimble-dev/nimble" />
<meta name="twitter:card" content="summary" />
<meta name="twitter:title" content="Chapter 11 Writing simple nimbleFunctions | NimbleUserManual.knit" />
<meta name="twitter:description" content="This is the NIMBLE User Manual." />
<meta name="twitter:image" content="/nimble-icon.png" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black" />
<link rel="prev" href="overview.html"/>
<link rel="next" href="cha-user-defined.html"/>
<script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
<style type="text/css">
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { color: #008000; } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { color: #008000; font-weight: bold; } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>
<style type="text/css">
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
</style>
<style type="text/css">
/* Used with Pandoc 2.11+ new --citeproc when CSL is used */
div.csl-bib-body { }
div.csl-entry {
clear: both;
margin-bottom: 0em;
}
.hanging div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}
</style>
<link rel="stylesheet" href="style.css" type="text/css" />
</head>
<body>
<div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
<div class="book-summary">
<nav role="navigation">
<ul class="summary">
<img src="./nimble-icon.png"
width=100>
<li><a href="./cha-welcome-nimble.html">NIMBLE User Manual, Version 1.3.0</a></li>
<li><a href="https://github.com/nimble-dev/nimble">NIMBLE Development Team</a></li>
<li><a href="https://R-nimble.org">https://R-nimble.org</a></li>
<li class="divider"></li>
<li class="part"><span><b>I Introduction</b></span></li>
<li class="chapter" data-level="1" data-path="cha-welcome-nimble.html"><a href="cha-welcome-nimble.html"><i class="fa fa-check"></i><b>1</b> Welcome to NIMBLE</a>
<ul>
<li class="chapter" data-level="1.1" data-path="cha-welcome-nimble.html"><a href="cha-welcome-nimble.html#sec:what-is-nimble"><i class="fa fa-check"></i><b>1.1</b> What does NIMBLE do?</a></li>
<li class="chapter" data-level="1.2" data-path="cha-welcome-nimble.html"><a href="cha-welcome-nimble.html#how-to-use-this-manual"><i class="fa fa-check"></i><b>1.2</b> How to use this manual</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html"><i class="fa fa-check"></i><b>2</b> Lightning introduction</a>
<ul>
<li class="chapter" data-level="2.1" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:brief-example"><i class="fa fa-check"></i><b>2.1</b> A brief example</a></li>
<li class="chapter" data-level="2.2" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:creating-model"><i class="fa fa-check"></i><b>2.2</b> Creating a model</a></li>
<li class="chapter" data-level="2.3" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:compiling-model"><i class="fa fa-check"></i><b>2.3</b> Compiling the model</a></li>
<li class="chapter" data-level="2.4" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:intro-runMCMC"><i class="fa fa-check"></i><b>2.4</b> One-line invocation of MCMC</a></li>
<li class="chapter" data-level="2.5" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:creating-mcmc"><i class="fa fa-check"></i><b>2.5</b> Creating, compiling and running a basic MCMC configuration</a></li>
<li class="chapter" data-level="2.6" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:customizing-mcmc"><i class="fa fa-check"></i><b>2.6</b> Customizing the MCMC</a></li>
<li class="chapter" data-level="2.7" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:running-mcem"><i class="fa fa-check"></i><b>2.7</b> Running MCEM</a></li>
<li class="chapter" data-level="2.8" data-path="cha-lightning-intro.html"><a href="cha-lightning-intro.html#sec:creating-your-own"><i class="fa fa-check"></i><b>2.8</b> Creating your own functions</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="cha-more-introduction.html"><a href="cha-more-introduction.html"><i class="fa fa-check"></i><b>3</b> More introduction</a>
<ul>
<li class="chapter" data-level="3.1" data-path="cha-more-introduction.html"><a href="cha-more-introduction.html#nimble-adopts-and-extends-the-bugs-language-for-specifying-models"><i class="fa fa-check"></i><b>3.1</b> NIMBLE adopts and extends the BUGS language for specifying models</a></li>
<li class="chapter" data-level="3.2" data-path="cha-more-introduction.html"><a href="cha-more-introduction.html#sec:nimble-lang-writ"><i class="fa fa-check"></i><b>3.2</b> nimbleFunctions for writing algorithms</a></li>
<li class="chapter" data-level="3.3" data-path="cha-more-introduction.html"><a href="cha-more-introduction.html#sec:nimble-algor-libr"><i class="fa fa-check"></i><b>3.3</b> The NIMBLE algorithm library</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html"><i class="fa fa-check"></i><b>4</b> Installing NIMBLE</a>
<ul>
<li class="chapter" data-level="4.1" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#sec:requ-run-nimble"><i class="fa fa-check"></i><b>4.1</b> Requirements to run NIMBLE</a></li>
<li class="chapter" data-level="4.2" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#sec:compiler"><i class="fa fa-check"></i><b>4.2</b> Installing a C++ compiler for NIMBLE to use</a>
<ul>
<li class="chapter" data-level="4.2.1" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#macos"><i class="fa fa-check"></i><b>4.2.1</b> MacOS</a></li>
<li class="chapter" data-level="4.2.2" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#linux"><i class="fa fa-check"></i><b>4.2.2</b> Linux</a></li>
<li class="chapter" data-level="4.2.3" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#windows"><i class="fa fa-check"></i><b>4.2.3</b> Windows</a></li>
</ul></li>
<li class="chapter" data-level="4.3" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#installing-the-nimble-package"><i class="fa fa-check"></i><b>4.3</b> Installing the NIMBLE package</a></li>
<li class="chapter" data-level="4.4" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#troubleshooting-installation-problems"><i class="fa fa-check"></i><b>4.4</b> Troubleshooting installation problems</a></li>
<li class="chapter" data-level="4.5" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#customizing-your-installation"><i class="fa fa-check"></i><b>4.5</b> Customizing your installation</a>
<ul>
<li class="chapter" data-level="4.5.1" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#using-your-own-copy-of-eigen"><i class="fa fa-check"></i><b>4.5.1</b> Using your own copy of Eigen</a></li>
<li class="chapter" data-level="4.5.2" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#using-libnimble"><i class="fa fa-check"></i><b>4.5.2</b> Using libnimble</a></li>
<li class="chapter" data-level="4.5.3" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#sec:blas"><i class="fa fa-check"></i><b>4.5.3</b> BLAS and LAPACK</a></li>
<li class="chapter" data-level="4.5.4" data-path="cha-installing-nimble.html"><a href="cha-installing-nimble.html#customizing-compilation-of-the-nimble-generated-c"><i class="fa fa-check"></i><b>4.5.4</b> Customizing compilation of the NIMBLE-generated C++</a></li>
</ul></li>
</ul></li>
<li class="part"><span><b>II Models in NIMBLE</b></span></li>
<li class="chapter" data-level="5" data-path="cha-writing-models.html"><a href="cha-writing-models.html"><i class="fa fa-check"></i><b>5</b> Writing models in NIMBLE’s dialect of BUGS</a>
<ul>
<li class="chapter" data-level="5.1" data-path="cha-writing-models.html"><a href="cha-writing-models.html#sec:supp-feat-bugs"><i class="fa fa-check"></i><b>5.1</b> Comparison to BUGS dialects supported by WinBUGS, OpenBUGS and JAGS</a>
<ul>
<li class="chapter" data-level="5.1.1" data-path="cha-writing-models.html"><a href="cha-writing-models.html#supported-features-of-bugs-and-jags"><i class="fa fa-check"></i><b>5.1.1</b> Supported features of BUGS and JAGS</a></li>
<li class="chapter" data-level="5.1.2" data-path="cha-writing-models.html"><a href="cha-writing-models.html#sec:extensions-bugs"><i class="fa fa-check"></i><b>5.1.2</b> NIMBLE’s Extensions to BUGS and JAGS</a></li>
<li class="chapter" data-level="5.1.3" data-path="cha-writing-models.html"><a href="cha-writing-models.html#sec:not-yet-supported"><i class="fa fa-check"></i><b>5.1.3</b> Not-supported features of BUGS and JAGS</a></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="cha-writing-models.html"><a href="cha-writing-models.html#writing-models"><i class="fa fa-check"></i><b>5.2</b> Writing models</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="cha-writing-models.html"><a href="cha-writing-models.html#declaring-stochastic-and-deterministic-nodes"><i class="fa fa-check"></i><b>5.2.1</b> Declaring stochastic and deterministic nodes</a></li>
<li class="chapter" data-level="5.2.2" data-path="cha-writing-models.html"><a href="cha-writing-models.html#sec:more-kinds-bugs"><i class="fa fa-check"></i><b>5.2.2</b> More kinds of BUGS declarations</a></li>
<li class="chapter" data-level="5.2.3" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:vectorized-versus-scalar-declarations"><i class="fa fa-check"></i><b>5.2.3</b> Vectorized versus scalar declarations</a></li>
<li class="chapter" data-level="5.2.4" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:dists-and-functions"><i class="fa fa-check"></i><b>5.2.4</b> Available distributions</a></li>
<li class="chapter" data-level="5.2.5" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:BUGS-lang-fxns"><i class="fa fa-check"></i><b>5.2.5</b> Available BUGS language functions</a></li>
<li class="chapter" data-level="5.2.6" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:BUGS-link"><i class="fa fa-check"></i><b>5.2.6</b> Available link functions</a></li>
<li class="chapter" data-level="5.2.7" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:trunc"><i class="fa fa-check"></i><b>5.2.7</b> Truncation, censoring, and constraints</a></li>
<li class="chapter" data-level="5.2.8" data-path="cha-writing-models.html"><a href="cha-writing-models.html#subsec:macros"><i class="fa fa-check"></i><b>5.2.8</b> Model macros</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="cha-building-models.html"><a href="cha-building-models.html"><i class="fa fa-check"></i><b>6</b> Building and using models</a>
<ul>
<li class="chapter" data-level="6.1" data-path="cha-building-models.html"><a href="cha-building-models.html#creating-model-objects"><i class="fa fa-check"></i><b>6.1</b> Creating model objects</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="cha-building-models.html"><a href="cha-building-models.html#using-nimblemodel-to-create-a-model"><i class="fa fa-check"></i><b>6.1.1</b> Using <em>nimbleModel</em> to create a model</a></li>
<li class="chapter" data-level="6.1.2" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:readBUGSmodel"><i class="fa fa-check"></i><b>6.1.2</b> Creating a model from standard BUGS and JAGS input files</a></li>
<li class="chapter" data-level="6.1.3" data-path="cha-building-models.html"><a href="cha-building-models.html#sub:multiple-instances"><i class="fa fa-check"></i><b>6.1.3</b> Making multiple instances from the same model definition</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:nodes-and-variables"><i class="fa fa-check"></i><b>6.2</b> NIMBLE models are objects you can query and manipulate</a>
<ul>
<li class="chapter" data-level="6.2.1" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:what-are-nodes-and-variables"><i class="fa fa-check"></i><b>6.2.1</b> What are variables and nodes?</a></li>
<li class="chapter" data-level="6.2.2" data-path="cha-building-models.html"><a href="cha-building-models.html#determining-the-nodes-and-variables-in-a-model"><i class="fa fa-check"></i><b>6.2.2</b> Determining the nodes and variables in a model</a></li>
<li class="chapter" data-level="6.2.3" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:accessing-nodes"><i class="fa fa-check"></i><b>6.2.3</b> Accessing nodes</a></li>
<li class="chapter" data-level="6.2.4" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:how-nodes-are"><i class="fa fa-check"></i><b>6.2.4</b> How nodes are named</a></li>
<li class="chapter" data-level="6.2.5" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:why-use-node"><i class="fa fa-check"></i><b>6.2.5</b> Why use node names?</a></li>
<li class="chapter" data-level="6.2.6" data-path="cha-building-models.html"><a href="cha-building-models.html#sec:cdisdata"><i class="fa fa-check"></i><b>6.2.6</b> Checking if a node holds data</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="cha-building-models.html"><a href="cha-building-models.html#using-models-in-parallel"><i class="fa fa-check"></i><b>6.3</b> Using models in parallel</a></li>
</ul></li>
<li class="part"><span><b>III Algorithms in NIMBLE</b></span></li>
<li class="chapter" data-level="7" data-path="cha-mcmc.html"><a href="cha-mcmc.html"><i class="fa fa-check"></i><b>7</b> MCMC</a>
<ul>
<li class="chapter" data-level="7.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:nimbleMCMC"><i class="fa fa-check"></i><b>7.1</b> One-line invocation of MCMC: <em>nimbleMCMC</em></a></li>
<li class="chapter" data-level="7.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:mcmc-configuration"><i class="fa fa-check"></i><b>7.2</b> The MCMC configuration</a>
<ul>
<li class="chapter" data-level="7.2.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:default-mcmc-conf"><i class="fa fa-check"></i><b>7.2.1</b> Default MCMC configuration</a></li>
<li class="chapter" data-level="7.2.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:customizing-mcmc-conf"><i class="fa fa-check"></i><b>7.2.2</b> Customizing the MCMC configuration</a></li>
</ul></li>
<li class="chapter" data-level="7.3" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:build-compile-mcmc"><i class="fa fa-check"></i><b>7.3</b> Building and compiling the MCMC</a></li>
<li class="chapter" data-level="7.4" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:initMCMC"><i class="fa fa-check"></i><b>7.4</b> Initializing MCMC</a></li>
<li class="chapter" data-level="7.5" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:runMCMC"><i class="fa fa-check"></i><b>7.5</b> User-friendly execution of MCMC algorithms: <em>runMCMC</em></a></li>
<li class="chapter" data-level="7.6" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:executing-the-mcmc-algorithm"><i class="fa fa-check"></i><b>7.6</b> Running the MCMC</a>
<ul>
<li class="chapter" data-level="7.6.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:mcmc-rerun"><i class="fa fa-check"></i><b>7.6.1</b> Rerunning versus restarting an MCMC</a></li>
<li class="chapter" data-level="7.6.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:sampler-time"><i class="fa fa-check"></i><b>7.6.2</b> Measuring sampler computation times: <em>getTimes</em></a></li>
<li class="chapter" data-level="7.6.3" data-path="cha-mcmc.html"><a href="cha-mcmc.html#assessing-the-adaption-process-of-rw-and-rw_block-samplers"><i class="fa fa-check"></i><b>7.6.3</b> Assessing the adaption process of <em>RW</em> and <em>RW_block</em> samplers</a></li>
</ul></li>
<li class="chapter" data-level="7.7" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:extracting-samples"><i class="fa fa-check"></i><b>7.7</b> Extracting MCMC samples</a></li>
<li class="chapter" data-level="7.8" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:WAIC"><i class="fa fa-check"></i><b>7.8</b> Calculating WAIC</a></li>
<li class="chapter" data-level="7.9" data-path="cha-mcmc.html"><a href="cha-mcmc.html#k-fold-cross-validation"><i class="fa fa-check"></i><b>7.9</b> k-fold cross-validation</a></li>
<li class="chapter" data-level="7.10" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:rjmcmc"><i class="fa fa-check"></i><b>7.10</b> Variable selection using Reversible Jump MCMC</a>
<ul>
<li class="chapter" data-level="7.10.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:rjmcmc-indicator"><i class="fa fa-check"></i><b>7.10.1</b> Using indicator variables</a></li>
<li class="chapter" data-level="7.10.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:rjmcmc-no-indicator"><i class="fa fa-check"></i><b>7.10.2</b> Without indicator variables</a></li>
</ul></li>
<li class="chapter" data-level="7.11" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:samplers-provided"><i class="fa fa-check"></i><b>7.11</b> Samplers provided with NIMBLE</a>
<ul>
<li class="chapter" data-level="7.11.1" data-path="cha-mcmc.html"><a href="cha-mcmc.html#conjugate-gibbs-samplers"><i class="fa fa-check"></i><b>7.11.1</b> Conjugate (‘Gibbs’) samplers</a></li>
<li class="chapter" data-level="7.11.2" data-path="cha-mcmc.html"><a href="cha-mcmc.html#subsec:HMC"><i class="fa fa-check"></i><b>7.11.2</b> Hamiltonian Monte Carlo (HMC)</a></li>
<li class="chapter" data-level="7.11.3" data-path="cha-mcmc.html"><a href="cha-mcmc.html#particle-filter-samplers"><i class="fa fa-check"></i><b>7.11.3</b> Particle filter samplers</a></li>
<li class="chapter" data-level="7.11.4" data-path="cha-mcmc.html"><a href="cha-mcmc.html#customized-log-likelihood-evaluations-rw_llfunction-sampler"><i class="fa fa-check"></i><b>7.11.4</b> Customized log-likelihood evaluations: <em>RW_llFunction sampler</em></a></li>
</ul></li>
<li class="chapter" data-level="7.12" data-path="cha-mcmc.html"><a href="cha-mcmc.html#sec:mcmc-example-litters"><i class="fa fa-check"></i><b>7.12</b> Detailed MCMC example: <em>litters</em></a></li>
<li class="chapter" data-level="7.13" data-path="cha-mcmc.html"><a href="cha-mcmc.html#mcmc-suite-compare-mcmcs"><i class="fa fa-check"></i><b>7.13</b> Comparing different MCMCs with <em>MCMCsuite</em> and <em>compareMCMCs</em></a></li>
<li class="chapter" data-level="7.14" data-path="cha-mcmc.html"><a href="cha-mcmc.html#running-mcmc-chains-in-parallel"><i class="fa fa-check"></i><b>7.14</b> Running MCMC chains in parallel</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html"><i class="fa fa-check"></i><b>8</b> Particle Filters, PMCMC, MCEM, Laplace approximation and quadrature</a>
<ul>
<li class="chapter" data-level="8.1" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#particle-filters-sequential-monte-carlo-and-iterated-filtering"><i class="fa fa-check"></i><b>8.1</b> Particle filters / sequential Monte Carlo and iterated filtering</a>
<ul>
<li class="chapter" data-level="8.1.1" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#filtering-algorithms"><i class="fa fa-check"></i><b>8.1.1</b> Filtering algorithms</a></li>
<li class="chapter" data-level="8.1.2" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#sec:particle-mcmc"><i class="fa fa-check"></i><b>8.1.2</b> Particle MCMC (PMCMC)</a></li>
</ul></li>
<li class="chapter" data-level="8.2" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#monte-carlo-expectation-maximization-mcem"><i class="fa fa-check"></i><b>8.2</b> Monte Carlo Expectation Maximization (MCEM)</a>
<ul>
<li class="chapter" data-level="8.2.1" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#sec:estimate-mcem-cov"><i class="fa fa-check"></i><b>8.2.1</b> Estimating the asymptotic covariance From MCEM</a></li>
</ul></li>
<li class="chapter" data-level="8.3" data-path="cha-algos-provided.html"><a href="cha-algos-provided.html#laplace-approximation-and-adaptive-gauss-hermite-quadrature"><i class="fa fa-check"></i><b>8.3</b> Laplace approximation and adaptive Gauss-Hermite quadrature</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="cha-spatial.html"><a href="cha-spatial.html"><i class="fa fa-check"></i><b>9</b> Spatial models</a>
<ul>
<li class="chapter" data-level="9.1" data-path="cha-spatial.html"><a href="cha-spatial.html#intrinsic-gaussian-car-model-dcar_normal"><i class="fa fa-check"></i><b>9.1</b> Intrinsic Gaussian CAR model: <em>dcar_normal</em></a>
<ul>
<li class="chapter" data-level="9.1.1" data-path="cha-spatial.html"><a href="cha-spatial.html#specification-and-density"><i class="fa fa-check"></i><b>9.1.1</b> Specification and density</a></li>
<li class="chapter" data-level="9.1.2" data-path="cha-spatial.html"><a href="cha-spatial.html#example"><i class="fa fa-check"></i><b>9.1.2</b> Example</a></li>
</ul></li>
<li class="chapter" data-level="9.2" data-path="cha-spatial.html"><a href="cha-spatial.html#proper-gaussian-car-model-dcar_proper"><i class="fa fa-check"></i><b>9.2</b> Proper Gaussian CAR model: <em>dcar_proper</em></a>
<ul>
<li class="chapter" data-level="9.2.1" data-path="cha-spatial.html"><a href="cha-spatial.html#specification-and-density-1"><i class="fa fa-check"></i><b>9.2.1</b> Specification and density</a></li>
<li class="chapter" data-level="9.2.2" data-path="cha-spatial.html"><a href="cha-spatial.html#example-1"><i class="fa fa-check"></i><b>9.2.2</b> Example</a></li>
</ul></li>
<li class="chapter" data-level="9.3" data-path="cha-spatial.html"><a href="cha-spatial.html#sec:spatial-mcmc-sampling-car"><i class="fa fa-check"></i><b>9.3</b> MCMC Sampling of CAR models</a>
<ul>
<li class="chapter" data-level="9.3.1" data-path="cha-spatial.html"><a href="cha-spatial.html#initial-values"><i class="fa fa-check"></i><b>9.3.1</b> Initial values</a></li>
<li class="chapter" data-level="9.3.2" data-path="cha-spatial.html"><a href="cha-spatial.html#zero-neighbor-regions"><i class="fa fa-check"></i><b>9.3.2</b> Zero-neighbor regions</a></li>
<li class="chapter" data-level="9.3.3" data-path="cha-spatial.html"><a href="cha-spatial.html#zero-mean-constraint"><i class="fa fa-check"></i><b>9.3.3</b> Zero-mean constraint</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="cha-bnp.html"><a href="cha-bnp.html"><i class="fa fa-check"></i><b>10</b> Bayesian nonparametric models</a>
<ul>
<li class="chapter" data-level="10.1" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:bnpmixtures"><i class="fa fa-check"></i><b>10.1</b> Bayesian nonparametric mixture models</a></li>
<li class="chapter" data-level="10.2" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:crp"><i class="fa fa-check"></i><b>10.2</b> Chinese Restaurant Process model</a>
<ul>
<li class="chapter" data-level="10.2.1" data-path="cha-bnp.html"><a href="cha-bnp.html#specification-and-density-2"><i class="fa fa-check"></i><b>10.2.1</b> Specification and density</a></li>
<li class="chapter" data-level="10.2.2" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:excrp"><i class="fa fa-check"></i><b>10.2.2</b> Example</a></li>
<li class="chapter" data-level="10.2.3" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:extensionscrp"><i class="fa fa-check"></i><b>10.2.3</b> Extensions</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:sb"><i class="fa fa-check"></i><b>10.3</b> Stick-breaking model</a>
<ul>
<li class="chapter" data-level="10.3.1" data-path="cha-bnp.html"><a href="cha-bnp.html#specification-and-function"><i class="fa fa-check"></i><b>10.3.1</b> Specification and function</a></li>
<li class="chapter" data-level="10.3.2" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:exsb"><i class="fa fa-check"></i><b>10.3.2</b> Example</a></li>
</ul></li>
<li class="chapter" data-level="10.4" data-path="cha-bnp.html"><a href="cha-bnp.html#mcmc-sampling-of-bnp-models"><i class="fa fa-check"></i><b>10.4</b> MCMC sampling of BNP models</a>
<ul>
<li class="chapter" data-level="10.4.1" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:mcmcdcrp"><i class="fa fa-check"></i><b>10.4.1</b> Sampling CRP models</a></li>
<li class="chapter" data-level="10.4.2" data-path="cha-bnp.html"><a href="cha-bnp.html#sec:mcmcsb"><i class="fa fa-check"></i><b>10.4.2</b> Sampling stick-breaking models</a></li>
</ul></li>
</ul></li>
<li class="part"><span><b>IV Programming with NIMBLE</b></span></li>
<li class="chapter" data-level="" data-path="overview.html"><a href="overview.html"><i class="fa fa-check"></i>Overview</a></li>
<li class="chapter" data-level="11" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html"><i class="fa fa-check"></i><b>11</b> Writing simple nimbleFunctions</a>
<ul>
<li class="chapter" data-level="11.1" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:RC-intro"><i class="fa fa-check"></i><b>11.1</b> Introduction to simple nimbleFunctions</a></li>
<li class="chapter" data-level="11.2" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:r-fiunctions-implemented"><i class="fa fa-check"></i><b>11.2</b> R functions (or variants) implemented in NIMBLE</a>
<ul>
<li class="chapter" data-level="11.2.1" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#finding-help-for-nimbles-versions-of-r-functions"><i class="fa fa-check"></i><b>11.2.1</b> Finding help for NIMBLE’s versions of R functions</a></li>
<li class="chapter" data-level="11.2.2" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#basic-operations"><i class="fa fa-check"></i><b>11.2.2</b> Basic operations</a></li>
<li class="chapter" data-level="11.2.3" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:basic-math-linear"><i class="fa fa-check"></i><b>11.2.3</b> Math and linear algebra</a></li>
<li class="chapter" data-level="11.2.4" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:nimble-dist-funs"><i class="fa fa-check"></i><b>11.2.4</b> Distribution functions</a></li>
<li class="chapter" data-level="11.2.5" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:basic-flow-control"><i class="fa fa-check"></i><b>11.2.5</b> Flow control: <em>if-then-else</em>, <em>for</em>, <em>while</em>, and <em>stop</em></a></li>
<li class="chapter" data-level="11.2.6" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:print"><i class="fa fa-check"></i><b>11.2.6</b> <em>print</em> and <em>cat</em></a></li>
<li class="chapter" data-level="11.2.7" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:check-user-interr"><i class="fa fa-check"></i><b>11.2.7</b> Checking for user interrupts: <em>checkInterrupt</em></a></li>
<li class="chapter" data-level="11.2.8" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#optimization-optim-and-nimoptim"><i class="fa fa-check"></i><b>11.2.8</b> Optimization: <em>optim</em> and <em>nimOptim</em></a></li>
<li class="chapter" data-level="11.2.9" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#integration-integrate-and-nimintegrate"><i class="fa fa-check"></i><b>11.2.9</b> Integration: <em>integrate</em> and <em>nimIntegrate</em></a></li>
<li class="chapter" data-level="11.2.10" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:altern-keyw-some"><i class="fa fa-check"></i><b>11.2.10</b> ‘nim’ synonyms for some functions</a></li>
</ul></li>
<li class="chapter" data-level="11.3" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:how-nimble-handles"><i class="fa fa-check"></i><b>11.3</b> How NIMBLE handles types of variables</a>
<ul>
<li class="chapter" data-level="11.3.1" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:nimbleList-RCFuns"><i class="fa fa-check"></i><b>11.3.1</b> nimbleList data structures</a></li>
<li class="chapter" data-level="11.3.2" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:how-types-work"><i class="fa fa-check"></i><b>11.3.2</b> How numeric types work</a></li>
</ul></li>
<li class="chapter" data-level="11.4" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:decl-argum-return"><i class="fa fa-check"></i><b>11.4</b> Declaring argument and return types</a></li>
<li class="chapter" data-level="11.5" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:comp-nimbl-pass"><i class="fa fa-check"></i><b>11.5</b> Compiled nimbleFunctions pass arguments by reference</a></li>
<li class="chapter" data-level="11.6" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:calling-external-code"><i class="fa fa-check"></i><b>11.6</b> Calling external compiled code</a></li>
<li class="chapter" data-level="11.7" data-path="cha-RCfunctions.html"><a href="cha-RCfunctions.html#sec:calling-R-code"><i class="fa fa-check"></i><b>11.7</b> Calling uncompiled R functions from compiled nimbleFunctions</a></li>
</ul></li>
<li class="chapter" data-level="12" data-path="cha-user-defined.html"><a href="cha-user-defined.html"><i class="fa fa-check"></i><b>12</b> Creating user-defined distributions and functions for models</a>
<ul>
<li class="chapter" data-level="12.1" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:user-functions"><i class="fa fa-check"></i><b>12.1</b> User-defined functions</a></li>
<li class="chapter" data-level="12.2" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:user-distributions"><i class="fa fa-check"></i><b>12.2</b> User-defined distributions</a>
<ul>
<li class="chapter" data-level="12.2.1" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:registerDistributions"><i class="fa fa-check"></i><b>12.2.1</b> Using <em>registerDistributions</em> for alternative parameterizations and providing other information</a></li>
</ul></li>
<li class="chapter" data-level="12.3" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:adv-user-def"><i class="fa fa-check"></i><b>12.3</b> Advanced user-defined functions and distributions</a></li>
<li class="chapter" data-level="12.4" data-path="cha-user-defined.html"><a href="cha-user-defined.html#sec:user-macros"><i class="fa fa-check"></i><b>12.4</b> User-defined model macros</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="cha-using-models.html"><a href="cha-using-models.html"><i class="fa fa-check"></i><b>13</b> Working with NIMBLE models</a>
<ul>
<li class="chapter" data-level="13.1" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:accessing-variables"><i class="fa fa-check"></i><b>13.1</b> The variables and nodes in a NIMBLE model</a>
<ul>
<li class="chapter" data-level="13.1.1" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:get-nodes"><i class="fa fa-check"></i><b>13.1.1</b> Determining the nodes in a model</a></li>
<li class="chapter" data-level="13.1.2" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:introduced-nodes"><i class="fa fa-check"></i><b>13.1.2</b> Understanding lifted nodes</a></li>
<li class="chapter" data-level="13.1.3" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:cdgetdependencies"><i class="fa fa-check"></i><b>13.1.3</b> Determining dependencies in a model</a></li>
</ul></li>
<li class="chapter" data-level="13.2" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:nodeInfo"><i class="fa fa-check"></i><b>13.2</b> Accessing information about nodes and variables</a>
<ul>
<li class="chapter" data-level="13.2.1" data-path="cha-using-models.html"><a href="cha-using-models.html#getting-distributional-information-about-a-node"><i class="fa fa-check"></i><b>13.2.1</b> Getting distributional information about a node</a></li>
<li class="chapter" data-level="13.2.2" data-path="cha-using-models.html"><a href="cha-using-models.html#getting-information-about-a-distribution"><i class="fa fa-check"></i><b>13.2.2</b> Getting information about a distribution</a></li>
<li class="chapter" data-level="13.2.3" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:getParam"><i class="fa fa-check"></i><b>13.2.3</b> Getting distribution parameter values for a node</a></li>
<li class="chapter" data-level="13.2.4" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:getBound"><i class="fa fa-check"></i><b>13.2.4</b> Getting distribution bounds for a node</a></li>
</ul></li>
<li class="chapter" data-level="13.3" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:cdcalc-cdsim-cdgetl"><i class="fa fa-check"></i><b>13.3</b> Carrying out model calculations</a>
<ul>
<li class="chapter" data-level="13.3.1" data-path="cha-using-models.html"><a href="cha-using-models.html#core-model-operations-calculation-and-simulation"><i class="fa fa-check"></i><b>13.3.1</b> Core model operations: calculation and simulation</a></li>
<li class="chapter" data-level="13.3.2" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:cdsimn-cdcalcn-cdget"><i class="fa fa-check"></i><b>13.3.2</b> Pre-defined nimbleFunctions for operating on model nodes: <em>simNodes</em>, <em>calcNodes</em>, and <em>getLogProbNodes</em></a></li>
<li class="chapter" data-level="13.3.3" data-path="cha-using-models.html"><a href="cha-using-models.html#sec:access-log-prob"><i class="fa fa-check"></i><b>13.3.3</b> Accessing log probabilities via <em>logProb</em> variables</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="14" data-path="cha-data-structures.html"><a href="cha-data-structures.html"><i class="fa fa-check"></i><b>14</b> Data structures in NIMBLE</a>
<ul>
<li class="chapter" data-level="14.1" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:modelValues-struct"><i class="fa fa-check"></i><b>14.1</b> The modelValues data structure</a>
<ul>
<li class="chapter" data-level="14.1.1" data-path="cha-data-structures.html"><a href="cha-data-structures.html#creating-modelvalues-objects"><i class="fa fa-check"></i><b>14.1.1</b> Creating modelValues objects</a></li>
<li class="chapter" data-level="14.1.2" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:access-cont-modelv"><i class="fa fa-check"></i><b>14.1.2</b> Accessing contents of modelValues</a></li>
</ul></li>
<li class="chapter" data-level="14.2" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:nimbleLists"><i class="fa fa-check"></i><b>14.2</b> The nimbleList data structure</a>
<ul>
<li class="chapter" data-level="14.2.1" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:predef-nimbleLists"><i class="fa fa-check"></i><b>14.2.1</b> Pre-defined nimbleList types</a></li>
<li class="chapter" data-level="14.2.2" data-path="cha-data-structures.html"><a href="cha-data-structures.html#sec:eigen-nimFunctions"><i class="fa fa-check"></i><b>14.2.2</b> Using <em>eigen</em> and <em>svd</em> in nimbleFunctions</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="15" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html"><i class="fa fa-check"></i><b>15</b> Writing nimbleFunctions to interact with models</a>
<ul>
<li class="chapter" data-level="15.1" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:writ-nimble-funct"><i class="fa fa-check"></i><b>15.1</b> Overview</a></li>
<li class="chapter" data-level="15.2" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:using-comp-nimbl"><i class="fa fa-check"></i><b>15.2</b> Using and compiling nimbleFunctions</a></li>
<li class="chapter" data-level="15.3" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#writing-setup-code"><i class="fa fa-check"></i><b>15.3</b> Writing setup code</a>
<ul>
<li class="chapter" data-level="15.3.1" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#useful-tools-for-setup-functions"><i class="fa fa-check"></i><b>15.3.1</b> Useful tools for setup functions</a></li>
<li class="chapter" data-level="15.3.2" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:access-modify-numer"><i class="fa fa-check"></i><b>15.3.2</b> Accessing and modifying numeric values from setup</a></li>
<li class="chapter" data-level="15.3.3" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#determining-numeric-types-in-nimblefunctions"><i class="fa fa-check"></i><b>15.3.3</b> Determining numeric types in nimbleFunctions</a></li>
<li class="chapter" data-level="15.3.4" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:determ-pers-texttts"><i class="fa fa-check"></i><b>15.3.4</b> Control of setup outputs</a></li>
</ul></li>
<li class="chapter" data-level="15.4" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:nimble-lang-comp"><i class="fa fa-check"></i><b>15.4</b> Writing run code</a>
<ul>
<li class="chapter" data-level="15.4.1" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:driv-models:-calc"><i class="fa fa-check"></i><b>15.4.1</b> Driving models: <em>calculate</em>, <em>calculateDiff</em>, <em>simulate</em>, <em>getLogProb</em></a></li>
<li class="chapter" data-level="15.4.2" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#getting-and-setting-variable-and-node-values"><i class="fa fa-check"></i><b>15.4.2</b> Getting and setting variable and node values</a></li>
<li class="chapter" data-level="15.4.3" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#getting-parameter-values-and-node-bounds"><i class="fa fa-check"></i><b>15.4.3</b> Getting parameter values and node bounds</a></li>
<li class="chapter" data-level="15.4.4" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:access-model-modelv"><i class="fa fa-check"></i><b>15.4.4</b> Using modelValues objects</a></li>
<li class="chapter" data-level="15.4.5" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:using-model-variable"><i class="fa fa-check"></i><b>15.4.5</b> Using model variables and modelValues in expressions</a></li>
<li class="chapter" data-level="15.4.6" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:incl-other-meth"><i class="fa fa-check"></i><b>15.4.6</b> Including other methods in a nimbleFunction</a></li>
<li class="chapter" data-level="15.4.7" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:using-other-nimbl"><i class="fa fa-check"></i><b>15.4.7</b> Using other nimbleFunctions</a></li>
<li class="chapter" data-level="15.4.8" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:virt-nimbl-nimbl"><i class="fa fa-check"></i><b>15.4.8</b> Virtual nimbleFunctions and nimbleFunctionLists</a></li>
<li class="chapter" data-level="15.4.9" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#character-objects"><i class="fa fa-check"></i><b>15.4.9</b> Character objects</a></li>
<li class="chapter" data-level="15.4.10" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:user-defined-data"><i class="fa fa-check"></i><b>15.4.10</b> User-defined data structures</a></li>
</ul></li>
<li class="chapter" data-level="15.5" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:user-samplers"><i class="fa fa-check"></i><b>15.5</b> Example: writing user-defined samplers to extend NIMBLE’s MCMC engine</a>
<ul>
<li class="chapter" data-level="15.5.1" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#user-defined-samplers-and-posterior-predictive-nodes"><i class="fa fa-check"></i><b>15.5.1</b> User-defined samplers and posterior predictive nodes</a></li>
</ul></li>
<li class="chapter" data-level="15.6" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#copying-nimblefunctions-and-nimble-models"><i class="fa fa-check"></i><b>15.6</b> Copying nimbleFunctions (and NIMBLE models)</a></li>
<li class="chapter" data-level="15.7" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#sec:debugging"><i class="fa fa-check"></i><b>15.7</b> Debugging nimbleFunctions</a></li>
<li class="chapter" data-level="15.8" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#timing-nimblefunctions-with-run.time"><i class="fa fa-check"></i><b>15.8</b> Timing nimbleFunctions with <em>run.time</em></a></li>
<li class="chapter" data-level="15.9" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#clearing-and-unloading-compiled-objects"><i class="fa fa-check"></i><b>15.9</b> Clearing and unloading compiled objects</a></li>
<li class="chapter" data-level="15.10" data-path="cha-progr-with-models.html"><a href="cha-progr-with-models.html#reducing-memory-usage"><i class="fa fa-check"></i><b>15.10</b> Reducing memory usage</a></li>
</ul></li>
<li class="part"><span><b>V Automatic Derivatives in NIMBLE</b></span></li>
<li class="chapter" data-level="16" data-path="cha-AD.html"><a href="cha-AD.html"><i class="fa fa-check"></i><b>16</b> Automatic Derivatives</a>
<ul>
<li class="chapter" data-level="16.1" data-path="cha-AD.html"><a href="cha-AD.html#sec:use-derivs"><i class="fa fa-check"></i><b>16.1</b> How to turn on derivatives in a model</a>
<ul>
<li class="chapter" data-level="16.1.1" data-path="cha-AD.html"><a href="cha-AD.html#finish-setting-up-the-glmm-example"><i class="fa fa-check"></i><b>16.1.1</b> Finish setting up the GLMM example</a></li>
</ul></li>
<li class="chapter" data-level="16.2" data-path="cha-AD.html"><a href="cha-AD.html#sec:AD-laplace"><i class="fa fa-check"></i><b>16.2</b> How to use Laplace approximation and adaptive Gauss-Hermite quadrature</a>
<ul>
<li class="chapter" data-level="16.2.1" data-path="cha-AD.html"><a href="cha-AD.html#using-the-laplace-approximation-methods-directly"><i class="fa fa-check"></i><b>16.2.1</b> Using the Laplace approximation methods directly</a></li>
<li class="chapter" data-level="16.2.2" data-path="cha-AD.html"><a href="cha-AD.html#changing-the-optimization-methods"><i class="fa fa-check"></i><b>16.2.2</b> Changing the optimization methods</a></li>
</ul></li>
<li class="chapter" data-level="16.3" data-path="cha-AD.html"><a href="cha-AD.html#sec:AD-user-def"><i class="fa fa-check"></i><b>16.3</b> How to support derivatives in user-defined functions and distributions</a></li>
<li class="chapter" data-level="16.4" data-path="cha-AD.html"><a href="cha-AD.html#what-operations-are-and-arent-supported-for-ad"><i class="fa fa-check"></i><b>16.4</b> What operations are and aren’t supported for AD</a></li>
<li class="chapter" data-level="16.5" data-path="cha-AD.html"><a href="cha-AD.html#basics-of-obtaining-derivatives-in-nimblefunctions"><i class="fa fa-check"></i><b>16.5</b> Basics of obtaining derivatives in <code>nimbleFunctions</code></a>
<ul>
<li class="chapter" data-level="16.5.1" data-path="cha-AD.html"><a href="cha-AD.html#checking-derivatives-with-uncompiled-execution"><i class="fa fa-check"></i><b>16.5.1</b> Checking derivatives with uncompiled execution</a></li>
<li class="chapter" data-level="16.5.2" data-path="cha-AD.html"><a href="cha-AD.html#sec:AD-holding-out"><i class="fa fa-check"></i><b>16.5.2</b> Holding some local variables out of derivative tracking</a></li>
<li class="chapter" data-level="16.5.3" data-path="cha-AD.html"><a href="cha-AD.html#sec:AD-multiple-NF"><i class="fa fa-check"></i><b>16.5.3</b> Using AD with multiple nimbleFunctions</a></li>
<li class="chapter" data-level="16.5.4" data-path="cha-AD.html"><a href="cha-AD.html#sec:understanding-more-AD"><i class="fa fa-check"></i><b>16.5.4</b> Understanding more about how AD works: <em>taping</em> of operations</a></li>
<li class="chapter" data-level="16.5.5" data-path="cha-AD.html"><a href="cha-AD.html#resetting-a-nimderivs-call"><i class="fa fa-check"></i><b>16.5.5</b> Resetting a <code>nimDerivs</code> call</a></li>
<li class="chapter" data-level="16.5.6" data-path="cha-AD.html"><a href="cha-AD.html#a-note-on-performance-benchmarking"><i class="fa fa-check"></i><b>16.5.6</b> A note on performance benchmarking</a></li>
</ul></li>
<li class="chapter" data-level="16.6" data-path="cha-AD.html"><a href="cha-AD.html#advanced-uses-double-taping"><i class="fa fa-check"></i><b>16.6</b> Advanced uses: double taping</a></li>
<li class="chapter" data-level="16.7" data-path="cha-AD.html"><a href="cha-AD.html#derivatives-involving-model-calculations"><i class="fa fa-check"></i><b>16.7</b> Derivatives involving model calculations</a>
<ul>
<li class="chapter" data-level="16.7.1" data-path="cha-AD.html"><a href="cha-AD.html#method-1-nimderivs-of-modelcalculate"><i class="fa fa-check"></i><b>16.7.1</b> Method 1: <code>nimDerivs</code> of <code>model$calculate</code></a></li>
<li class="chapter" data-level="16.7.2" data-path="cha-AD.html"><a href="cha-AD.html#method-2-nimderivs-of-a-method-that-calls-modelcalculate"><i class="fa fa-check"></i><b>16.7.2</b> Method 2: <code>nimDerivs</code> of a method that calls <code>model$calculate</code></a></li>
</ul></li>
<li class="chapter" data-level="16.8" data-path="cha-AD.html"><a href="cha-AD.html#sec:parameter-transform"><i class="fa fa-check"></i><b>16.8</b> Parameter transformations</a></li>
</ul></li>
<li class="chapter" data-level="17" data-path="example-maximum-likelihood-estimation-using-optim-with-gradients-from-nimderivs..html"><a href="example-maximum-likelihood-estimation-using-optim-with-gradients-from-nimderivs..html"><i class="fa fa-check"></i><b>17</b> Example: maximum likelihood estimation using <code>optim</code> with gradients from <code>nimDerivs</code>.</a></li>
<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
</ul>
</nav>
</div>
<div class="book-body">
<div class="body-inner">
<div class="book-header" role="navigation">
<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./"></a>
</h1>
</div>
<div class="page-wrapper" tabindex="-1" role="main">
<div class="page-inner">
<section class="normal" id="section-">
<div id="cha-RCfunctions" class="section level1 hasAnchor" number="11">
<h1><span class="header-section-number">Chapter 11</span> Writing simple nimbleFunctions<a href="cha-RCfunctions.html#cha-RCfunctions" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="sec:RC-intro" class="section level2 hasAnchor" number="11.1">
<h2><span class="header-section-number">11.1</span> Introduction to simple nimbleFunctions<a href="cha-RCfunctions.html#sec:RC-intro" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><em>nimbleFunctions</em> are the heart of programming in NIMBLE. In this
chapter, we introduce simple nimbleFunctions that contain only one
function to be executed, in either compiled or uncompiled form, but no
setup function or additional methods.</p>
<p>Defining a simple nimbleFunction is like defining an R function:
<code>nimbleFunction</code> returns a function that can be executed, and it
can also be compiled. Simple nimbleFunctions are useful for doing math or the other
kinds of processing available in NIMBLE when no model or modelValues
is needed. These can be used for any purpose in R programming. They
can also be used as new functions and distributions in NIMBLE’s
extension of BUGS (Chapter <a href="cha-user-defined.html#cha-user-defined">12</a>).</p>
<p>Here’s a basic example implementing the textbook calculation of
least squares estimation of linear regression parameters<a href="#fn21" class="footnote-ref" id="fnref21"><sup>21</sup></a>:</p>
<div class="sourceCode" id="cb237"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb237-1"><a href="cha-RCfunctions.html#cb237-1" tabindex="-1"></a>solveLeastSquares <span class="ot"><-</span> <span class="fu">nimbleFunction</span>(</span>
<span id="cb237-2"><a href="cha-RCfunctions.html#cb237-2" tabindex="-1"></a> <span class="at">run =</span> <span class="cf">function</span>(<span class="at">X =</span> <span class="fu">double</span>(<span class="dv">2</span>), <span class="at">y =</span> <span class="fu">double</span>(<span class="dv">1</span>)) { <span class="co"># type declarations</span></span>
<span id="cb237-3"><a href="cha-RCfunctions.html#cb237-3" tabindex="-1"></a> ans <span class="ot"><-</span> <span class="fu">inverse</span>(<span class="fu">t</span>(X) <span class="sc">%*%</span> X) <span class="sc">%*%</span> (<span class="fu">t</span>(X) <span class="sc">%*%</span> y)</span>
<span id="cb237-4"><a href="cha-RCfunctions.html#cb237-4" tabindex="-1"></a> <span class="fu">return</span>(ans)</span>
<span id="cb237-5"><a href="cha-RCfunctions.html#cb237-5" tabindex="-1"></a> <span class="fu">returnType</span>(<span class="fu">double</span>(<span class="dv">2</span>)) <span class="co"># return type declaration</span></span>
<span id="cb237-6"><a href="cha-RCfunctions.html#cb237-6" tabindex="-1"></a> } )</span>
<span id="cb237-7"><a href="cha-RCfunctions.html#cb237-7" tabindex="-1"></a></span>
<span id="cb237-8"><a href="cha-RCfunctions.html#cb237-8" tabindex="-1"></a>X <span class="ot"><-</span> <span class="fu">matrix</span>(<span class="fu">rnorm</span>(<span class="dv">400</span>), <span class="at">nrow =</span> <span class="dv">100</span>)</span>
<span id="cb237-9"><a href="cha-RCfunctions.html#cb237-9" tabindex="-1"></a>y <span class="ot"><-</span> <span class="fu">rnorm</span>(<span class="dv">100</span>)</span>
<span id="cb237-10"><a href="cha-RCfunctions.html#cb237-10" tabindex="-1"></a><span class="fu">solveLeastSquares</span>(X, y)</span></code></pre></div>
<pre><code>## [,1]
## [1,] 0.088547575
## [2,] 0.002025635
## [3,] -0.090387283
## [4,] -0.072660391</code></pre>
<div class="sourceCode" id="cb239"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb239-1"><a href="cha-RCfunctions.html#cb239-1" tabindex="-1"></a>CsolveLeastSquares <span class="ot"><-</span> <span class="fu">compileNimble</span>(solveLeastSquares)</span>
<span id="cb239-2"><a href="cha-RCfunctions.html#cb239-2" tabindex="-1"></a><span class="fu">CsolveLeastSquares</span>(X, y)</span></code></pre></div>
<pre><code>## [,1]
## [1,] 0.088547575
## [2,] 0.002025635
## [3,] -0.090387283
## [4,] -0.072660391</code></pre>
<p>In this example, we fit a linear model for 100 random response values (<code>y</code>) to four columns of
randomly generated explanatory variables (<code>X</code>). We ran the
nimbleFunction
<code>solveLeastSquares</code> uncompiled,
natively in R, allowing testing and debugging (Section <a href="cha-progr-with-models.html#sec:debugging">15.7</a>). Then we compiled it and showed that the compiled version does the same thing,
but faster<a href="#fn22" class="footnote-ref" id="fnref22"><sup>22</sup></a>. NIMBLE’s compiler creates C++ that uses the Eigen (<a href="http://eigen.tuxfamily.org">http://eigen.tuxfamily.org</a>)
library for linear algebra.</p>
<p>Notice that the actual NIMBLE code is written as an R function
definition that is passed to <code>nimbleFunction</code> as the <code>run</code>
argument. Hence we call it the <em>run</em> code. run code is
written in the NIMBLE language. This is similar to a narrow subset of
R with some additional features. Formally, we view it as a distinct language
that encompasses what can be compiled from a nimbleFunction.</p>
<p>To write nimbleFunctions, you will need to learn:</p>
<ul>
<li>what R functions are supported for NIMBLE compilation and any
ways they differ from their regular R counterparts;</li>
<li>how NIMBLE handles types of variables;</li>
<li>how to declare types of <code>nimbleFunction</code> arguments and return values;</li>
<li>that compiled nimbleFunctions always pass arguments to each
other by reference.
<!--- 1. how to use nimbleList data structures. --></li>
</ul>
<p>The next sections cover each of these topics in turn.</p>
</div>
<div id="sec:r-fiunctions-implemented" class="section level2 hasAnchor" number="11.2">
<h2><span class="header-section-number">11.2</span> R functions (or variants) implemented in NIMBLE<a href="cha-RCfunctions.html#sec:r-fiunctions-implemented" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="finding-help-for-nimbles-versions-of-r-functions" class="section level3 hasAnchor" number="11.2.1">
<h3><span class="header-section-number">11.2.1</span> Finding help for NIMBLE’s versions of R functions<a href="cha-RCfunctions.html#finding-help-for-nimbles-versions-of-r-functions" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>Often, R help pages are available for NIMBLE’s versions of R functions
using the prefix ‘nim’ and capitalizing the next letter. For
example, help on NIMBLE’s version of <code>numeric</code> can be found by <code>help(nimNumeric)</code>. In some cases help is found directly using the name of the function as it appears in R.</p>
</div>
<div id="basic-operations" class="section level3 hasAnchor" number="11.2.2">
<h3><span class="header-section-number">11.2.2</span> Basic operations<a href="cha-RCfunctions.html#basic-operations" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>Basic R operations supported for NIMBLE compilation are listed in
Table <a href="cha-RCfunctions.html#tab:coreR">11.1</a>.</p>
<table>
<caption><span id="tab:coreR">Table 11.1: </span> Basic R manipulation functions in NIMBLE. For some of these functions, in addition to the usual use of <code>help()</code>, you can find help in R for NIMBLE’s version of a function by using the “nim” prefix and capitalizing the next letter. E.g. <code>help(nimC)</code> for help with <code>c()</code>.</caption>
<thead>
<tr class="header">
<th align="left">Function</th>
<th align="left">Comments (differences from R)</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left"><code>c()</code></td>
<td align="left">No <code>recursive</code> argument.</td>
</tr>
<tr class="even">
<td align="left"><code>rep()</code></td>
<td align="left">No <code>rep.int</code> or <code>rep_len</code> arguments.</td>
</tr>
<tr class="odd">
<td align="left"><code>seq()</code> and ‘:’</td>
<td align="left">Negative integer sequences from ‘:’, e.g. , <code>2:1</code> do not work.</td>
</tr>
<tr class="even">
<td align="left"><code>which()</code></td>
<td align="left">No <code>arr.ind</code> or <code>useNames</code> arguments.</td>
</tr>
<tr class="odd">
<td align="left"><code>diag()</code></td>
<td align="left">Works like R in three ways: <code>diag(vector)</code> returns a matrix with <code>vector</code> on the diagonal;</td>
</tr>
<tr class="even">
<td align="left"></td>
<td align="left"><code>diag(matrix)</code> returns the diagonal vector of <code>matrix</code>;</td>
</tr>
<tr class="odd">
<td align="left"></td>
<td align="left"><code>diag(n)</code> returns an <span class="math inline">\(n \times n\)</span> identity matrix. No <code>nrow</code> or <code>ncol</code> arguments.</td>
</tr>
<tr class="even">
<td align="left"><code>diag()<-</code></td>
<td align="left">Works for assigning the diagonal vector of a matrix.</td>
</tr>
<tr class="odd">
<td align="left"><code>dim()</code></td>
<td align="left">Works on a vector as well as higher-dimensional arguments.</td>
</tr>
<tr class="even">
<td align="left"><code>length()</code></td>
<td align="left"></td>
</tr>
<tr class="odd">
<td align="left"><code>is.na()</code></td>
<td align="left">Does not correctly handle NAs (or NaNs) from R that are type <code>'logical'</code> or <code>'integer'</code>,</td>
</tr>
<tr class="even">
<td align="left"></td>
<td align="left">so convert these using <code>as.numeric()</code> before passing from R to NIMBLE.</td>
</tr>
<tr class="odd">
<td align="left"><code>is.nan()</code></td>
<td align="left"></td>
</tr>
<tr class="even">
<td align="left"><code>any()</code></td>
<td align="left">One argument only; NAs treated as FALSE.</td>
</tr>
<tr class="odd">
<td align="left"><code>all()</code></td>
<td align="left">One argument only; NAs treated as FALSE.</td>
</tr>
<tr class="even">
<td align="left"><code>numeric()</code></td>
<td align="left">Allows additional arguments to control initialization.</td>
</tr>
<tr class="odd">
<td align="left"><code>logical()</code></td>
<td align="left">Allows additional arguments to control initialization.</td>
</tr>
<tr class="even">
<td align="left"><code>integer()</code></td>
<td align="left">Allows additional arguments to control initialization.</td>
</tr>
<tr class="odd">
<td align="left"><code>matrix()</code></td>
<td align="left">Allows additional arguments to control initialization.</td>
</tr>
<tr class="even">
<td align="left"><code>array()</code></td>
<td align="left">Allows additional arguments to control initialization.</td>
</tr>
<tr class="odd">
<td align="left">indexing</td>
<td align="left">Arbitrary integer and logical indexing is supported for objects of one or two dimensions.</td>
</tr>
<tr class="even">
<td align="left"></td>
<td align="left">For higher-dimensional objects, only <code>:</code> indexing works and then only to create an object</td>
</tr>
<tr class="odd">
<td align="left"></td>
<td align="left">of at most two dimensions.</td>
</tr>
</tbody>
</table>
<p>In addition to the above functions, we provide functions <code>any_na()</code> and <code>any_nan()</code> for finding if there are any <code>NA</code> or <code>NaN</code> values in a vector. These are equivalent to using <code>any(is.na())</code> and <code>any(is.nan())</code> in R, with the exception noted in the table above regarding <code>is.na()</code>.</p>
<p>Other R functions with numeric arguments and return value can be called during compiled execution by wrapping them as a <code>nimbleRcall</code> (see Section <a href="cha-RCfunctions.html#sec:calling-R-code">11.7</a>).</p>
<p>Next we cover some of these functions in more detail.</p>
<div id="numeric-integer-logical-matrix-and-array" class="section level4 hasAnchor" number="11.2.2.1">
<h4><span class="header-section-number">11.2.2.1</span> <em>numeric</em>, <em>integer</em>, <em>logical</em>, <em>matrix</em> and <em>array</em><a href="cha-RCfunctions.html#numeric-integer-logical-matrix-and-array" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p><code>numeric</code>, <code>integer</code>, or <code>logical</code> will create a 1-dimensional vector of
floating-point (or ‘double’ [precision]), integer, or logical values, respectively. The <code>length</code> argument specifies the vector
length (default 0), and the <code>value</code> argument specifies the initial
value either as a scalar (used for all vector elements, with default
0) or a vector. If a vector and its length is not equal to <code>length</code>, the remaining values will be filled by R-style recycling if the <code>recycle</code> argument is <code>TRUE</code> (which is the default). The <code>init</code> argument specifies
whether or not to initialize the elements in compiled code (default <code>TRUE</code>). If
first use of the variable does not rely on initial values, using
<code>init = FALSE</code> will yield slightly more efficient performance.</p>
<p><code>matrix</code> creates a 2-dimensional matrix object of either floating-point (if
<code>type = "double"</code>, the default), integer (if <code>type = "integer"</code>), or logical (if <code>type = "logical"</code>) values.
As in R, <code>nrow</code> and <code>ncol</code> arguments specify the number of rows and columns, respectively.
The <code>value</code> and <code>init</code> arguments are used in the same way as for
<code>numeric</code>, <code>integer</code>, and <code>logical</code>.</p>
<p><code>array</code> creates a vector or higher-dimensional object, depending
on the <code>dim</code> argument, which takes a vector of sizes for each
dimension. The <code>type</code>, <code>value</code> and <code>init</code> argument behave
the same as for <code>matrix</code>.</p>
<p>The best way to create an identity matrix is with <code>diag(n)</code>, which
returns an <span class="math inline">\(n \times n\)</span> identity matrix. NIMBLE also provides a deprecated
nimbleFunction <code>identityMatrix</code> that does the same thing.</p>
<p>Examples of these functions, and the related function <span class="math inline">\(`setSize`\)</span>
for changing the size of a numeric object, are given in Section <a href="cha-RCfunctions.html#sec:chang-sizes-exist">11.3.2.4</a>.</p>
</div>
<div id="sec:query-chang-sizes" class="section level4 hasAnchor" number="11.2.2.2">
<h4><span class="header-section-number">11.2.2.2</span> <em>length</em> and <em>dim</em><a href="cha-RCfunctions.html#sec:query-chang-sizes" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p><code>length</code> behaves like R’s <code>length</code> function. It
returns the <em>entire</em> length of X. That means if <code>X</code> is
multivariate, <code>length(X)</code> returns the product of the sizes of
the dimensions. NIMBLE’s version of <code>dim</code>, which has synonym <code>nimDim</code>, behaves like R’s
<code>dim</code> function for matrices or arrays and like R’s
<code>length</code> function for vectors. In other words, regardless of
whether the number of dimensions is 1 or more, it returns a vector
of the sizes.</p>
</div>
<div id="deprecated-creation-of-non-scalar-objects-using-declare" class="section level4 hasAnchor" number="11.2.2.3">
<h4><span class="header-section-number">11.2.2.3</span> Deprecated creation of non-scalar objects using <em>declare</em><a href="cha-RCfunctions.html#deprecated-creation-of-non-scalar-objects-using-declare" class="anchor-section" aria-label="Anchor link to header"></a></h4>
<p>Previous versions of NIMBLE provided a function <code>declare</code> for
declaring variables. The more R-like functions <code>numeric</code>,
<code>integer</code>, <code>logical</code>, <code>matrix</code> and <code>array</code> are intended to replace
<code>declare</code>, but <code>declare</code> is still supported for backward
compatibility. In a future version of NIMBLE, <code>declare</code> may be removed.</p>
</div>
</div>
<div id="sec:basic-math-linear" class="section level3 hasAnchor" number="11.2.3">
<h3><span class="header-section-number">11.2.3</span> Math and linear algebra<a href="cha-RCfunctions.html#sec:basic-math-linear" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>Numeric scalar and matrix mathematical operations are listed in Tables <a href="cha-RCfunctions.html#tab:functions2">11.2</a>-<a href="cha-RCfunctions.html#tab:functionsMatrix2">11.3</a>.</p>
<!---
would need to do some sed manipulation to be able to automate this cross-ref
\@ref(tab:functions) and \@ref(tab:functionsMatrix).
-->
<p>As in R, many scalar operations in NIMBLE will work component-wise on vectors or
higher dimensional objects. For example if B and C are vectors, <code>A = B + C</code> will add them and create vector C by component-wise
addition of B and C. In the current version of NIMBLE, component-wise operations
generally only work for vectors and matrices, not arrays with more
than two dimensions. The only exception is assignment: <code>A = B</code> will
work up to NIMBLE’s current limit of four dimensions.</p>
<table>
<caption><span id="tab:functions2">Table 11.2: </span> Functions operating on scalars, many of which can operate on each element (component-wise) of
vectors and matrices. Status column indicates if the function is currently provided in NIMBLE. Vector input column
indicates if the function can take a vector as an argument (i.e., if the function is vectorized).</caption>
<thead>
<tr class="header">
<th align="left">Usage</th>
<th align="left">Description</th>
<th align="left">Comments</th>
<th>Status</th>
<th>Vector input</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left"><code>x | y</code>, <code>x & y</code></td>
<td align="left">logical OR (<span class="math inline">\(|\)</span>) and AND(&)</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>!x</code></td>
<td align="left">logical not</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>x > y, x >= y</code></td>
<td align="left">greater than (and or equal to)</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>x < y, x <= y</code></td>
<td align="left">less than (and or equal to)</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>x != y, x == y</code></td>
<td align="left">(not) equals</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>x + y, x - y, x * y</code></td>
<td align="left">component-wise operators</td>
<td align="left">mix of scalar and vector</td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>x / y</code></td>
<td align="left">component-wise division</td>
<td align="left">vector <span class="math inline">\(x\)</span> and scalar <span class="math inline">\(y\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>x^y, pow(x, y)</code></td>
<td align="left">power</td>
<td align="left"><span class="math inline">\(x^y\)</span>; vector <span class="math inline">\(x\)</span>,scalar <span class="math inline">\(y\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>x %% y</code></td>
<td align="left">modulo (remainder)</td>
<td align="left"></td>
<td>yes</td>
<td>no</td>
</tr>
<tr class="even">
<td align="left"><code>min(x1, x2),</code></td>
<td align="left">min. (max.) of two scalars</td>
<td align="left"></td>
<td>yes</td>
<td>See <code>pmin</code>,</td>
</tr>
<tr class="odd">
<td align="left"><code>max(x1, x2)</code></td>
<td align="left"></td>
<td align="left"></td>
<td></td>
<td><code>pmax</code></td>
</tr>
<tr class="even">
<td align="left"><code>exp(x)</code></td>
<td align="left">exponential</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>log(x)</code></td>
<td align="left">natural logarithm</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>sqrt(x)</code></td>
<td align="left">square root</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>abs(x)</code></td>
<td align="left">absolute value</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>step(x)</code></td>
<td align="left">step function at 0</td>
<td align="left">0 if <span class="math inline">\(x<0\)</span>, 1 if <span class="math inline">\(x>=0\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>equals(x, y)</code></td>
<td align="left">equality of two scalars</td>
<td align="left">1 if <span class="math inline">\(x==y\)</span>, 0 if <span class="math inline">\(x != y\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>cube(x)</code></td>
<td align="left">third power</td>
<td align="left"><span class="math inline">\(x^3\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>sin(x), cos(x),</code></td>
<td align="left">trigonometric functions</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>tan(x)</code></td>
<td align="left"></td>
<td align="left"></td>
<td></td>
<td></td>
</tr>
<tr class="odd">
<td align="left"><code>asin(x), acos(x),</code></td>
<td align="left">inverse trigonometric functions</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>atan(x)</code></td>
<td align="left"></td>
<td align="left"></td>
<td></td>
<td></td>
</tr>
<tr class="odd">
<td align="left"><code>asinh(x), acosh(x),</code></td>
<td align="left">inv. hyperbolic trig. functions</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>atanh(x)</code></td>
<td align="left"></td>
<td align="left"></td>
<td></td>
<td></td>
</tr>
<tr class="odd">
<td align="left"><code>logit(x)</code></td>
<td align="left">logit</td>
<td align="left"><span class="math inline">\(\log(x/(1-x))\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>ilogit(x), expit(x)</code></td>
<td align="left">inverse logit</td>
<td align="left"><span class="math inline">\(\exp(x)/(1 + \exp(x))\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>probit(x)</code></td>
<td align="left">probit (Gaussian quantile)</td>
<td align="left"><span class="math inline">\(\Phi^{-1}(x)\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>iprobit(x), phi(x)</code></td>
<td align="left">inverse probit (Gaussian CDF)</td>
<td align="left"><span class="math inline">\(\Phi(x)\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>cloglog(x)</code></td>
<td align="left">complementary log log</td>
<td align="left"><span class="math inline">\(\log(-\log(1-x))\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>icloglog(x)</code></td>
<td align="left">inverse complementary log log</td>
<td align="left"><span class="math inline">\(1 - \exp(-\exp(x))\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>ceiling(x)</code></td>
<td align="left">ceiling function</td>
<td align="left"><span class="math inline">\(\lceil(x)\rceil\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>floor(x)</code></td>
<td align="left">floor function</td>
<td align="left"><span class="math inline">\(\lfloor(x)\rfloor\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>round(x)</code></td>
<td align="left">round to integer</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>trunc(x)</code></td>
<td align="left">truncation to integer</td>
<td align="left"></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="odd">
<td align="left"><code>lgamma(x), loggam(x)</code></td>
<td align="left">log gamma function</td>
<td align="left"><span class="math inline">\(\log \Gamma(x)\)</span></td>
<td>yes</td>
<td>yes</td>
</tr>
<tr class="even">
<td align="left"><code>besselK(x, nu,</code></td>
<td align="left">modified bessel function</td>
<td align="left">returns vector even if</td>
<td>yes</td>
<td>yes</td>