Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Compile Jags Model from a Hyde NetworkDescriptionGenerates the JAGS code from the Hyde network and uses it to create an object representing a Bayesian graphical model. UsagecompileJagsModel(network, data = NULL, ...) Arguments
Details
ValueReturns a Author(s)Benjamin Nutter See Also
Examples
data(PE, package="HydeNet")
Net <- HydeNetwork(~ wells +
pe | wells +
d.dimer | pregnant*pe +
angio | pe +
treat | d.dimer*angio +
death | pe*treat,
data = PE)
compiledNet <- compileJagsModel(Net, n.chains=5)
#* Generate the posterior distribution
Posterior <- HydePosterior(compiledNet,
variable.names = c("d.dimer", "death"),
n.iter = 1000)
Posterior
#* For a single model (ie, not a decision model), the user may choose to
#* use the code{rjags} function code{coda.samples}.
#* However, this does not have a succinct print method
s <- coda.samples(compiledNet$jags,
variable.names = c("d.dimer", "death"),
n.iter=1000)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(HydeNet)
Loading required package: nnet
Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.1.0
Loaded modules: basemod,bugs
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HydeNet/compileJagsModel.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compileJagsModel
> ### Title: Compile Jags Model from a Hyde Network
> ### Aliases: compileJagsModel
>
> ### ** Examples
>
> data(PE, package="HydeNet")
> Net <- HydeNetwork(~ wells +
+ pe | wells +
+ d.dimer | pregnant*pe +
+ angio | pe +
+ treat | d.dimer*angio +
+ death | pe*treat,
+ data = PE)
>
>
> compiledNet <- compileJagsModel(Net, n.chains=5)
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 0
Unobserved stochastic nodes: 7
Total graph size: 90
Initializing model
Warning messages:
1: In bind_rows_(x, .id) :
binding factor and character vector, coercing into character vector
2: In bind_rows_(x, .id) :
binding factor and character vector, coercing into character vector
3: In bind_rows_(x, .id) :
binding factor and character vector, coercing into character vector
4: In bind_rows_(x, .id) :
binding factor and character vector, coercing into character vector
>
> #* Generate the posterior distribution
> Posterior <- HydePosterior(compiledNet,
+ variable.names = c("d.dimer", "death"),
+ n.iter = 1000)
> Posterior
d.dimer death chain_index obs_index
1 240.0554 No 1 1
2 228.9688 No 1 2
3 236.8301 No 1 3
4 235.9967 No 1 4
5 236.8104 No 1 5
6 243.2212 No 1 6
7 241.8320 No 1 7
8 234.8408 No 1 8
9 241.5265 No 1 9
10 237.7027 No 1 10
11 236.6772 No 1 11
12 236.6804 No 1 12
13 237.6084 No 1 13
14 243.5160 No 1 14
15 236.8758 No 1 15
16 233.9627 No 1 16
17 242.0520 No 1 17
18 240.3758 No 1 18
19 242.9079 No 1 19
20 233.9463 No 1 20
21 237.7165 No 1 21
22 240.2489 No 1 22
23 244.0848 No 1 23
24 248.4026 No 1 24
25 229.5003 No 1 25
26 233.0004 No 1 26
27 251.4121 No 1 27
28 241.6711 No 1 28
29 263.1135 No 1 29
30 238.9652 No 1 30
31 236.6187 Yes 1 31
32 238.3798 No 1 32
33 247.0881 Yes 1 33
34 356.6785 No 1 34
35 239.9796 No 1 35
36 235.6587 No 1 36
37 240.4534 No 1 37
38 235.3943 No 1 38
39 264.6220 No 1 39
40 321.6461 No 1 40
41 240.2583 No 1 41
42 240.3618 No 1 42
43 316.9179 No 1 43
44 240.5303 No 1 44
45 238.2582 No 1 45
46 239.0557 No 1 46
47 233.9876 No 1 47
48 236.1256 No 1 48
49 237.2944 No 1 49
50 239.6672 No 1 50
51 233.0045 No 1 51
52 236.8800 No 1 52
53 243.7963 No 1 53
54 233.2028 No 1 54
55 240.3231 No 1 55
56 246.8852 No 1 56
57 264.9559 No 1 57
58 300.2878 No 1 58
59 244.0375 No 1 59
60 236.5748 No 1 60
61 235.8641 No 1 61
62 242.9417 No 1 62
63 242.2320 No 1 63
64 230.0906 No 1 64
65 234.1900 No 1 65
66 235.6543 Yes 1 66
67 240.8381 No 1 67
68 258.0946 No 1 68
69 240.6204 No 1 69
70 233.0573 No 1 70
71 243.2229 No 1 71
72 237.2404 No 1 72
73 235.0120 No 1 73
74 233.0425 No 1 74
75 243.8169 No 1 75
76 279.6995 No 1 76
77 263.5627 No 1 77
78 304.4741 No 1 78
79 305.0717 No 1 79
80 251.1467 No 1 80
81 237.7738 No 1 81
82 303.5272 No 1 82
83 266.3612 No 1 83
84 236.7266 No 1 84
85 236.6102 No 1 85
86 313.4194 No 1 86
87 240.2179 No 1 87
88 238.6489 No 1 88
89 239.2500 No 1 89
90 245.2279 No 1 90
91 240.8836 No 1 91
92 239.9402 No 1 92
93 240.7574 Yes 1 93
94 237.1998 No 1 94
95 303.2442 No 1 95
96 228.0362 No 1 96
97 313.8207 No 1 97
98 244.0377 No 1 98
99 245.4594 No 1 99
100 333.2056 No 1 100
101 305.3218 No 1 101
102 233.2238 No 1 102
103 292.1871 No 1 103
104 234.4522 Yes 1 104
105 240.5637 No 1 105
106 238.0909 No 1 106
107 307.2861 No 1 107
108 247.8391 No 1 108
109 313.9613 No 1 109
110 239.4559 No 1 110
111 240.7908 No 1 111
112 236.2179 No 1 112
113 232.7067 No 1 113
114 308.6162 No 1 114
115 246.1673 No 1 115
116 304.4818 No 1 116
117 229.8164 No 1 117
118 237.5734 No 1 118
119 246.6249 Yes 1 119
120 234.8245 No 1 120
121 231.9740 No 1 121
122 239.9252 No 1 122
123 250.1992 No 1 123
124 235.4092 No 1 124
125 309.1576 Yes 1 125
126 240.0302 No 1 126
127 236.6945 No 1 127
128 308.0390 No 1 128
129 306.1418 No 1 129
130 249.5918 No 1 130
131 308.6025 Yes 1 131
132 236.1138 No 1 132
133 236.4675 Yes 1 133
134 337.8868 No 1 134
135 238.1912 No 1 135
136 233.2491 No 1 136
137 240.3126 No 1 137
138 301.6226 Yes 1 138
139 244.8686 No 1 139
140 230.3803 No 1 140
141 244.4653 No 1 141
142 267.7222 No 1 142
143 268.1041 No 1 143
144 239.2603 No 1 144
145 239.1956 No 1 145
146 307.1732 Yes 1 146
147 241.4490 No 1 147
148 306.9009 No 1 148
149 232.0773 No 1 149
150 237.4446 No 1 150
151 321.4513 No 1 151
152 243.7489 No 1 152
153 240.5240 No 1 153
154 247.2318 No 1 154
155 302.0321 No 1 155
156 235.5921 No 1 156
157 261.1949 No 1 157
158 234.9331 No 1 158
159 246.2207 No 1 159
160 302.0851 Yes 1 160
161 235.7651 No 1 161
162 240.5852 No 1 162
163 274.5652 No 1 163
164 248.4437 No 1 164
165 246.0420 No 1 165
166 239.5404 No 1 166
167 246.8227 No 1 167
168 295.8808 No 1 168
169 241.2402 No 1 169
170 252.6831 No 1 170
171 291.6038 Yes 1 171
172 231.4190 No 1 172
173 236.9986 No 1 173
174 333.4928 Yes 1 174
175 238.2346 No 1 175
176 240.4645 No 1 176
177 347.7333 Yes 1 177
178 234.0712 No 1 178
179 238.9691 No 1 179
180 232.2598 No 1 180
181 314.0694 No 1 181
182 234.8495 No 1 182
183 233.5854 No 1 183
184 267.7642 No 1 184
185 314.5363 No 1 185
186 228.9505 No 1 186
187 236.4884 No 1 187
188 234.2897 No 1 188
189 243.2411 No 1 189
190 237.8269 No 1 190
191 237.6370 No 1 191
192 306.4623 No 1 192
193 236.9449 No 1 193
194 242.6451 No 1 194
195 311.6332 No 1 195
196 241.0308 No 1 196
197 273.5399 No 1 197
198 251.8375 Yes 1 198
199 235.0187 No 1 199
200 234.0214 No 1 200
201 232.4204 No 1 201
202 244.7440 No 1 202
203 243.6298 No 1 203
204 245.1712 No 1 204
205 240.3253 No 1 205
206 241.7494 No 1 206
207 239.3493 Yes 1 207
208 236.2473 No 1 208
209 232.0085 No 1 209
210 233.2606 No 1 210
211 248.8653 No 1 211
212 253.9008 No 1 212
213 232.8948 No 1 213
214 311.0262 No 1 214
215 242.9728 No 1 215
216 267.6113 Yes 1 216
217 241.9458 Yes 1 217
218 239.6723 No 1 218
219 341.9919 No 1 219
220 272.2647 No 1 220
221 245.4182 No 1 221
222 241.8452 No 1 222
223 236.1154 No 1 223
224 334.4767 Yes 1 224
225 238.6235 No 1 225
226 309.7394 Yes 1 226
227 239.8097 No 1 227
228 247.2449 No 1 228
229 234.0084 No 1 229
230 238.0224 No 1 230
231 235.0480 No 1 231
232 236.8967 No 1 232
233 245.2227 No 1 233
234 232.2395 No 1 234
235 312.5140 No 1 235
236 308.4960 Yes 1 236
237 236.7503 No 1 237
238 234.6722 No 1 238
239 237.6541 No 1 239
240 240.8878 No 1 240
241 312.0095 Yes 1 241
242 231.5671 No 1 242
243 260.7936 No 1 243
244 236.7478 No 1 244
245 240.7593 No 1 245
246 231.0260 No 1 246
247 239.5327 No 1 247
248 242.8355 No 1 248
249 239.9659 No 1 249
250 243.6496 No 1 250
251 308.6733 No 1 251
252 247.3427 No 1 252
253 243.3965 No 1 253
254 236.4139 No 1 254
255 237.4108 No 1 255
256 251.4074 No 1 256
257 274.2904 No 1 257
258 240.5974 No 1 258
259 307.1792 No 1 259
260 252.9318 No 1 260
261 247.6187 No 1 261
262 299.3641 No 1 262
263 241.7724 No 1 263
264 233.2476 No 1 264
265 245.8048 No 1 265
266 310.9647 No 1 266
267 246.5929 No 1 267
268 234.1665 No 1 268
269 254.0425 No 1 269
270 239.0180 No 1 270
271 305.0225 No 1 271
272 243.4413 No 1 272
273 242.2036 No 1 273
274 317.3357 No 1 274
275 270.8245 No 1 275
276 226.8104 No 1 276
277 230.9723 No 1 277
278 275.9748 No 1 278
279 250.4573 No 1 279
280 240.6471 No 1 280
281 250.6662 No 1 281
282 235.5732 No 1 282
283 244.4798 No 1 283
284 234.0997 No 1 284
285 306.4812 No 1 285
286 248.5174 No 1 286
287 244.9128 No 1 287
288 241.8046 No 1 288
289 302.8245 No 1 289
290 240.0165 No 1 290
291 273.7086 No 1 291
292 231.7180 No 1 292
293 243.3711 No 1 293
294 235.5345 No 1 294
295 236.4194 No 1 295
296 303.9472 No 1 296
297 236.0634 No 1 297
298 312.8428 No 1 298
299 243.0947 No 1 299
300 238.8568 No 1 300
301 235.8516 No 1 301
302 303.1704 No 1 302
303 243.2326 No 1 303
304 231.1800 No 1 304
305 341.7638 No 1 305
306 244.9423 No 1 306
307 246.5463 No 1 307
308 306.6596 Yes 1 308
309 242.7666 No 1 309
310 235.1357 No 1 310
311 232.2319 No 1 311
312 232.5253 Yes 1 312
313 240.7247 No 1 313
314 235.2562 No 1 314
315 242.0085 No 1 315
316 302.7058 Yes 1 316
317 240.5972 No 1 317
318 243.0508 No 1 318
319 310.6307 Yes 1 319
320 239.3277 No 1 320
321 244.1874 No 1 321
322 242.7881 No 1 322
323 241.0625 No 1 323
324 237.4599 No 1 324
325 233.0354 No 1 325
326 239.7789 No 1 326
327 303.6891 No 1 327
328 245.5611 No 1 328
329 240.4593 No 1 329
330 307.9586 Yes 1 330
331 234.6394 No 1 331
332 267.8695 Yes 1 332
333 240.3092 No 1 333
334 232.0038 No 1 334
335 239.3490 No 1 335
336 233.8993 No 1 336
337 235.8179 No 1 337
338 340.6429 No 1 338
339 236.3423 No 1 339
340 311.3741 Yes 1 340
341 228.1563 No 1 341
342 235.6080 No 1 342
343 237.1641 No 1 343
344 278.8061 No 1 344
345 301.4899 No 1 345
346 240.3732 No 1 346
347 339.7007 No 1 347
348 238.1614 No 1 348
349 309.4602 No 1 349
350 240.8313 No 1 350
351 233.9137 No 1 351
352 304.6886 No 1 352
353 233.7468 No 1 353
354 240.4547 No 1 354
355 304.6932 Yes 1 355
356 245.1033 No 1 356
357 242.6141 No 1 357
358 242.6034 No 1 358
359 308.4275 No 1 359
360 239.0835 No 1 360
361 240.9989 No 1 361
362 236.5532 No 1 362
363 265.3860 No 1 363
364 242.5568 No 1 364
365 241.8813 No 1 365
366 247.4449 No 1 366
367 308.5176 No 1 367
368 307.1464 No 1 368
369 269.2151 No 1 369
370 236.7683 No 1 370
371 232.7996 No 1 371
372 243.8774 Yes 1 372
373 263.9413 No 1 373
374 314.2993 No 1 374
375 241.9901 No 1 375
376 243.3460 No 1 376
377 240.7871 No 1 377
378 236.4621 No 1 378
379 245.2165 No 1 379
380 281.9419 No 1 380
381 234.2493 No 1 381
382 242.0849 No 1 382
383 240.9983 No 1 383
384 236.0189 No 1 384
385 240.9716 No 1 385
386 269.3173 No 1 386
387 237.4571 No 1 387
388 239.0852 No 1 388
389 236.7594 No 1 389
390 307.2145 No 1 390
391 243.5391 No 1 391
392 242.0075 No 1 392
393 249.9576 No 1 393
394 240.9574 No 1 394
395 291.8259 No 1 395
396 261.2630 No 1 396
397 255.0137 No 1 397
398 332.8382 No 1 398
399 243.5118 No 1 399
400 242.6284 No 1 400
401 306.5232 Yes 1 401
402 240.4316 No 1 402
403 272.2747 Yes 1 403
404 316.4411 No 1 404
405 270.4623 No 1 405
406 241.5676 No 1 406
407 307.1282 No 1 407
408 272.3460 No 1 408
409 232.9105 No 1 409
410 302.1516 No 1 410
411 238.9420 No 1 411
412 240.0428 No 1 412
413 243.9045 No 1 413
414 311.1270 Yes 1 414
415 262.2377 No 1 415
416 226.1526 No 1 416
417 239.4075 No 1 417
418 262.7464 No 1 418
419 237.1992 No 1 419
420 239.1140 No 1 420
421 269.8893 No 1 421
422 242.4586 No 1 422
423 246.5022 No 1 423
424 224.3018 No 1 424
425 233.1978 No 1 425
426 244.9693 No 1 426
427 307.2683 Yes 1 427
428 229.1313 No 1 428
429 236.8495 No 1 429
430 231.2805 No 1 430
431 274.9995 No 1 431
432 236.2897 No 1 432
433 244.8840 No 1 433
434 304.4227 Yes 1 434
435 239.1514 No 1 435
436 239.1729 No 1 436
437 247.3503 No 1 437
438 224.9750 No 1 438
439 232.2488 No 1 439
440 270.8350 No 1 440
441 239.1676 No 1 441
442 240.3677 No 1 442
443 232.2874 No 1 443
444 241.9341 No 1 444
445 262.8751 No 1 445
446 243.1060 No 1 446
447 240.7895 No 1 447
448 308.4634 Yes 1 448
449 248.9335 No 1 449
450 249.0457 No 1 450
451 247.0744 No 1 451
452 239.7668 No 1 452
453 247.6795 No 1 453
454 306.6280 No 1 454
455 235.1047 No 1 455
456 303.9795 No 1 456
457 239.7722 No 1 457
458 262.6511 No 1 458
459 239.2911 No 1 459
460 245.8000 No 1 460
461 242.3339 No 1 461
462 231.1512 No 1 462
463 240.8658 No 1 463
464 241.8280 No 1 464
465 236.3678 No 1 465
466 279.4997 No 1 466
467 243.0329 No 1 467
468 275.9841 No 1 468
469 241.5224 No 1 469
470 239.2879 No 1 470
471 239.5034 No 1 471
472 245.1415 No 1 472
473 304.5580 No 1 473
474 237.1774 No 1 474
475 240.8737 No 1 475
476 244.9624 No 1 476
477 243.7947 No 1 477
478 251.8780 No 1 478
479 232.4435 No 1 479
480 234.5323 No 1 480
481 247.2508 No 1 481
482 244.2422 No 1 482
483 241.5419 No 1 483
484 318.8758 No 1 484
485 244.3784 No 1 485
486 299.2707 Yes 1 486
487 239.2751 No 1 487
488 240.9240 No 1 488
489 242.9651 No 1 489
490 243.6111 No 1 490
491 234.5892 No 1 491
492 244.0379 No 1 492
493 269.0530 No 1 493
494 265.8738 No 1 494
495 242.0566 No 1 495
496 240.9841 No 1 496
497 246.2239 No 1 497
498 302.3615 No 1 498
499 231.9864 No 1 499
500 248.4218 No 1 500
501 244.4063 No 1 501
502 244.8031 No 1 502
503 235.4623 No 1 503
504 309.4585 Yes 1 504
505 239.3600 No 1 505
506 247.1160 No 1 506
507 270.1305 No 1 507
508 236.3439 Yes 1 508
509 242.2468 No 1 509
510 239.0807 No 1 510
511 270.9809 No 1 511
512 240.0600 Yes 1 512
513 269.4741 No 1 513
514 308.1178 Yes 1 514
515 240.2096 No 1 515
516 241.3405 No 1 516
517 233.5454 No 1 517
518 310.0776 Yes 1 518
519 234.1974 No 1 519
520 242.0505 No 1 520
521 241.9222 No 1 521
522 238.2666 No 1 522
523 234.0851 No 1 523
524 308.0969 Yes 1 524
525 307.6915 No 1 525
526 237.6406 No 1 526
527 304.6651 Yes 1 527
528 240.5769 No 1 528
529 260.8309 No 1 529
530 243.9493 No 1 530
531 238.7649 No 1 531
532 236.0359 No 1 532
533 268.3616 No 1 533
534 241.8040 Yes 1 534
535 234.4815 No 1 535
536 243.7400 No 1 536
537 238.6310 No 1 537
538 243.9569 No 1 538
539 247.6912 No 1 539
540 306.5151 No 1 540
541 239.2594 No 1 541
542 307.4474 No 1 542
543 234.8883 No 1 543
544 248.0528 No 1 544
545 243.1140 No 1 545
546 241.0461 No 1 546
547 231.3711 No 1 547
548 245.2213 No 1 548
549 236.4754 No 1 549
550 271.8141 No 1 550
551 235.5341 No 1 551
552 235.6722 No 1 552
553 234.0819 No 1 553
554 244.5249 No 1 554
555 236.4663 No 1 555
556 303.7446 No 1 556
557 240.7544 No 1 557
558 243.7189 No 1 558
559 231.9391 No 1 559
560 309.7779 No 1 560
561 337.0425 No 1 561
562 237.5868 No 1 562
563 242.7798 No 1 563
564 236.2231 No 1 564
565 306.7160 No 1 565
566 232.3664 No 1 566
567 248.0793 No 1 567
568 237.3606 Yes 1 568
569 309.4453 No 1 569
570 234.8863 No 1 570
571 277.6786 No 1 571
572 234.5649 No 1 572
573 232.0807 No 1 573
574 238.3002 No 1 574
575 237.7041 No 1 575
576 237.0918 No 1 576
577 242.9315 No 1 577
578 262.2703 No 1 578
579 316.4800 No 1 579
580 265.8577 No 1 580
581 251.3631 No 1 581
582 229.6346 No 1 582
583 250.2157 No 1 583
584 338.5449 No 1 584
585 241.5222 No 1 585
586 241.7962 No 1 586
587 271.1830 No 1 587
588 238.7672 No 1 588
589 233.0706 No 1 589
590 236.0410 No 1 590
591 233.9203 No 1 591
592 298.2036 Yes 1 592
593 243.1053 No 1 593
594 315.8495 No 1 594
595 230.8304 No 1 595
596 244.5070 No 1 596
597 235.1002 No 1 597
598 234.0205 No 1 598
599 237.0283 No 1 599
600 249.0888 No 1 600
601 237.2412 No 1 601
602 233.9538 No 1 602
603 234.5847 No 1 603
604 241.5171 No 1 604
605 238.2759 No 1 605
606 309.1580 Yes 1 606
607 233.3175 No 1 607
608 239.5378 No 1 608
609 229.4378 No 1 609
610 247.8263 No 1 610
611 249.2420 No 1 611
612 307.9031 No 1 612
613 267.9032 No 1 613
614 238.9962 No 1 614
615 245.8479 No 1 615
616 235.8448 No 1 616
617 228.5330 No 1 617
618 238.7552 No 1 618
619 279.2717 No 1 619
620 248.2473 No 1 620
621 245.0854 No 1 621
622 271.2500 No 1 622
623 234.0937 No 1 623
624 238.3286 No 1 624
625 309.4446 Yes 1 625
626 239.8316 No 1 626
627 241.6313 No 1 627
628 300.0900 No 1 628
629 242.6895 No 1 629
630 234.5550 No 1 630
631 272.7999 No 1 631
632 308.5198 No 1 632
633 231.7385 No 1 633
634 269.5142 No 1 634
635 244.6430 No 1 635
636 238.4095 No 1 636
637 253.1682 No 1 637
638 241.4307 No 1 638
639 267.8274 No 1 639
640 312.6152 No 1 640
641 240.8667 No 1 641
642 244.1488 No 1 642
643 314.4889 No 1 643
644 245.4820 No 1 644
645 242.9923 No 1 645
646 253.8542 No 1 646
647 306.8319 No 1 647
648 242.8578 No 1 648
649 233.9700 No 1 649
650 236.9383 No 1 650
651 238.8203 No 1 651
652 312.3609 Yes 1 652
653 308.1697 No 1 653
654 239.8117 No 1 654
655 247.9824 No 1 655
656 242.8285 No 1 656
657 235.7331 No 1 657
658 239.4835 No 1 658
659 241.0515 No 1 659
660 306.7133 Yes 1 660
661
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and