Returns the posterior mean main effects, pairwise effects, and edge inclusion indicators from a bgms model fit.
Usage
# S3 method for class 'bgms'
coef(object, ...)Value
A list with the following components:
- main
Posterior mean of the main-effect parameters.
NULLfor GGM models (no main effects). For OMRF models this is a numeric matrix (p x max_categories) of category thresholds. For mixed MRF models this is a list with$discrete(p x max_categories matrix) and$continuous(q x 1 matrix of means).- pairwise
Posterior mean of the partial association matrix (zero diagonal). Use
extract_precision()for the full precision matrix.- indicator
Posterior mean of the edge inclusion indicators (if available).
- mean_allocations
Posterior mean block allocations. Present only for Stochastic-Block edge-prior fits.
- mode_allocations
Posterior mode block allocations. Present only for Stochastic-Block edge-prior fits.
- num_blocks
Data frame of the posterior distribution over the number of blocks. Present only for Stochastic-Block edge-prior fits.
See also
bgm(), print.bgms(), summary.bgms()
Other posterior-methods:
coef.bgmCompare(),
print.bgmCompare(),
print.bgms(),
summary.bgmCompare(),
summary.bgms()
Examples
# \donttest{
fit = bgm(x = Wenchuan[, 1:3])
#> 2 rows with missing values excluded (n = 360 remaining).
#> To impute missing values instead, use na_action = "impute".
#> Chain 1 (Warmup): ⦗╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 50/4000 (1.2%)
#> Chain 2 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 54/4000 (1.4%)
#> Chain 3 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 62/4000 (1.6%)
#> Chain 4 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 68/4000 (1.7%)
#> Total (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 234/16000 (1.5%)
#> Elapsed: 0s | ETA: 0s
#> Chain 1 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 100/4000 (2.5%)
#> Chain 2 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 98/4000 (2.5%)
#> Chain 3 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 170/4000 (4.2%)
#> Chain 4 (Warmup): ⦗━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 139/4000 (3.5%)
#> Total (Warmup): ⦗━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 507/16000 (3.2%)
#> Elapsed: 1s | ETA: 31s
#> Chain 1 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 200/4000 (5.0%)
#> Chain 2 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 669/4000 (16.7%)
#> Chain 3 (Warmup): ⦗━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 304/4000 (7.6%)
#> Chain 4 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 766/4000 (19.1%)
#> Total (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1939/16000 (12.1%)
#> Elapsed: 2s | ETA: 15s
#> Chain 1 (Warmup): ⦗━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 450/4000 (11.2%)
#> Chain 2 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 960/4000 (24.0%)
#> Chain 3 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 453/4000 (11.3%)
#> Chain 4 (Warmup): ⦗━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1026/4000 (25.7%)
#> Total (Warmup): ⦗━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 2889/16000 (18.1%)
#> Elapsed: 3s | ETA: 14s
#> Chain 1 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 500/4000 (12.5%)
#> Chain 2 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1584/4000 (39.6%)
#> Chain 3 (Warmup): ⦗━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 701/4000 (17.5%)
#> Chain 4 (Warmup): ⦗━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━⦘ 1641/4000 (41.0%)
#> Total (Warmup): ⦗━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4426/16000 (27.7%)
#> Elapsed: 4s | ETA: 10s
#> Chain 1 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 800/4000 (20.0%)
#> Chain 2 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1656/4000 (41.4%)
#> Chain 3 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 996/4000 (24.9%)
#> Chain 4 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1896/4000 (47.4%)
#> Total (Warmup): ⦗━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 5348/16000 (33.4%)
#> Elapsed: 4s | ETA: 8s
#> Chain 1 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1100/4000 (27.5%)
#> Chain 2 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1694/4000 (42.4%)
#> Chain 3 (Warmup): ⦗━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1331/4000 (33.3%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 2157/4000 (53.9%)
#> Total (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 6282/16000 (39.3%)
#> Elapsed: 5s | ETA: 8s
#> Chain 1 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1400/4000 (35.0%)
#> Chain 2 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1899/4000 (47.5%)
#> Chain 3 (Warmup): ⦗━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━⦘ 1650/4000 (41.2%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━⦘ 2412/4000 (60.3%)
#> Total (Warmup): ⦗━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━⦘ 7361/16000 (46.0%)
#> Elapsed: 5s | ETA: 6s
#> Chain 1 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1700/4000 (42.5%)
#> Chain 2 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 2598/4000 (65.0%)
#> Chain 3 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1855/4000 (46.4%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━⦘ 3101/4000 (77.5%)
#> Total (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━⦘ 9254/16000 (57.8%)
#> Elapsed: 7s | ETA: 5s
#> Chain 1 (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 1900/4000 (47.5%)
#> Chain 2 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 2869/4000 (71.7%)
#> Chain 3 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 2084/4000 (52.1%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 3359/4000 (84.0%)
#> Total (Warmup): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 10212/16000 (63.8%)
#> Elapsed: 7s | ETA: 4s
#> Chain 1 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━⦘ 2150/4000 (53.8%)
#> Chain 2 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 3173/4000 (79.3%)
#> Chain 3 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 2364/4000 (59.1%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━⦘ 3650/4000 (91.2%)
#> Total (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━⦘ 11337/16000 (70.9%)
#> Elapsed: 8s | ETA: 3s
#> Chain 1 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 2400/4000 (60.0%)
#> Chain 2 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 3475/4000 (86.9%)
#> Chain 3 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━⦘ 2630/4000 (65.8%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺⦘ 3932/4000 (98.3%)
#> Total (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━⦘ 12437/16000 (77.7%)
#> Elapsed: 8s | ETA: 2s
#> Chain 1 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 2800/4000 (70.0%)
#> Chain 2 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 3779/4000 (94.5%)
#> Chain 3 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━⦘ 2904/4000 (72.6%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4000/4000 (100.0%)
#> Total (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 13483/16000 (84.3%)
#> Elapsed: 9s | ETA: 2s
#> Chain 1 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━⦘ 3250/4000 (81.2%)
#> Chain 2 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4000/4000 (100.0%)
#> Chain 3 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━⦘ 3243/4000 (81.1%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4000/4000 (100.0%)
#> Total (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━⦘ 14493/16000 (90.6%)
#> Elapsed: 9s | ETA: 1s
#> Chain 1 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 3700/4000 (92.5%)
#> Chain 2 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4000/4000 (100.0%)
#> Chain 3 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━⦘ 3731/4000 (93.3%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4000/4000 (100.0%)
#> Total (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 15431/16000 (96.4%)
#> Elapsed: 10s | ETA: 0s
#> Chain 1 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4000/4000 (100.0%)
#> Chain 2 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4000/4000 (100.0%)
#> Chain 3 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4000/4000 (100.0%)
#> Chain 4 (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 4000/4000 (100.0%)
#> Total (Sampling): ⦗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━⦘ 16000/16000 (100.0%)
#> Elapsed: 10s | ETA: 0s
coef(fit)
#> $main
#> cat (1) cat (2) cat (3) cat (4)
#> intrusion 0.8095135 -1.171906 -3.531671 -7.435522
#> dreams -0.3990840 -3.290096 -6.346986 -10.439243
#> flash 0.0709138 -2.134114 -4.581322 -8.424787
#>
#> $pairwise
#> intrusion dreams flash
#> intrusion 0.0000000 0.3493653 0.2138557
#> dreams 0.3493653 0.0000000 0.2801950
#> flash 0.2138557 0.2801950 0.0000000
#>
#> $indicator
#> intrusion dreams flash
#> intrusion 0 1 1
#> dreams 1 0 1
#> flash 1 1 0
#>
# }