Computes a battery of convergence tests and diagnostic plots for an
hbmfit object. This is the primary convergence diagnostic function
in hbsaems (supersedes the deprecated hbcc).
Arguments
- model
An
hbmfitorbrmsfitobject.- diag_tests
Character vector of tests to run. Any subset of
c("rhat", "geweke", "heidel", "raftery").- plot_types
Character vector of plot types to generate. Any subset of
c("trace", "dens", "acf", "nuts_energy", "rhat", "neff").- ...
Additional arguments passed to the underlying brms or coda routines.
Value
An hbcc_results object containing:
rhat_essMatrix with columns
Rhat,Bulk_ESS,Tail_ESS.geweke,raftery,heidelOutputs from the corresponding coda routines, or
NULLwhen the test fails.plotsNamed list of
ggplot/bayesplotobjects.
Details
For each parameter \(\theta_j\), the Gelman-Rubin statistic is computed as $$\widehat{R}_j = \sqrt{\frac{\widehat{\mathrm{var}}^+(\theta_j)}{W_j}}$$ where \(W_j\) is the within-chain variance and \(\widehat{\mathrm{var}}^+\) is the marginal posterior variance estimate. Values close to 1 (typically below 1.1) indicate convergence.
Examples
# \donttest{
library(hbsaems)
library(brms)
data("data_fhnorm")
# Uses brms's default MCMC settings (chains = 4, iter = 2000,
# warmup = 1000). For challenging posteriors (e.g. funnel
# geometries in Fay-Herriot with small D_i), consider
# chains = 4, iter = 4000, warmup = 2000 and
# control = list(adapt_delta = 0.99).
model <- hbm(brms::bf(y ~ x1 + x2 + x3),
data = data_fhnorm,
re = ~ (1 | regency), # area-level random effect
chains = 4, iter = 2000, warmup = 1000,
cores = 1, seed = 123, refresh = 0)
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 25 divergent transitions after warmup. See
#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 4 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> https://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.35, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> https://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> https://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> https://mc-stan.org/misc/warnings.html#tail-ess
diag <- convergence_check(model)
#> Warning: Low E-BFMI (< 0.3) in 4 chain(s); the posterior may have heavy tails the sampler explores poorly. Consider reparameterisation or longer warmup.
#> Warning: 25 divergent transition(s) detected; estimates may be biased. Increase adapt_delta (e.g. 0.99) or reparameterise.
summary(diag)
#>
#> ===== Convergence Diagnostics Summary =====
#>
#> Divergent transitions: 25 (0.62%) <-- WARNING
#> E-BFMI (min over chains): 0.008 <-- WARNING (< 0.3)
#> Max-treedepth hit rate: 0.00%
#>
#> R-hat:
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> 1.005 1.049 1.073 1.078 1.095 1.346
#>
#> Bulk ESS:
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> 9.364 31.783 114.041 456.203 680.919 2670.063
#>
#> Tail ESS:
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> 12.63 601.22 792.12 855.54 1032.55 2115.53
#>
#> Geweke test (Z-scores):
#> [[1]]
#>
#> Fraction in 1st window = 0.1
#> Fraction in 2nd window = 0.5
#>
#> b_Intercept b_x1
#> -0.15824 1.60612
#> b_x2 b_x3
#> 0.88420 -0.53576
#> sd_regency__Intercept sigma
#> -2.52915 2.29708
#> Intercept r_regency[regency_001,Intercept]
#> -0.27931 2.88638
#> r_regency[regency_002,Intercept] r_regency[regency_003,Intercept]
#> 0.65180 1.96971
#> r_regency[regency_004,Intercept] r_regency[regency_005,Intercept]
#> 1.56594 -0.71116
#> r_regency[regency_006,Intercept] r_regency[regency_007,Intercept]
#> -1.89830 1.92871
#> r_regency[regency_008,Intercept] r_regency[regency_009,Intercept]
#> -1.62656 1.90548
#> r_regency[regency_010,Intercept] r_regency[regency_011,Intercept]
#> 1.26861 -0.32483
#> r_regency[regency_012,Intercept] r_regency[regency_013,Intercept]
#> -2.41782 3.13014
#> r_regency[regency_014,Intercept] r_regency[regency_015,Intercept]
#> 2.26103 -3.13972
#> r_regency[regency_016,Intercept] r_regency[regency_017,Intercept]
#> 2.19214 2.61427
#> r_regency[regency_018,Intercept] r_regency[regency_019,Intercept]
#> 3.12511 2.31012
#> r_regency[regency_020,Intercept] r_regency[regency_021,Intercept]
#> -2.59151 -2.34553
#> r_regency[regency_022,Intercept] r_regency[regency_023,Intercept]
#> -2.18168 -2.37945
#> r_regency[regency_024,Intercept] r_regency[regency_025,Intercept]
#> -2.08990 -1.77198
#> r_regency[regency_026,Intercept] r_regency[regency_027,Intercept]
#> -0.43900 1.34708
#> r_regency[regency_028,Intercept] r_regency[regency_029,Intercept]
#> -2.59289 2.07400
#> r_regency[regency_030,Intercept] r_regency[regency_031,Intercept]
#> 1.30394 0.17685
#> r_regency[regency_032,Intercept] r_regency[regency_033,Intercept]
#> 0.46099 -2.30008
#> r_regency[regency_034,Intercept] r_regency[regency_035,Intercept]
#> -1.78855 3.67220
#> r_regency[regency_036,Intercept] r_regency[regency_037,Intercept]
#> 1.00633 1.96558
#> r_regency[regency_038,Intercept] r_regency[regency_039,Intercept]
#> -0.37151 -2.37390
#> r_regency[regency_040,Intercept] r_regency[regency_041,Intercept]
#> -2.09146 -1.99156
#> r_regency[regency_042,Intercept] r_regency[regency_043,Intercept]
#> -1.91026 -1.31370
#> r_regency[regency_044,Intercept] r_regency[regency_045,Intercept]
#> -3.04051 2.58990
#> r_regency[regency_046,Intercept] r_regency[regency_047,Intercept]
#> -3.08812 -2.00331
#> r_regency[regency_048,Intercept] r_regency[regency_049,Intercept]
#> 3.39274 -0.75400
#> r_regency[regency_050,Intercept] r_regency[regency_051,Intercept]
#> 0.92543 -2.41609
#> r_regency[regency_052,Intercept] r_regency[regency_053,Intercept]
#> 2.00808 1.54248
#> r_regency[regency_054,Intercept] r_regency[regency_055,Intercept]
#> -1.41961 -0.61713
#> r_regency[regency_056,Intercept] r_regency[regency_057,Intercept]
#> 1.41193 -0.29367
#> r_regency[regency_058,Intercept] r_regency[regency_059,Intercept]
#> -2.10775 -3.65790
#> r_regency[regency_060,Intercept] r_regency[regency_061,Intercept]
#> 2.28392 -2.09853
#> r_regency[regency_062,Intercept] r_regency[regency_063,Intercept]
#> -2.67487 -1.52616
#> r_regency[regency_064,Intercept] r_regency[regency_065,Intercept]
#> 2.64206 3.16218
#> r_regency[regency_066,Intercept] r_regency[regency_067,Intercept]
#> 2.48188 -2.25529
#> r_regency[regency_068,Intercept] r_regency[regency_069,Intercept]
#> 2.04454 3.01248
#> r_regency[regency_070,Intercept] r_regency[regency_071,Intercept]
#> 3.32831 -2.42450
#> r_regency[regency_072,Intercept] r_regency[regency_073,Intercept]
#> 2.85159 2.40675
#> r_regency[regency_074,Intercept] r_regency[regency_075,Intercept]
#> -1.45759 1.49635
#> r_regency[regency_076,Intercept] r_regency[regency_077,Intercept]
#> -2.05644 1.26249
#> r_regency[regency_078,Intercept] r_regency[regency_079,Intercept]
#> 2.91413 -2.15001
#> r_regency[regency_080,Intercept] r_regency[regency_081,Intercept]
#> -0.85733 3.69162
#> r_regency[regency_082,Intercept] r_regency[regency_083,Intercept]
#> 2.20703 0.91390
#> r_regency[regency_084,Intercept] r_regency[regency_085,Intercept]
#> 0.15637 -2.90992
#> r_regency[regency_086,Intercept] r_regency[regency_087,Intercept]
#> -1.91843 -0.54891
#> r_regency[regency_088,Intercept] r_regency[regency_089,Intercept]
#> -0.23481 -2.63679
#> r_regency[regency_090,Intercept] r_regency[regency_091,Intercept]
#> 1.92409 -2.02769
#> r_regency[regency_092,Intercept] r_regency[regency_093,Intercept]
#> 2.39729 4.36079
#> r_regency[regency_094,Intercept] r_regency[regency_095,Intercept]
#> -2.38297 0.02689
#> r_regency[regency_096,Intercept] r_regency[regency_097,Intercept]
#> 4.00009 -2.27511
#> r_regency[regency_098,Intercept] r_regency[regency_099,Intercept]
#> -0.25542 -1.92359
#> r_regency[regency_100,Intercept] lprior
#> 2.62163 -0.37048
#> lp__ z_1[1,1]
#> -2.28691 2.11962
#> z_1[1,2] z_1[1,3]
#> 0.17088 2.61201
#> z_1[1,4] z_1[1,5]
#> 1.24362 -1.13379
#> z_1[1,6] z_1[1,7]
#> -1.09598 2.06534
#> z_1[1,8] z_1[1,9]
#> -0.78965 2.58728
#> z_1[1,10] z_1[1,11]
#> 1.87922 -0.60529
#> z_1[1,12] z_1[1,13]
#> -2.61012 3.89437
#> z_1[1,14] z_1[1,15]
#> 2.64685 -3.34579
#> z_1[1,16] z_1[1,17]
#> 2.11491 2.40921
#> z_1[1,18] z_1[1,19]
#> 3.45070 2.70676
#> z_1[1,20] z_1[1,21]
#> -2.48499 -2.12125
#> z_1[1,22] z_1[1,23]
#> -2.00494 -1.20430
#> z_1[1,24] z_1[1,25]
#> -1.68542 -2.43801
#> z_1[1,26] z_1[1,27]
#> 0.54678 1.53436
#> z_1[1,28] z_1[1,29]
#> -2.19845 0.74513
#> z_1[1,30] z_1[1,31]
#> 1.05580 0.15998
#> z_1[1,32] z_1[1,33]
#> 0.03103 -2.27982
#> z_1[1,34] z_1[1,35]
#> -2.39870 2.94442
#> z_1[1,36] z_1[1,37]
#> -0.02712 2.69929
#> z_1[1,38] z_1[1,39]
#> -0.27441 -2.51660
#> z_1[1,40] z_1[1,41]
#> -2.65653 -2.48684
#> z_1[1,42] z_1[1,43]
#> -1.45412 -0.63725
#> z_1[1,44] z_1[1,45]
#> -2.01200 2.40829
#> z_1[1,46] z_1[1,47]
#> -3.80717 -1.68514
#> z_1[1,48] z_1[1,49]
#> 2.42407 -1.43542
#> z_1[1,50] z_1[1,51]
#> 1.02343 -3.09506
#> z_1[1,52] z_1[1,53]
#> 2.06200 0.15922
#> z_1[1,54] z_1[1,55]
#> -0.30823 -0.51112
#> z_1[1,56] z_1[1,57]
#> 0.39254 0.85266
#> z_1[1,58] z_1[1,59]
#> -2.40147 -2.56096
#> z_1[1,60] z_1[1,61]
#> 3.11313 -2.24344
#> z_1[1,62] z_1[1,63]
#> -3.31091 0.31605
#> z_1[1,64] z_1[1,65]
#> 2.06285 3.29296
#> z_1[1,66] z_1[1,67]
#> 1.76390 -1.70594
#> z_1[1,68] z_1[1,69]
#> 2.34826 3.17592
#> z_1[1,70] z_1[1,71]
#> 3.03904 -1.71170
#> z_1[1,72] z_1[1,73]
#> 1.68881 3.09550
#> z_1[1,74] z_1[1,75]
#> -0.34911 0.54012
#> z_1[1,76] z_1[1,77]
#> -2.43748 0.84206
#> z_1[1,78] z_1[1,79]
#> 2.06353 -2.33366
#> z_1[1,80] z_1[1,81]
#> -1.59284 2.28628
#> z_1[1,82] z_1[1,83]
#> 1.78741 0.66343
#> z_1[1,84] z_1[1,85]
#> -0.91615 -2.18634
#> z_1[1,86] z_1[1,87]
#> -2.18771 -0.48931
#> z_1[1,88] z_1[1,89]
#> -1.41842 -1.63330
#> z_1[1,90] z_1[1,91]
#> 0.87632 -2.02861
#> z_1[1,92] z_1[1,93]
#> 2.03824 1.55679
#> z_1[1,94] z_1[1,95]
#> -3.47342 0.84319
#> z_1[1,96] z_1[1,97]
#> 0.69043 -1.61334
#> z_1[1,98] z_1[1,99]
#> 0.02948 -1.67558
#> z_1[1,100]
#> 3.30813
#>
#>
#> [[2]]
#>
#> Fraction in 1st window = 0.1
#> Fraction in 2nd window = 0.5
#>
#> b_Intercept b_x1
#> -1.95358 -7.60496
#> b_x2 b_x3
#> 4.08080 0.36287
#> sd_regency__Intercept sigma
#> 3.92596 -4.61273
#> Intercept r_regency[regency_001,Intercept]
#> -1.37008 -4.66496
#> r_regency[regency_002,Intercept] r_regency[regency_003,Intercept]
#> -1.16556 -3.38597
#> r_regency[regency_004,Intercept] r_regency[regency_005,Intercept]
#> 4.54002 6.47226
#> r_regency[regency_006,Intercept] r_regency[regency_007,Intercept]
#> 5.94546 -2.67606
#> r_regency[regency_008,Intercept] r_regency[regency_009,Intercept]
#> 4.47313 -2.71448
#> r_regency[regency_010,Intercept] r_regency[regency_011,Intercept]
#> -3.56064 -2.25937
#> r_regency[regency_012,Intercept] r_regency[regency_013,Intercept]
#> 2.95943 -2.09253
#> r_regency[regency_014,Intercept] r_regency[regency_015,Intercept]
#> -1.33955 4.79756
#> r_regency[regency_016,Intercept] r_regency[regency_017,Intercept]
#> -3.53830 -3.13828
#> r_regency[regency_018,Intercept] r_regency[regency_019,Intercept]
#> -1.90589 -2.78391
#> r_regency[regency_020,Intercept] r_regency[regency_021,Intercept]
#> 3.64799 3.74094
#> r_regency[regency_022,Intercept] r_regency[regency_023,Intercept]
#> 1.38284 2.40322
#> r_regency[regency_024,Intercept] r_regency[regency_025,Intercept]
#> 3.94104 6.11481
#> r_regency[regency_026,Intercept] r_regency[regency_027,Intercept]
#> 4.95190 2.71749
#> r_regency[regency_028,Intercept] r_regency[regency_029,Intercept]
#> 4.41540 -2.35089
#> r_regency[regency_030,Intercept] r_regency[regency_031,Intercept]
#> 2.54996 2.35183
#> r_regency[regency_032,Intercept] r_regency[regency_033,Intercept]
#> 8.73909 4.57671
#> r_regency[regency_034,Intercept] r_regency[regency_035,Intercept]
#> 2.84530 -2.73561
#> r_regency[regency_036,Intercept] r_regency[regency_037,Intercept]
#> -0.86591 -2.95689
#> r_regency[regency_038,Intercept] r_regency[regency_039,Intercept]
#> 6.41156 3.91242
#> r_regency[regency_040,Intercept] r_regency[regency_041,Intercept]
#> 3.54186 3.36529
#> r_regency[regency_042,Intercept] r_regency[regency_043,Intercept]
#> 3.42232 2.95368
#> r_regency[regency_044,Intercept] r_regency[regency_045,Intercept]
#> 5.12949 -2.68025
#> r_regency[regency_046,Intercept] r_regency[regency_047,Intercept]
#> 4.97750 5.05569
#> r_regency[regency_048,Intercept] r_regency[regency_049,Intercept]
#> -1.46592 1.20026
#> r_regency[regency_050,Intercept] r_regency[regency_051,Intercept]
#> -0.25201 2.28409
#> r_regency[regency_052,Intercept] r_regency[regency_053,Intercept]
#> -4.36636 -1.60295
#> r_regency[regency_054,Intercept] r_regency[regency_055,Intercept]
#> 10.33209 0.13763
#> r_regency[regency_056,Intercept] r_regency[regency_057,Intercept]
#> -1.63304 0.85220
#> r_regency[regency_058,Intercept] r_regency[regency_059,Intercept]
#> 5.07435 1.21834
#> r_regency[regency_060,Intercept] r_regency[regency_061,Intercept]
#> -4.00153 3.15308
#> r_regency[regency_062,Intercept] r_regency[regency_063,Intercept]
#> 4.04068 4.78043
#> r_regency[regency_064,Intercept] r_regency[regency_065,Intercept]
#> -3.70226 -3.16944
#> r_regency[regency_066,Intercept] r_regency[regency_067,Intercept]
#> -3.08322 2.35621
#> r_regency[regency_068,Intercept] r_regency[regency_069,Intercept]
#> -4.18234 1.02832
#> r_regency[regency_070,Intercept] r_regency[regency_071,Intercept]
#> -3.49818 5.24672
#> r_regency[regency_072,Intercept] r_regency[regency_073,Intercept]
#> -3.84102 -2.83323
#> r_regency[regency_074,Intercept] r_regency[regency_075,Intercept]
#> 0.45650 1.01657
#> r_regency[regency_076,Intercept] r_regency[regency_077,Intercept]
#> 4.05114 1.69138
#> r_regency[regency_078,Intercept] r_regency[regency_079,Intercept]
#> -2.33362 3.28153
#> r_regency[regency_080,Intercept] r_regency[regency_081,Intercept]
#> 9.24354 -4.21282
#> r_regency[regency_082,Intercept] r_regency[regency_083,Intercept]
#> -2.51509 -0.47672
#> r_regency[regency_084,Intercept] r_regency[regency_085,Intercept]
#> -1.24322 3.39027
#> r_regency[regency_086,Intercept] r_regency[regency_087,Intercept]
#> 4.21053 6.63743
#> r_regency[regency_088,Intercept] r_regency[regency_089,Intercept]
#> 6.50785 5.93525
#> r_regency[regency_090,Intercept] r_regency[regency_091,Intercept]
#> -3.22985 7.61296
#> r_regency[regency_092,Intercept] r_regency[regency_093,Intercept]
#> -3.00287 -2.76285
#> r_regency[regency_094,Intercept] r_regency[regency_095,Intercept]
#> 3.35161 -0.80392
#> r_regency[regency_096,Intercept] r_regency[regency_097,Intercept]
#> -1.58111 3.74010
#> r_regency[regency_098,Intercept] r_regency[regency_099,Intercept]
#> 9.19121 3.83075
#> r_regency[regency_100,Intercept] lprior
#> -3.12281 0.25977
#> lp__ z_1[1,1]
#> 7.54083 -4.21147
#> z_1[1,2] z_1[1,3]
#> 0.19295 -3.44074
#> z_1[1,4] z_1[1,5]
#> 3.90997 5.29122
#> z_1[1,6] z_1[1,7]
#> 7.26798 -2.49447
#> z_1[1,8] z_1[1,9]
#> 3.20150 -2.13547
#> z_1[1,10] z_1[1,11]
#> -3.13490 -1.82488
#> z_1[1,12] z_1[1,13]
#> 2.30047 -1.78469
#> z_1[1,14] z_1[1,15]
#> -0.29988 3.88001
#> z_1[1,16] z_1[1,17]
#> -3.28691 -2.65156
#> z_1[1,18] z_1[1,19]
#> -1.55187 -2.33990
#> z_1[1,20] z_1[1,21]
#> 3.74930 3.94971
#> z_1[1,22] z_1[1,23]
#> 0.75840 2.62373
#> z_1[1,24] z_1[1,25]
#> 3.14306 6.41276
#> z_1[1,26] z_1[1,27]
#> 4.83589 5.38955
#> z_1[1,28] z_1[1,29]
#> 3.88941 -1.87839
#> z_1[1,30] z_1[1,31]
#> 2.69289 1.99825
#> z_1[1,32] z_1[1,33]
#> 6.31600 5.36197
#> z_1[1,34] z_1[1,35]
#> 2.44164 -2.27807
#> z_1[1,36] z_1[1,37]
#> -0.62864 -2.61372
#> z_1[1,38] z_1[1,39]
#> 5.50224 4.09869
#> z_1[1,40] z_1[1,41]
#> 3.63843 3.92030
#> z_1[1,42] z_1[1,43]
#> 4.54465 2.57441
#> z_1[1,44] z_1[1,45]
#> 4.83986 -2.42157
#> z_1[1,46] z_1[1,47]
#> 5.84947 4.98051
#> z_1[1,48] z_1[1,49]
#> -0.20457 1.03576
#> z_1[1,50] z_1[1,51]
#> -0.24082 2.00922
#> z_1[1,52] z_1[1,53]
#> -3.33487 -0.67367
#> z_1[1,54] z_1[1,55]
#> 9.52758 0.34512
#> z_1[1,56] z_1[1,57]
#> -0.67135 0.80572
#> z_1[1,58] z_1[1,59]
#> 4.69380 0.78473
#> z_1[1,60] z_1[1,61]
#> -4.13058 2.88603
#> z_1[1,62] z_1[1,63]
#> 4.46975 3.79994
#> z_1[1,64] z_1[1,65]
#> -3.42287 -1.96022
#> z_1[1,66] z_1[1,67]
#> -2.63962 1.96729
#> z_1[1,68] z_1[1,69]
#> -4.66713 3.09414
#> z_1[1,70] z_1[1,71]
#> -2.59709 5.90209
#> z_1[1,72] z_1[1,73]
#> -2.92235 -2.52277
#> z_1[1,74] z_1[1,75]
#> 0.23165 2.01532
#> z_1[1,76] z_1[1,77]
#> 4.38227 1.34967
#> z_1[1,78] z_1[1,79]
#> -1.78014 2.75461
#> z_1[1,80] z_1[1,81]
#> 10.15230 -3.52112
#> z_1[1,82] z_1[1,83]
#> -1.69371 -0.06622
#> z_1[1,84] z_1[1,85]
#> -0.84943 2.63431
#> z_1[1,86] z_1[1,87]
#> 3.64757 6.21705
#> z_1[1,88] z_1[1,89]
#> 4.14507 5.31947
#> z_1[1,90] z_1[1,91]
#> -2.23136 7.58994
#> z_1[1,92] z_1[1,93]
#> -2.36636 -2.18725
#> z_1[1,94] z_1[1,95]
#> 2.69595 -0.97403
#> z_1[1,96] z_1[1,97]
#> -1.05842 5.51356
#> z_1[1,98] z_1[1,99]
#> 7.72840 3.29455
#> z_1[1,100]
#> -3.24142
#>
#>
#> [[3]]
#>
#> Fraction in 1st window = 0.1
#> Fraction in 2nd window = 0.5
#>
#> b_Intercept b_x1
#> -0.33615 2.61820
#> b_x2 b_x3
#> 1.63275 1.18901
#> sd_regency__Intercept sigma
#> 2.57078 -2.12549
#> Intercept r_regency[regency_001,Intercept]
#> -0.57831 -2.46299
#> r_regency[regency_002,Intercept] r_regency[regency_003,Intercept]
#> -0.33961 -1.85363
#> r_regency[regency_004,Intercept] r_regency[regency_005,Intercept]
#> 4.34994 6.97587
#> r_regency[regency_006,Intercept] r_regency[regency_007,Intercept]
#> 2.79184 -1.69408
#> r_regency[regency_008,Intercept] r_regency[regency_009,Intercept]
#> 3.29772 -1.12953
#> r_regency[regency_010,Intercept] r_regency[regency_011,Intercept]
#> -0.18530 -0.70729
#> r_regency[regency_012,Intercept] r_regency[regency_013,Intercept]
#> 1.38534 -2.04923
#> r_regency[regency_014,Intercept] r_regency[regency_015,Intercept]
#> -1.33950 2.94184
#> r_regency[regency_016,Intercept] r_regency[regency_017,Intercept]
#> -1.98671 -2.37257
#> r_regency[regency_018,Intercept] r_regency[regency_019,Intercept]
#> -1.30640 -1.84580
#> r_regency[regency_020,Intercept] r_regency[regency_021,Intercept]
#> 5.00190 1.83303
#> r_regency[regency_022,Intercept] r_regency[regency_023,Intercept]
#> 5.96547 2.78556
#> r_regency[regency_024,Intercept] r_regency[regency_025,Intercept]
#> 2.99181 2.18277
#> r_regency[regency_026,Intercept] r_regency[regency_027,Intercept]
#> 1.30718 -1.90331
#> r_regency[regency_028,Intercept] r_regency[regency_029,Intercept]
#> 2.99975 -2.08964
#> r_regency[regency_030,Intercept] r_regency[regency_031,Intercept]
#> 3.32208 -0.42922
#> r_regency[regency_032,Intercept] r_regency[regency_033,Intercept]
#> 2.31243 1.66747
#> r_regency[regency_034,Intercept] r_regency[regency_035,Intercept]
#> 1.67823 -1.65864
#> r_regency[regency_036,Intercept] r_regency[regency_037,Intercept]
#> 0.88746 -0.92504
#> r_regency[regency_038,Intercept] r_regency[regency_039,Intercept]
#> 4.11681 2.61317
#> r_regency[regency_040,Intercept] r_regency[regency_041,Intercept]
#> 2.09196 1.79843
#> r_regency[regency_042,Intercept] r_regency[regency_043,Intercept]
#> 2.05046 1.22541
#> r_regency[regency_044,Intercept] r_regency[regency_045,Intercept]
#> 5.24039 -1.45629
#> r_regency[regency_046,Intercept] r_regency[regency_047,Intercept]
#> 1.77451 2.60953
#> r_regency[regency_048,Intercept] r_regency[regency_049,Intercept]
#> -1.57636 0.49798
#> r_regency[regency_050,Intercept] r_regency[regency_051,Intercept]
#> -0.33022 5.55240
#> r_regency[regency_052,Intercept] r_regency[regency_053,Intercept]
#> -3.43673 -1.76407
#> r_regency[regency_054,Intercept] r_regency[regency_055,Intercept]
#> 1.44958 2.03856
#> r_regency[regency_056,Intercept] r_regency[regency_057,Intercept]
#> -0.75024 0.10786
#> r_regency[regency_058,Intercept] r_regency[regency_059,Intercept]
#> 2.35615 2.86265
#> r_regency[regency_060,Intercept] r_regency[regency_061,Intercept]
#> -3.34030 1.81799
#> r_regency[regency_062,Intercept] r_regency[regency_063,Intercept]
#> 1.76286 0.83788
#> r_regency[regency_064,Intercept] r_regency[regency_065,Intercept]
#> -1.57042 -2.59346
#> r_regency[regency_066,Intercept] r_regency[regency_067,Intercept]
#> -2.19599 1.47350
#> r_regency[regency_068,Intercept] r_regency[regency_069,Intercept]
#> -2.44086 -1.31605
#> r_regency[regency_070,Intercept] r_regency[regency_071,Intercept]
#> -3.15755 3.20485
#> r_regency[regency_072,Intercept] r_regency[regency_073,Intercept]
#> -1.66828 -2.91003
#> r_regency[regency_074,Intercept] r_regency[regency_075,Intercept]
#> 2.40241 -1.40687
#> r_regency[regency_076,Intercept] r_regency[regency_077,Intercept]
#> 3.39491 -3.47794
#> r_regency[regency_078,Intercept] r_regency[regency_079,Intercept]
#> -2.11954 1.78426
#> r_regency[regency_080,Intercept] r_regency[regency_081,Intercept]
#> 3.28672 -2.13282
#> r_regency[regency_082,Intercept] r_regency[regency_083,Intercept]
#> -1.15450 -1.15865
#> r_regency[regency_084,Intercept] r_regency[regency_085,Intercept]
#> 0.65410 1.31614
#> r_regency[regency_086,Intercept] r_regency[regency_087,Intercept]
#> 2.62817 -2.42291
#> r_regency[regency_088,Intercept] r_regency[regency_089,Intercept]
#> 2.84586 1.93853
#> r_regency[regency_090,Intercept] r_regency[regency_091,Intercept]
#> 0.05776 3.24772
#> r_regency[regency_092,Intercept] r_regency[regency_093,Intercept]
#> -2.02220 -1.69903
#> r_regency[regency_094,Intercept] r_regency[regency_095,Intercept]
#> 2.24011 0.67441
#> r_regency[regency_096,Intercept] r_regency[regency_097,Intercept]
#> -2.39041 2.09650
#> r_regency[regency_098,Intercept] r_regency[regency_099,Intercept]
#> 0.60892 6.41766
#> r_regency[regency_100,Intercept] lprior
#> -3.11250 -0.48636
#> lp__ z_1[1,1]
#> 2.22015 -2.57215
#> z_1[1,2] z_1[1,3]
#> 0.15098 -1.57463
#> z_1[1,4] z_1[1,5]
#> 3.34179 4.59979
#> z_1[1,6] z_1[1,7]
#> 1.94838 -2.10966
#> z_1[1,8] z_1[1,9]
#> 2.71813 -0.49367
#> z_1[1,10] z_1[1,11]
#> 0.13045 -0.57648
#> z_1[1,12] z_1[1,13]
#> 1.31344 -2.56096
#> z_1[1,14] z_1[1,15]
#> -0.79196 2.70977
#> z_1[1,16] z_1[1,17]
#> -1.92924 -2.37459
#> z_1[1,18] z_1[1,19]
#> -1.33476 -2.31377
#> z_1[1,20] z_1[1,21]
#> 4.70778 1.42784
#> z_1[1,22] z_1[1,23]
#> 5.37145 2.67931
#> z_1[1,24] z_1[1,25]
#> 3.32091 2.33938
#> z_1[1,26] z_1[1,27]
#> 0.68386 -1.74830
#> z_1[1,28] z_1[1,29]
#> 3.35196 -1.48279
#> z_1[1,30] z_1[1,31]
#> 3.01263 -0.50463
#> z_1[1,32] z_1[1,33]
#> 1.49737 1.42724
#> z_1[1,34] z_1[1,35]
#> 0.86990 -1.91494
#> z_1[1,36] z_1[1,37]
#> 1.28205 -0.22859
#> z_1[1,38] z_1[1,39]
#> 2.90272 2.53025
#> z_1[1,40] z_1[1,41]
#> 1.68602 1.80361
#> z_1[1,42] z_1[1,43]
#> 1.89609 0.65115
#> z_1[1,44] z_1[1,45]
#> 5.21451 -1.28369
#> z_1[1,46] z_1[1,47]
#> 2.18709 2.39232
#> z_1[1,48] z_1[1,49]
#> -1.51789 0.03439
#> z_1[1,50] z_1[1,51]
#> -0.04333 5.05168
#> z_1[1,52] z_1[1,53]
#> -3.05517 -1.54686
#> z_1[1,54] z_1[1,55]
#> 1.17467 2.48659
#> z_1[1,56] z_1[1,57]
#> -0.07149 -0.02887
#> z_1[1,58] z_1[1,59]
#> 2.23867 2.21328
#> z_1[1,60] z_1[1,61]
#> -2.87877 1.25077
#> z_1[1,62] z_1[1,63]
#> 1.45702 0.51686
#> z_1[1,64] z_1[1,65]
#> -0.83717 -2.33342
#> z_1[1,66] z_1[1,67]
#> -1.46761 0.89563
#> z_1[1,68] z_1[1,69]
#> -2.41142 -0.79586
#> z_1[1,70] z_1[1,71]
#> -2.58466 2.60683
#> z_1[1,72] z_1[1,73]
#> -1.26957 -2.13064
#> z_1[1,74] z_1[1,75]
#> 1.93720 -1.33290
#> z_1[1,76] z_1[1,77]
#> 2.80733 -1.85324
#> z_1[1,78] z_1[1,79]
#> -1.77678 1.76344
#> z_1[1,80] z_1[1,81]
#> 2.52932 -1.70323
#> z_1[1,82] z_1[1,83]
#> -0.83905 -0.82037
#> z_1[1,84] z_1[1,85]
#> 1.73662 1.05846
#> z_1[1,86] z_1[1,87]
#> 3.11650 -2.41838
#> z_1[1,88] z_1[1,89]
#> 2.34459 2.82350
#> z_1[1,90] z_1[1,91]
#> 0.75884 3.46833
#> z_1[1,92] z_1[1,93]
#> -1.84745 -1.37934
#> z_1[1,94] z_1[1,95]
#> 2.83016 0.56784
#> z_1[1,96] z_1[1,97]
#> -1.98180 2.06597
#> z_1[1,98] z_1[1,99]
#> 1.13812 5.11925
#> z_1[1,100]
#> -2.55534
#>
#>
#> [[4]]
#>
#> Fraction in 1st window = 0.1
#> Fraction in 2nd window = 0.5
#>
#> b_Intercept b_x1
#> 4.306798 0.138522
#> b_x2 b_x3
#> 3.217878 2.091704
#> sd_regency__Intercept sigma
#> 1.706977 -1.169097
#> Intercept r_regency[regency_001,Intercept]
#> 4.821207 -2.644912
#> r_regency[regency_002,Intercept] r_regency[regency_003,Intercept]
#> -3.584002 -1.455519
#> r_regency[regency_004,Intercept] r_regency[regency_005,Intercept]
#> 0.153535 -0.807236
#> r_regency[regency_006,Intercept] r_regency[regency_007,Intercept]
#> -0.671253 -2.015644
#> r_regency[regency_008,Intercept] r_regency[regency_009,Intercept]
#> -1.611947 -2.168900
#> r_regency[regency_010,Intercept] r_regency[regency_011,Intercept]
#> -3.845515 -3.349155
#> r_regency[regency_012,Intercept] r_regency[regency_013,Intercept]
#> -0.598528 -3.966197
#> r_regency[regency_014,Intercept] r_regency[regency_015,Intercept]
#> -1.672882 0.216526
#> r_regency[regency_016,Intercept] r_regency[regency_017,Intercept]
#> -2.156602 -1.444862
#> r_regency[regency_018,Intercept] r_regency[regency_019,Intercept]
#> -1.199866 -0.998165
#> r_regency[regency_020,Intercept] r_regency[regency_021,Intercept]
#> 1.913834 -0.734336
#> r_regency[regency_022,Intercept] r_regency[regency_023,Intercept]
#> -0.771281 -0.390361
#> r_regency[regency_024,Intercept] r_regency[regency_025,Intercept]
#> -0.550246 0.270728
#> r_regency[regency_026,Intercept] r_regency[regency_027,Intercept]
#> -0.358525 -2.610382
#> r_regency[regency_028,Intercept] r_regency[regency_029,Intercept]
#> 0.406868 -4.840734
#> r_regency[regency_030,Intercept] r_regency[regency_031,Intercept]
#> -0.979597 -0.853206
#> r_regency[regency_032,Intercept] r_regency[regency_033,Intercept]
#> -2.902062 0.240789
#> r_regency[regency_034,Intercept] r_regency[regency_035,Intercept]
#> -0.397651 -2.277866
#> r_regency[regency_036,Intercept] r_regency[regency_037,Intercept]
#> -2.937674 -1.476411
#> r_regency[regency_038,Intercept] r_regency[regency_039,Intercept]
#> -1.087061 1.066855
#> r_regency[regency_040,Intercept] r_regency[regency_041,Intercept]
#> 0.299457 -0.321866
#> r_regency[regency_042,Intercept] r_regency[regency_043,Intercept]
#> -0.589560 -2.213468
#> r_regency[regency_044,Intercept] r_regency[regency_045,Intercept]
#> 1.681134 -1.509631
#> r_regency[regency_046,Intercept] r_regency[regency_047,Intercept]
#> 0.925785 -0.632817
#> r_regency[regency_048,Intercept] r_regency[regency_049,Intercept]
#> -2.446031 -2.232771
#> r_regency[regency_050,Intercept] r_regency[regency_051,Intercept]
#> -7.190352 0.474496
#> r_regency[regency_052,Intercept] r_regency[regency_053,Intercept]
#> -3.287363 -2.971393
#> r_regency[regency_054,Intercept] r_regency[regency_055,Intercept]
#> -0.223817 -1.068024
#> r_regency[regency_056,Intercept] r_regency[regency_057,Intercept]
#> -1.703835 -2.756484
#> r_regency[regency_058,Intercept] r_regency[regency_059,Intercept]
#> 1.366060 -2.107006
#> r_regency[regency_060,Intercept] r_regency[regency_061,Intercept]
#> -2.950260 -2.068420
#> r_regency[regency_062,Intercept] r_regency[regency_063,Intercept]
#> 0.008517 -2.754926
#> r_regency[regency_064,Intercept] r_regency[regency_065,Intercept]
#> -2.891131 -2.954195
#> r_regency[regency_066,Intercept] r_regency[regency_067,Intercept]
#> -2.561695 -0.826576
#> r_regency[regency_068,Intercept] r_regency[regency_069,Intercept]
#> -2.247551 -2.188642
#> r_regency[regency_070,Intercept] r_regency[regency_071,Intercept]
#> -2.864885 -0.082241
#> r_regency[regency_072,Intercept] r_regency[regency_073,Intercept]
#> -2.836939 -1.789548
#> r_regency[regency_074,Intercept] r_regency[regency_075,Intercept]
#> -0.639663 -2.895855
#> r_regency[regency_076,Intercept] r_regency[regency_077,Intercept]
#> 1.193387 -4.021551
#> r_regency[regency_078,Intercept] r_regency[regency_079,Intercept]
#> -2.827248 0.313596
#> r_regency[regency_080,Intercept] r_regency[regency_081,Intercept]
#> -1.961982 -3.726726
#> r_regency[regency_082,Intercept] r_regency[regency_083,Intercept]
#> -1.527196 -1.400072
#> r_regency[regency_084,Intercept] r_regency[regency_085,Intercept]
#> -3.429709 -2.150009
#> r_regency[regency_086,Intercept] r_regency[regency_087,Intercept]
#> 0.470954 -2.224197
#> r_regency[regency_088,Intercept] r_regency[regency_089,Intercept]
#> -1.953428 0.275214
#> r_regency[regency_090,Intercept] r_regency[regency_091,Intercept]
#> -3.368603 1.368208
#> r_regency[regency_092,Intercept] r_regency[regency_093,Intercept]
#> -2.588248 -6.612935
#> r_regency[regency_094,Intercept] r_regency[regency_095,Intercept]
#> 0.374481 -1.361233
#> r_regency[regency_096,Intercept] r_regency[regency_097,Intercept]
#> -2.805933 -0.144346
#> r_regency[regency_098,Intercept] r_regency[regency_099,Intercept]
#> -3.280423 1.071588
#> r_regency[regency_100,Intercept] lprior
#> -2.344496 -1.531353
#> lp__ z_1[1,1]
#> 1.421865 -3.344242
#> z_1[1,2] z_1[1,3]
#> -3.376196 -1.438500
#> z_1[1,4] z_1[1,5]
#> 0.014319 -1.054411
#> z_1[1,6] z_1[1,7]
#> -0.892320 -2.136647
#> z_1[1,8] z_1[1,9]
#> -2.031110 -1.706400
#> z_1[1,10] z_1[1,11]
#> -4.171387 -3.491678
#> z_1[1,12] z_1[1,13]
#> -1.201080 -4.206893
#> z_1[1,14] z_1[1,15]
#> -1.994205 -0.163600
#> z_1[1,16] z_1[1,17]
#> -3.612151 -1.618987
#> z_1[1,18] z_1[1,19]
#> -1.478478 -1.174784
#> z_1[1,20] z_1[1,21]
#> 2.215308 -1.359440
#> z_1[1,22] z_1[1,23]
#> -1.158873 -0.955924
#> z_1[1,24] z_1[1,25]
#> -1.014166 -0.126942
#> z_1[1,26] z_1[1,27]
#> -0.083022 -2.283947
#> z_1[1,28] z_1[1,29]
#> 0.258311 -5.540468
#> z_1[1,30] z_1[1,31]
#> -1.072474 -0.668203
#> z_1[1,32] z_1[1,33]
#> -3.187014 -0.329338
#> z_1[1,34] z_1[1,35]
#> -1.187802 -2.917143
#> z_1[1,36] z_1[1,37]
#> -2.326368 -1.424360
#> z_1[1,38] z_1[1,39]
#> -1.306850 1.167718
#> z_1[1,40] z_1[1,41]
#> -0.256971 -0.701562
#> z_1[1,42] z_1[1,43]
#> -1.059850 -2.241285
#> z_1[1,44] z_1[1,45]
#> 2.072568 -1.736575
#> z_1[1,46] z_1[1,47]
#> 0.822205 -1.024810
#> z_1[1,48] z_1[1,49]
#> -3.182766 -2.597025
#> z_1[1,50] z_1[1,51]
#> -7.173679 0.390322
#> z_1[1,52] z_1[1,53]
#> -3.745516 -2.990428
#> z_1[1,54] z_1[1,55]
#> -0.284172 -0.839273
#> z_1[1,56] z_1[1,57]
#> -1.723342 -2.960291
#> z_1[1,58] z_1[1,59]
#> 1.286633 -1.668382
#> z_1[1,60] z_1[1,61]
#> -3.166122 -2.188757
#> z_1[1,62] z_1[1,63]
#> -0.459177 -3.252710
#> z_1[1,64] z_1[1,65]
#> -3.304451 -4.120516
#> z_1[1,66] z_1[1,67]
#> -3.395075 -1.403177
#> z_1[1,68] z_1[1,69]
#> -3.186673 -2.766750
#> z_1[1,70] z_1[1,71]
#> -5.505045 -0.579112
#> z_1[1,72] z_1[1,73]
#> -3.373123 -2.061582
#> z_1[1,74] z_1[1,75]
#> -1.024341 -2.988373
#> z_1[1,76] z_1[1,77]
#> 1.440211 -4.601670
#> z_1[1,78] z_1[1,79]
#> -7.355370 -0.180179
#> z_1[1,80] z_1[1,81]
#> -2.029339 -4.108763
#> z_1[1,82] z_1[1,83]
#> -2.675617 -1.095311
#> z_1[1,84] z_1[1,85]
#> -2.762787 -2.060242
#> z_1[1,86] z_1[1,87]
#> 0.312556 -1.927770
#> z_1[1,88] z_1[1,89]
#> -2.632345 0.041515
#> z_1[1,90] z_1[1,91]
#> -3.821679 1.472091
#> z_1[1,92] z_1[1,93]
#> -2.983358 -6.157606
#> z_1[1,94] z_1[1,95]
#> 0.163359 -1.215103
#> z_1[1,96] z_1[1,97]
#> -2.892911 -0.496275
#> z_1[1,98] z_1[1,99]
#> -2.250915 1.082417
#> z_1[1,100]
#> -2.974943
#>
#>
is_converged(model)
#> [1] FALSE
is_converged(model, threshold = 1.05)
#> [1] FALSE
# }