Would it be possible for you to confirm that the following, which should be an equivalent model using the MLwiN example data works for you?
Code: Select all
> library(R2MLwiN)
> data(bang, package = "R2MLwiN")
> f <- logit(use) ~ 1 + age + (1 | district)
> m <- runMLwiN(f, D = "Binomial", data = bang, estoptions = list(EstM = 1, resi.store.levs = 2))
MLwiN is running, please wait......
/nogui option ignored
ECHO 0
Echoing is ON
BATC 1
Batch mode is ON
MAXI 2
STAR
iteration 0
iteration 1
Convergence not achieved
TOLE 2
MAXI 20
BATC 1
Batch mode is ON
NEXT
iteration 2
iteration 3
Convergence achieved
ECHO 0
Echoing is ON
MCMC 0 500 1 5.8 50 10 G30[1] G30[2] 2 2 2 1 1 2
Adapting for 100 iterations (Maximum 5000)
-2 * Loglike = 3664.513281
Adapting for 200 iterations (Maximum 5000)
-2 * Loglike = 3675.038874
Adapting for 300 iterations (Maximum 5000)
-2 * Loglike = 3649.538587
Adapting for 400 iterations (Maximum 5000)
-2 * Loglike = 3667.799866
Adapting for 500 iterations (Maximum 5000)
-2 * Loglike = 3664.345650
Adapting for 600 iterations (Maximum 5000)
-2 * Loglike = 3674.114156
Adapting finished and took 700 iterations
Adapting took 700 iterations
Burning in for 50 iterations out of 500
-2 * Loglike = 3686.568077
Burning in for 100 iterations out of 500
-2 * Loglike = 3661.594681
Burning in for 150 iterations out of 500
-2 * Loglike = 3667.214322
Burning in for 200 iterations out of 500
-2 * Loglike = 3699.944267
Burning in for 250 iterations out of 500
-2 * Loglike = 3679.787350
Burning in for 300 iterations out of 500
-2 * Loglike = 3668.379318
Burning in for 350 iterations out of 500
-2 * Loglike = 3667.081363
Burning in for 400 iterations out of 500
-2 * Loglike = 3686.565542
Burning in for 450 iterations out of 500
-2 * Loglike = 3654.455906
Burning in for 500 iterations out of 500
-2 * Loglike = 3677.422240
ERAS G30
LINK 0 G30
ERAS c1090 c1091
MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 2
Actual update 50 of 5000, Stored update 50 of 5000
-2 * Loglike = 3669.157477
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 3690.762939
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 3659.555989
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 3667.042260
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 3663.279540
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 3656.446703
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 3666.999108
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 3668.527913
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 3664.416065
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 3673.814288
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 3669.170097
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 3663.119560
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 3669.742923
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 3655.928702
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 3651.024209
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 3676.265238
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 3668.511777
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 3680.540518
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 3676.362890
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 3683.259330
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 3671.928428
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 3670.340797
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 3673.658199
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 3649.047230
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 3655.178298
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 3676.099379
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 3675.893582
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 3656.202755
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 3648.981335
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 3671.907135
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 3677.990007
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 3665.339884
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 3682.618214
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 3674.281851
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 3660.587857
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 3670.883736
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 3668.332403
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 3671.818755
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 3670.815446
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 3664.924050
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 3661.779303
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 3681.575585
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 3664.805556
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 3663.249264
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 3669.328327
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 3671.101815
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 3654.358531
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 3657.859758
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 3643.240362
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 3674.082202
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 3684.617607
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 3668.119802
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 3658.854313
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 3663.035269
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 3665.758922
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 3686.073061
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 3660.994303
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 3686.100308
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 3675.657456
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 3664.530635
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 3677.985721
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 3672.863453
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 3658.006029
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 3662.529219
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 3685.448858
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 3658.961703
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 3692.839117
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 3671.752911
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 3661.961702
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 3662.482558
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 3667.867827
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 3675.799613
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 3654.314314
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 3694.211916
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 3687.939762
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 3656.649947
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 3645.126272
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 3671.422200
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 3673.229740
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 3657.888886
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 3669.300364
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 3680.648578
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 3658.576698
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 3660.124417
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 3653.214706
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 3668.825515
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 3668.790373
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 3666.745836
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 3666.585785
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 3660.311943
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 3673.205105
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 3662.646247
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 3662.548578
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 3657.482480
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 3661.774784
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 3674.294638
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 3659.444877
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 3660.129958
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 3659.726315
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 3682.569027
PUPN c1003 c1004
AVER c1091 b99 b100
Count = 5000
Average = 3668.0
S.D. = 10.962
S.E.M. = 0.15503
ECHO 0
Execution completed
> summary(m@resi.chains$resi_lev2)
Iterations = 1:5000
Thinning interval = 1
Number of chains = 1
Sample size per chain = 5000
1. Empirical mean and standard deviation for each variable,
plus standard error of the mean:
Mean SD Naive SE Time-series SE
u_0_1 -0.458134 0.1825 0.002581 0.007736
u_0_2 -0.448389 0.3250 0.004597 0.010665
u_0_3 0.205684 0.4881 0.006903 0.015413
u_0_4 0.177572 0.2684 0.003796 0.008854
u_0_5 0.105015 0.2635 0.003727 0.008975
u_0_6 -0.333035 0.2182 0.003086 0.007187
u_0_7 -0.230364 0.3355 0.004744 0.010042
u_0_8 0.206828 0.2435 0.003443 0.007803
u_0_9 0.007713 0.2993 0.004233 0.009437
u_0_10 -0.701055 0.4020 0.005685 0.013758
u_0_11 -1.025663 0.3973 0.005619 0.012805
u_0_12 -0.181517 0.2754 0.003895 0.008726
u_0_13 -0.119728 0.2862 0.004048 0.008678
u_0_14 0.990507 0.1736 0.002455 0.009352
u_0_15 0.154600 0.3070 0.004342 0.009532
u_0_16 0.478458 0.3172 0.004486 0.009942
u_0_17 -0.191479 0.2908 0.004112 0.008986
u_0_18 -0.107678 0.2460 0.003479 0.008312
u_0_19 -0.091118 0.2735 0.003868 0.008784
u_0_20 -0.064001 0.3332 0.004712 0.010453
u_0_21 -0.065431 0.3203 0.004530 0.010529
u_0_22 -0.415348 0.3473 0.004912 0.011125
u_0_23 -0.372913 0.3469 0.004906 0.010675
u_0_24 -0.610874 0.4048 0.005724 0.012710
u_0_25 0.278112 0.2085 0.002948 0.009072
u_0_26 0.002928 0.3647 0.005157 0.011061
u_0_27 -0.688298 0.2669 0.003774 0.009743
u_0_28 -0.437259 0.2302 0.003256 0.008235
u_0_29 -0.234661 0.2809 0.003973 0.009530
u_0_30 0.352584 0.1966 0.002780 0.008944
u_0_31 0.205744 0.2400 0.003394 0.007355
u_0_32 -0.449208 0.3197 0.004521 0.010492
u_0_33 0.176187 0.3564 0.005041 0.011094
u_0_34 0.890955 0.2957 0.004181 0.010886
u_0_35 0.426823 0.2427 0.003432 0.007670
u_0_36 -0.562676 0.3288 0.004649 0.010300
u_0_37 0.544954 0.3797 0.005370 0.013180
u_0_38 -0.275673 0.3824 0.005407 0.011869
u_0_39 0.617692 0.2974 0.004205 0.009935
u_0_40 0.264772 0.2400 0.003394 0.007408
u_0_41 0.231205 0.2939 0.004156 0.009555
u_0_42 0.470649 0.3909 0.005529 0.011900
u_0_43 0.709908 0.2366 0.003346 0.009872
u_0_44 -0.549111 0.3296 0.004662 0.010142
u_0_45 0.104335 0.2749 0.003888 0.010568
u_0_46 0.465912 0.1906 0.002695 0.008120
u_0_47 0.384260 0.3587 0.005073 0.012064
u_0_48 0.526294 0.2433 0.003441 0.009490
u_0_49 -0.115629 0.4521 0.006394 0.013768
u_0_50 0.393097 0.3252 0.004599 0.010766
u_0_51 0.308005 0.2645 0.003740 0.009198
u_0_52 0.322801 0.2145 0.003033 0.008390
u_0_53 0.012495 0.3448 0.004876 0.011205
u_0_54 -0.244853 0.4413 0.006241 0.013109
u_0_55 1.044065 0.2608 0.003688 0.010718
u_0_56 -0.487930 0.2868 0.004056 0.008953
u_0_57 0.158462 0.2738 0.003872 0.009115
u_0_58 -0.250409 0.3799 0.005373 0.011763
u_0_59 -0.160288 0.2688 0.003801 0.008044
u_0_60 -0.358112 0.2637 0.003729 0.009379
2. Quantiles for each variable:
2.5% 25% 50% 75% 97.5%
u_0_1 -0.83197 -0.58377 -0.453769 -0.334627 -0.100284
u_0_2 -1.12877 -0.65640 -0.437310 -0.225007 0.158028
u_0_3 -0.74740 -0.11301 0.202043 0.534916 1.158240
u_0_4 -0.34109 -0.01065 0.177372 0.354776 0.702519
u_0_5 -0.38614 -0.07932 0.100110 0.287144 0.622100
u_0_6 -0.77384 -0.47556 -0.326650 -0.181899 0.077483
u_0_7 -0.88078 -0.46032 -0.238205 0.003834 0.428506
u_0_8 -0.27723 0.03915 0.207953 0.369147 0.682832
u_0_9 -0.57917 -0.20049 0.014003 0.211992 0.578642
u_0_10 -1.55828 -0.94964 -0.682941 -0.424791 0.046348
u_0_11 -1.85638 -1.27404 -1.011984 -0.736860 -0.295525
u_0_12 -0.71764 -0.36460 -0.184496 0.006459 0.358724
u_0_13 -0.68288 -0.31336 -0.115741 0.079314 0.417048
u_0_14 0.66453 0.87125 0.990110 1.101741 1.352699
u_0_15 -0.45629 -0.04616 0.149643 0.367483 0.754268
u_0_16 -0.16430 0.26660 0.484531 0.689499 1.107564
u_0_17 -0.75157 -0.39521 -0.182218 0.009870 0.358007
u_0_18 -0.59486 -0.26747 -0.106194 0.052425 0.388038
u_0_19 -0.61506 -0.28471 -0.092972 0.109771 0.437304
u_0_20 -0.75075 -0.27536 -0.056439 0.166027 0.571247
u_0_21 -0.68449 -0.28831 -0.063846 0.149168 0.561796
u_0_22 -1.11530 -0.64838 -0.400777 -0.171878 0.224982
u_0_23 -1.03669 -0.61878 -0.367690 -0.134439 0.309260
u_0_24 -1.41809 -0.88389 -0.603174 -0.316183 0.121217
u_0_25 -0.11725 0.13673 0.275865 0.421773 0.696074
u_0_26 -0.72756 -0.23291 0.001719 0.233864 0.730602
u_0_27 -1.22769 -0.86759 -0.687703 -0.502590 -0.168136
u_0_28 -0.88190 -0.59322 -0.425266 -0.279324 0.003607
u_0_29 -0.79458 -0.41425 -0.231115 -0.056453 0.309746
u_0_30 -0.02640 0.22019 0.349911 0.481584 0.763770
u_0_31 -0.25966 0.04735 0.210114 0.353872 0.695036
u_0_32 -1.07169 -0.67259 -0.444090 -0.220104 0.160235
u_0_33 -0.49495 -0.06633 0.172255 0.413151 0.894935
u_0_34 0.30936 0.69788 0.890459 1.077885 1.498042
u_0_35 -0.05708 0.25704 0.430821 0.591454 0.901804
u_0_36 -1.21573 -0.77462 -0.547616 -0.338077 0.057216
u_0_37 -0.20408 0.28793 0.536989 0.798905 1.303553
u_0_38 -1.04568 -0.53406 -0.265525 -0.027311 0.486679
u_0_39 0.04935 0.42217 0.613493 0.810934 1.228556
u_0_40 -0.19347 0.09499 0.254834 0.423536 0.720623
u_0_41 -0.35384 0.02948 0.237657 0.426341 0.815847
u_0_42 -0.27362 0.21170 0.456172 0.710916 1.275744
u_0_43 0.25557 0.54841 0.709225 0.861571 1.182722
u_0_44 -1.22909 -0.76740 -0.523897 -0.327473 0.079335
u_0_45 -0.47146 -0.07065 0.109485 0.287100 0.633941
u_0_46 0.10165 0.34009 0.466894 0.586928 0.857343
u_0_47 -0.31163 0.13049 0.379903 0.618616 1.120280
u_0_48 0.05188 0.37080 0.521297 0.689609 1.004935
u_0_49 -0.96252 -0.41598 -0.125847 0.188332 0.766450
u_0_50 -0.22287 0.17086 0.381537 0.596876 1.063914
u_0_51 -0.21611 0.13615 0.309293 0.484640 0.831334
u_0_52 -0.09621 0.17584 0.325612 0.465715 0.744192
u_0_53 -0.65524 -0.22721 0.020296 0.235135 0.678905
u_0_54 -1.14092 -0.54273 -0.224948 0.045622 0.619311
u_0_55 0.51828 0.87202 1.034364 1.225256 1.550763
u_0_56 -1.06305 -0.67854 -0.477751 -0.302533 0.078348
u_0_57 -0.36142 -0.02857 0.154032 0.334027 0.693253
u_0_58 -0.98589 -0.50944 -0.238941 0.004218 0.525048
u_0_59 -0.66585 -0.34349 -0.162197 0.017408 0.346201
u_0_60 -0.90571 -0.53458 -0.355667 -0.175062 0.149264