R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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. Natural language support but running in an English locale 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. > ############################################################################ > # MLwiN MCMC Manual > # > # 15 Cross Classified Models . . . . . . . . . . . . . . . . . . . . . .215 > # > # Browne, W.J. (2009) MCMC Estimation in MLwiN, v2.13. Centre for > # Multilevel Modelling, University of Bristol. > ############################################################################ > # R script to replicate all analyses using R2MLwiN > # > # Zhang, Z., Charlton, C., Parker, R, Leckie, G., and Browne, W.J. > # Centre for Multilevel Modelling, 2012 > # http://www.bristol.ac.uk/cmm/software/R2MLwiN/ > ############################################################################ > > # 15.1 Classifications and levels . . . . . . . . . . . . . . . . . . . .216 > > # 15.2 Notation . . . . . . . . . . . . . . . . . . . . . . . . . . . . .217 > > # 15.3 The Fife educational dataset . . . . . . . . . . . . . . . . . . .217 > > library(R2MLwiN) R2MLwiN: A package to run models implemented in MLwiN from R Copyright 2013-2024 Zhengzheng Zhang, Christopher M. J. Charlton, Richard M. A. Parker, William J. Browne and George Leckie Support provided by the Economic and Social Research Council (ESRC) (Grants RES-149-25-1084, RES-576-25-0032 and ES/K007246/1) To cite R2MLwiN in publications use: Zhengzheng Zhang, Richard M. A. Parker, Christopher M. J. Charlton, George Leckie, William J. Browne (2016). R2MLwiN: A Package to Run MLwiN from within R. Journal of Statistical Software, 72(10), 1-43. doi:10.18637/jss.v072.i10 A BibTeX entry for LaTeX users is @Article{, title = {{R2MLwiN}: A Package to Run {MLwiN} from within {R}}, author = {Zhengzheng Zhang and Richard M. A. Parker and Christopher M. J. Charlton and George Leckie and William J. Browne}, journal = {Journal of Statistical Software}, year = {2016}, volume = {72}, number = {10}, pages = {1--43}, doi = {10.18637/jss.v072.i10}, } The MLwiN_path option is currently set to C:/Program Files/MLwiN v3.09/ To change this use: options(MLwiN_path="") > # MLwiN folder > mlwin <- getOption("MLwiN_path") > while (!file.access(mlwin, mode = 1) == 0) { + cat("Please specify the root MLwiN folder or the full path to the MLwiN executable:\n") + mlwin <- scan(what = character(0), sep = "\n") + mlwin <- gsub("\\", "/", mlwin, fixed = TRUE) + } > options(MLwiN_path = mlwin) > > ## Read xc1 data > data(xc1, package = "R2MLwiN") > > (mymodel <- runMLwiN(attain ~ 1 + (1 | sid) + (1 | pupil), estoptions = list(EstM = 1), data = xc1)) 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 Convergence achieved ECHO 0 Echoing is ON MCMC 0 500 1 5.8 50 10 G30[1] G30[2] 1 1 1 1 1 1 BURNING IN... Burning in for 50 iterations out of 500 -2 * Loglike = 17285.909568 Burning in for 100 iterations out of 500 -2 * Loglike = 17284.270025 Burning in for 150 iterations out of 500 -2 * Loglike = 17285.573561 Burning in for 200 iterations out of 500 -2 * Loglike = 17300.519822 Burning in for 250 iterations out of 500 -2 * Loglike = 17291.925701 Burning in for 300 iterations out of 500 -2 * Loglike = 17294.202575 Burning in for 350 iterations out of 500 -2 * Loglike = 17287.831050 Burning in for 400 iterations out of 500 -2 * Loglike = 17287.578736 Burning in for 450 iterations out of 500 -2 * Loglike = 17287.994352 Burning in for 500 iterations out of 500 -2 * Loglike = 17286.841894 ERAS G30 LINK 0 G30 ERAS c1090 c1091 MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 1 Actual update 50 of 5000, Stored update 50 of 5000 -2 * Loglike = 17290.038706 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 17295.044305 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 17292.418206 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 17303.974563 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 17289.965701 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 17278.064967 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 17295.266448 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 17290.860328 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 17288.636293 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 17298.645767 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 17315.649634 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 17285.657302 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 17297.368973 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 17286.315917 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 17291.938496 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 17293.896427 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 17289.932542 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 17294.282109 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 17288.349605 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 17287.629929 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 17284.887942 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 17291.622405 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 17290.261472 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 17289.560961 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 17291.264308 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 17299.799103 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 17313.578259 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 17292.640850 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 17286.210371 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 17287.835996 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 17288.243355 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 17294.784527 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 17286.911809 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 17292.184459 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 17292.954871 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 17290.139025 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 17296.481682 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 17283.972198 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 17295.954669 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 17293.268030 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 17284.239847 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 17287.627600 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 17287.645519 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 17290.009890 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 17292.873793 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 17292.119250 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 17283.031832 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 17294.650142 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 17296.079082 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 17292.327103 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 17283.827075 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 17288.791893 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 17291.485339 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 17284.324411 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 17287.036129 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 17286.369055 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 17285.360808 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 17296.234723 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 17283.729159 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 17291.999910 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 17293.126175 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 17287.963146 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 17292.009969 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 17280.683123 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 17293.795783 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 17290.619314 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 17300.210163 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 17282.710932 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 17291.448655 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 17290.283105 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 17294.085301 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 17287.813408 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 17296.224114 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 17296.861478 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 17294.595234 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 17291.275361 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 17291.871309 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 17283.738987 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 17297.990176 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 17285.516099 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 17285.117672 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 17296.777899 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 17295.483751 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 17298.626157 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 17297.176698 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 17287.302558 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 17282.765107 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 17293.538269 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 17296.386626 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 17286.570797 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 17296.390045 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 17283.161212 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 17284.314172 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 17296.817914 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 17289.762092 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 17291.583249 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 17294.532550 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 17283.734512 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 17305.113125 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 17290.306962 PUPN c1003 c1004 AVER c1091 b99 b100 Count = 5000 Average = 17292. S.D. = 6.6533 S.E.M. = 0.094092 ECHO 0 Execution completed -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- MLwiN (version: 3.09) multilevel model (Normal) N min mean max N_complete min_complete mean_complete max_complete sid 19 92 180.7895 290 19 92 180.7895 290 Estimation algorithm: MCMC Elapsed time : 0.9s Number of obs: 3435 (from total 3435) Number of iter.: 5000 Chains: 1 Burn-in: 500 Bayesian Deviance Information Criterion (DIC) Dbar D(thetabar) pD DIC 17291.828 17273.631 18.196 17310.024 --------------------------------------------------------------------------------------------------- The model formula: attain ~ 1 + (1 | sid) + (1 | pupil) Level 2: sid Level 1: pupil --------------------------------------------------------------------------------------------------- The fixed part estimates: Coef. Std. Err. z Pr(>|z|) [95% Cred. Interval] ESS Intercept 5.58647 0.16139 34.61 1.536e-262 *** 5.28239 5.92269 262 Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 --------------------------------------------------------------------------------------------------- The random part estimates at the sid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 0.49285 0.20836 0.22120 1.03009 1707 --------------------------------------------------------------------------------------------------- The random part estimates at the pupil level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 8.99649 0.21806 8.56580 9.43000 5000 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > # 15.4 A Cross-classified model . . . . . . . . . . . . . . . . . . . . .220 > > (mymodel <- runMLwiN(attain ~ 1 + (1 | sid) + (1 | pid) + (1 | pupil), estoptions = list(xc = TRUE, EstM = 1, resi.store = TRUE, + resi.store.levs = c(2, 3)), data = xc1)) 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 1 1 1 1 1 1 Setting up XC/MM data structures - may take a while Setting up XC/MM data structures - may take a while BURNING IN... Burning in for 50 iterations out of 500 -2 * Loglike = 17123.478432 Burning in for 100 iterations out of 500 -2 * Loglike = 16925.132039 Burning in for 150 iterations out of 500 -2 * Loglike = 16927.319784 Burning in for 200 iterations out of 500 -2 * Loglike = 16965.778132 Burning in for 250 iterations out of 500 -2 * Loglike = 16955.606213 Burning in for 300 iterations out of 500 -2 * Loglike = 16951.951786 Burning in for 350 iterations out of 500 -2 * Loglike = 16945.378302 Burning in for 400 iterations out of 500 -2 * Loglike = 16936.190225 Burning in for 450 iterations out of 500 -2 * Loglike = 16938.670195 Burning in for 500 iterations out of 500 -2 * Loglike = 16944.131202 ERAS c1090 c1091 MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 1 Actual update 50 of 5000, Stored update 50 of 5000 -2 * Loglike = 16930.772442 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 16958.858121 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 16923.352158 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 16940.009091 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 16914.697370 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 16944.496305 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 16928.528828 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 16943.248884 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 16971.423563 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 16922.090209 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 16935.816563 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 16947.385281 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 16920.685707 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 16928.587477 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 16965.325040 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 16943.473388 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 16919.308571 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 16933.128381 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 16930.758854 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 16957.083477 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 16943.888128 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 16965.964038 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 16921.824422 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 16953.658403 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 16934.451904 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 16951.781743 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 16941.251399 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 16935.745317 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 16955.226145 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 16941.287823 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 16948.896067 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 16945.849652 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 16937.136389 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 16945.958267 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 16974.412385 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 16900.602337 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 16924.854301 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 16937.713106 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 16959.782756 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 16923.766420 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 16976.590347 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 16913.081205 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 16926.910271 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 16990.699766 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 16931.869506 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 16962.784537 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 16946.179259 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 16943.240212 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 16962.278310 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 16920.934529 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 16936.105403 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 16930.767958 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 16932.632149 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 16946.364085 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 16949.664128 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 16927.858466 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 16943.524799 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 16961.762232 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 16948.996842 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 16936.466011 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 16960.544148 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 16935.903257 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 16952.645922 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 16925.194814 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 16949.719875 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 16981.039761 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 16938.904884 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 16931.690513 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 16919.876730 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 16978.709435 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 16943.686070 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 16949.382953 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 16945.388982 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 16978.610147 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 16922.976755 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 16955.136803 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 16937.102960 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 16960.278801 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 16960.759430 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 16927.385112 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 16913.975066 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 16948.521937 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 16923.748220 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 16919.286295 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 16975.125515 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 16961.544313 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 16943.126667 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 16918.061191 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 16945.876429 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 16951.286047 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 16947.170759 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 16952.497550 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 16949.644793 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 16923.183576 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 16941.651856 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 16934.280588 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 16970.783108 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 16919.141551 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 16954.922789 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 16920.466341 PUPN c1003 c1004 AVER c1091 b99 b100 Count = 5000 Average = 16941. S.D. = 18.665 S.E.M. = 0.26397 ECHO 0 Execution completed -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- MLwiN (version: 3.09) multilevel model (Normal) N min mean max N_complete min_complete mean_complete max_complete sid 19 92 180.78947 290 19 92 180.78947 290 pid 148 1 23.20946 72 148 1 23.20946 72 Estimation algorithm: MCMC Cross-classified Elapsed time : 2.77s Number of obs: 3435 (from total 3435) Number of iter.: 5000 Chains: 1 Burn-in: 500 Bayesian Deviance Information Criterion (DIC) Dbar D(thetabar) pD DIC 16940.799 16833.534 107.265 17048.064 --------------------------------------------------------------------------------------------------- The model formula: attain ~ 1 + (1 | sid) + (1 | pid) + (1 | pupil) Level 3: sid Level 2: pid Level 1: pupil --------------------------------------------------------------------------------------------------- The fixed part estimates: Coef. Std. Err. z Pr(>|z|) [95% Cred. Interval] ESS Intercept 5.50851 0.19195 28.70 4.091e-181 *** 5.11068 5.88199 167 Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 --------------------------------------------------------------------------------------------------- The random part estimates at the sid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 0.42008 0.21979 0.14039 0.97629 992 --------------------------------------------------------------------------------------------------- The random part estimates at the pid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 1.14487 0.21097 0.78224 1.59964 1092 --------------------------------------------------------------------------------------------------- The random part estimates at the pupil level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 8.12044 0.19749 7.73796 8.51995 4052 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > # 15.5 Residuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223 > > lencateg <- length(unique(xc1$sid)) > resi.chain0 <- mymodel@resi.chains$resi_lev3 > residual0 <- apply(resi.chain0, 2, mean) > rankno <- order(residual0) > plot(x = 1:lencateg, y = residual0[rankno], pch = 24, bg = "black", xlab = "rank", ylab = "cons") > abline(h = 0, lty = "dotted") > > ## Common caterpillar > #lencateg <- length(unique(xc1[["sid"]])) > #resi.chain0 <- mymodel@resi.chains$resi_lev3 > #u0rank <- apply(resi.chain0,1,rank) > #u0rankmn <- apply(u0rank, 1,mean) > #u0ranklo <- apply(u0rank, 1, function(x) quantile(x,.025)) > #u0rankmd <- apply(u0rank, 1,median) > #u0rankhi <- apply(u0rank, 1, function(x) quantile(x,.975)) > #rankno <- order(u0rankmn) > #caterpillar(y=u0rankmn[rankno],x=1:lencateg,qtlow=u0ranklo[rankno],qtup=u0rankhi[rankno]],ylim=c(0,20)) > > lencateg <- length(unique(xc1$pid)) > resi.chain1 <- mymodel@resi.chains$resi_lev2 > residual1 <- apply(resi.chain1, 2, mean) > rankno <- order(residual1) > plot(x = 1:length(residual1), y = residual1[rankno], pch = 24, bg = "black", xlab = "rank", ylab = "cons") > abline(h = 0, lty = "dotted") > > ## Common caterpillar > #lencateg <- length(unique(xc1[["pid"]])) > #resi.chain1 <- mymodel@resi.chains$resi_lev2 > #u0rank <- apply(resi.chain1,1,rank) > #u0rankmn <- apply(u0rank, 1,mean) > #u0ranklo <- apply(u0rank, 1, function(x) quantile(x,.025)) > #u0rankmd <- apply(u0rank, 1,median) > #u0rankhi <- apply(u0rank, 1, function(x) quantile(x,.975)) > #rankno <- order(u0rankmn) > #caterpillar(y=u0rankmn[rankno],x=1:lencateg,qtlow=u0ranklo[rankno],qtup=u0rankhi[rankno],ylim=c(0,150)) > > # 15.6 Adding predictors to the model . . . . . . . . . . . . . . . . . .225 > > (mymodel <- runMLwiN(attain ~ 1 + vrq + (1 | sid) + (1 | pid) + (1 | pupil), estoptions = list(xc = TRUE, EstM = 1, + resi.store = TRUE, resi.store.levs = c(2, 3)), data = xc1)) 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 iteration 4 Convergence achieved ECHO 0 Echoing is ON MCMC 0 500 1 5.8 50 10 1 1 1 1 1 1 Setting up XC/MM data structures - may take a while Setting up XC/MM data structures - may take a while BURNING IN... Burning in for 50 iterations out of 500 -2 * Loglike = 14750.271688 Burning in for 100 iterations out of 500 -2 * Loglike = 14756.268718 Burning in for 150 iterations out of 500 -2 * Loglike = 14720.387502 Burning in for 200 iterations out of 500 -2 * Loglike = 14702.616047 Burning in for 250 iterations out of 500 -2 * Loglike = 14689.885661 Burning in for 300 iterations out of 500 -2 * Loglike = 14751.800723 Burning in for 350 iterations out of 500 -2 * Loglike = 14717.883985 Burning in for 400 iterations out of 500 -2 * Loglike = 14758.778053 Burning in for 450 iterations out of 500 -2 * Loglike = 14692.462744 Burning in for 500 iterations out of 500 -2 * Loglike = 14698.334400 ERAS c1090 c1091 MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 1 Actual update 50 of 5000, Stored update 50 of 5000 -2 * Loglike = 14726.648579 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 14708.714934 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 14714.156163 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 14735.330478 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 14734.042778 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 14739.708099 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 14752.506555 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 14740.239289 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 14727.309772 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 14721.726667 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 14714.389422 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 14711.916622 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 14681.220960 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 14674.656496 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 14727.075393 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 14719.969649 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 14736.055298 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 14703.640240 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 14756.012828 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 14704.864211 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 14736.595543 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 14731.070254 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 14717.911687 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 14726.494190 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 14720.718827 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 14713.861942 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 14728.561725 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 14740.709757 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 14684.390330 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 14738.195483 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 14720.894981 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 14693.576354 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 14723.661223 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 14751.851688 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 14698.131898 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 14704.121020 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 14741.156313 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 14719.522535 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 14728.577139 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 14759.939863 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 14757.172614 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 14775.295571 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 14705.696392 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 14765.639895 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 14742.580987 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 14701.808431 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 14726.716032 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 14742.999784 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 14720.563505 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 14724.121023 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 14718.655198 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 14738.223266 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 14708.135042 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 14754.479651 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 14692.458198 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 14708.373264 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 14718.282669 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 14756.200885 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 14718.416358 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 14741.032734 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 14727.273098 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 14741.744425 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 14734.561902 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 14737.104623 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 14722.846389 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 14734.937030 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 14735.546971 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 14753.414005 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 14730.752953 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 14752.522119 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 14750.762575 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 14725.702641 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 14722.347351 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 14717.141178 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 14734.485929 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 14754.107879 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 14719.361029 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 14741.677095 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 14692.661731 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 14732.591274 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 14727.174417 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 14710.941255 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 14732.130742 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 14723.453708 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 14718.365732 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 14731.990425 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 14733.629703 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 14727.363105 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 14718.171860 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 14750.048340 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 14724.507326 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 14726.439207 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 14721.973578 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 14723.217022 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 14705.344556 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 14716.198173 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 14694.202998 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 14730.204470 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 14728.997299 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 14700.117407 PUPN c1003 c1004 AVER c1091 b99 b100 Count = 5000 Average = 14725. S.D. = 17.480 S.E.M. = 0.24721 ECHO 0 Execution completed -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- MLwiN (version: 3.09) multilevel model (Normal) N min mean max N_complete min_complete mean_complete max_complete sid 19 92 180.78947 290 19 92 180.78947 290 pid 148 1 23.20946 72 148 1 23.20946 72 Estimation algorithm: MCMC Cross-classified Elapsed time : 2.82s Number of obs: 3435 (from total 3435) Number of iter.: 5000 Chains: 1 Burn-in: 500 Bayesian Deviance Information Criterion (DIC) Dbar D(thetabar) pD DIC 14724.880 14643.739 81.140 14806.020 --------------------------------------------------------------------------------------------------- The model formula: attain ~ 1 + vrq + (1 | sid) + (1 | pid) + (1 | pupil) Level 3: sid Level 2: pid Level 1: pupil --------------------------------------------------------------------------------------------------- The fixed part estimates: Coef. Std. Err. z Pr(>|z|) [95% Cred. Interval] ESS Intercept -10.02868 0.28266 -35.48 9.917e-276 *** -10.58560 -9.48717 3257 vrq 0.16007 0.00281 57.03 0 *** 0.15469 0.16555 3361 Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 --------------------------------------------------------------------------------------------------- The random part estimates at the sid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 0.01883 0.02230 0.00088 0.08230 242 --------------------------------------------------------------------------------------------------- The random part estimates at the pid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 0.27758 0.06345 0.17069 0.41836 795 --------------------------------------------------------------------------------------------------- The random part estimates at the pupil level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 4.26071 0.10741 4.05558 4.47272 4577 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > (mymodel <- runMLwiN(attain ~ 1 + vrq + sc + fed + med + choice + (1 | sid) + (1 | pid) + (1 | pupil), estoptions = list(xc = TRUE, + EstM = 1, resi.store = TRUE, resi.store.levs = c(2, 3)), data = xc1)) 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 Convergence achieved ECHO 0 Echoing is ON MCMC 0 500 1 5.8 50 10 1 1 1 1 1 1 Setting up XC/MM data structures - may take a while Setting up XC/MM data structures - may take a while BURNING IN... Burning in for 50 iterations out of 500 -2 * Loglike = 14675.513215 Burning in for 100 iterations out of 500 -2 * Loglike = 14652.195104 Burning in for 150 iterations out of 500 -2 * Loglike = 14655.099287 Burning in for 200 iterations out of 500 -2 * Loglike = 14665.019162 Burning in for 250 iterations out of 500 -2 * Loglike = 14629.390700 Burning in for 300 iterations out of 500 -2 * Loglike = 14649.617653 Burning in for 350 iterations out of 500 -2 * Loglike = 14638.124829 Burning in for 400 iterations out of 500 -2 * Loglike = 14686.030940 Burning in for 450 iterations out of 500 -2 * Loglike = 14661.771561 Burning in for 500 iterations out of 500 -2 * Loglike = 14688.200300 ERAS c1090 c1091 MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 1 Actual update 50 of 5000, Stored update 50 of 5000 -2 * Loglike = 14679.376773 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 14641.810588 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 14666.500588 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 14641.401546 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 14635.320983 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 14647.757255 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 14666.399816 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 14680.225576 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 14646.719328 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 14653.629456 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 14663.247373 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 14663.166383 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 14623.362675 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 14648.959982 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 14682.272659 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 14631.651263 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 14678.292383 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 14676.230064 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 14600.697207 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 14622.248422 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 14652.077714 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 14661.253404 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 14616.772688 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 14636.717837 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 14621.236534 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 14624.461124 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 14662.041581 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 14637.869993 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 14643.210049 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 14647.059409 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 14658.830118 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 14647.954858 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 14631.747291 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 14678.843687 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 14653.660527 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 14639.676210 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 14650.086730 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 14644.398255 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 14644.334021 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 14663.169198 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 14627.092625 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 14671.669183 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 14654.016073 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 14624.677805 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 14660.749279 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 14637.927120 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 14630.408438 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 14654.228305 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 14651.845121 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 14700.393522 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 14639.948022 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 14631.695146 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 14667.894944 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 14664.207667 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 14628.299313 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 14652.232609 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 14685.598433 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 14645.771594 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 14680.756184 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 14632.324442 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 14665.017052 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 14666.857168 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 14623.348656 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 14643.540452 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 14635.519251 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 14649.183132 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 14631.240600 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 14665.814006 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 14650.228770 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 14651.549533 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 14676.010278 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 14651.651278 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 14678.975894 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 14660.893059 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 14624.452191 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 14691.541839 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 14675.433298 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 14591.758074 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 14664.185367 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 14669.680852 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 14653.494510 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 14651.558343 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 14640.057913 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 14640.013710 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 14682.729861 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 14666.378125 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 14615.834262 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 14645.033148 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 14635.905153 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 14671.160661 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 14674.040885 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 14635.752531 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 14642.617929 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 14633.221338 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 14654.384598 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 14615.675892 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 14659.704523 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 14663.130306 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 14642.802389 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 14662.170416 PUPN c1003 c1004 AVER c1091 b99 b100 Count = 5000 Average = 14651. S.D. = 17.602 S.E.M. = 0.24893 ECHO 0 Execution completed -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- MLwiN (version: 3.09) multilevel model (Normal) N min mean max N_complete min_complete mean_complete max_complete sid 19 92 180.78947 290 19 92 180.78947 290 pid 148 1 23.20946 72 148 1 23.20946 72 Estimation algorithm: MCMC Cross-classified Elapsed time : 3.05s Number of obs: 3435 (from total 3435) Number of iter.: 5000 Chains: 1 Burn-in: 500 Bayesian Deviance Information Criterion (DIC) Dbar D(thetabar) pD DIC 14650.707 14573.783 76.923 14727.630 --------------------------------------------------------------------------------------------------- The model formula: attain ~ 1 + vrq + sc + fed + med + choice + (1 | sid) + (1 | pid) + (1 | pupil) Level 3: sid Level 2: pid Level 1: pupil --------------------------------------------------------------------------------------------------- The fixed part estimates: Coef. Std. Err. z Pr(>|z|) [95% Cred. Interval] ESS Intercept -9.71794 0.28873 -33.66 2.4e-248 *** -10.27783 -9.16000 3383 vrq 0.15511 0.00277 55.92 0 *** 0.14968 0.16049 3989 sc 0.02713 0.00334 8.12 4.828e-16 *** 0.02065 0.03381 3966 fed 0.21638 0.09157 2.36 0.01812 * 0.03846 0.39776 5000 med 0.21950 0.08699 2.52 0.01162 * 0.05016 0.38986 4784 choice -0.12010 0.05564 -2.16 0.03088 * -0.23030 -0.01263 4554 Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 --------------------------------------------------------------------------------------------------- The random part estimates at the sid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 0.01572 0.01805 0.00062 0.06576 368 --------------------------------------------------------------------------------------------------- The random part estimates at the pid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 0.20750 0.05143 0.12241 0.32150 668 --------------------------------------------------------------------------------------------------- The random part estimates at the pupil level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 4.16641 0.10375 3.97095 4.37889 4534 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > lencateg <- length(unique(xc1$sid)) > resi.chain0 <- mymodel@resi.chains$resi_lev3 > residual0 <- apply(resi.chain0, 2, mean) > rankno <- order(residual0) > plot(x = 1:lencateg, y = residual0[rankno], pch = 24, bg = "black", xlab = "rank", ylab = "cons") > abline(h = 0, lty = "dotted") > > xc1$school19 <- as.integer(xc1$sid == 19) > > (mymodel <- runMLwiN(attain ~ 1 + vrq + sc + fed + med + choice + school19 + (0 | sid) + (1 | pid) + (1 | pupil), + estoptions = list(xc = TRUE, EstM = 1), data = xc1)) 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 Convergence achieved ECHO 0 Echoing is ON MCMC 0 500 1 5.8 50 10 1 1 1 1 1 1 Setting up XC/MM data structures - may take a while BURNING IN... Burning in for 50 iterations out of 500 -2 * Loglike = 14663.391429 Burning in for 100 iterations out of 500 -2 * Loglike = 14643.843824 Burning in for 150 iterations out of 500 -2 * Loglike = 14632.127506 Burning in for 200 iterations out of 500 -2 * Loglike = 14637.233003 Burning in for 250 iterations out of 500 -2 * Loglike = 14635.889097 Burning in for 300 iterations out of 500 -2 * Loglike = 14675.977559 Burning in for 350 iterations out of 500 -2 * Loglike = 14644.365144 Burning in for 400 iterations out of 500 -2 * Loglike = 14644.713333 Burning in for 450 iterations out of 500 -2 * Loglike = 14664.811831 Burning in for 500 iterations out of 500 -2 * Loglike = 14641.234403 ERAS c1090 c1091 MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 1 Actual update 50 of 5000, Stored update 50 of 5000 -2 * Loglike = 14658.124372 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 14631.453098 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 14670.012662 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 14646.710094 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 14631.391128 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 14646.882373 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 14644.421965 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 14638.195790 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 14635.584568 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 14655.224766 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 14644.792136 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 14640.885268 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 14636.426626 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 14667.851975 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 14669.135444 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 14635.990403 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 14664.731046 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 14658.885293 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 14644.842758 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 14653.781739 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 14636.528212 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 14653.644905 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 14649.255312 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 14646.779802 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 14647.095919 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 14662.502106 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 14622.972822 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 14625.262790 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 14648.398602 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 14686.396646 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 14648.653773 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 14652.037106 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 14667.308937 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 14655.344662 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 14651.807486 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 14633.501848 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 14655.357351 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 14647.304128 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 14661.682785 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 14673.156462 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 14620.846111 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 14639.797871 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 14661.197489 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 14659.558025 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 14644.221559 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 14643.669466 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 14644.362567 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 14656.079602 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 14627.044174 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 14669.341883 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 14645.885148 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 14645.059617 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 14664.210435 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 14658.345298 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 14683.375766 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 14627.340484 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 14657.071732 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 14648.068665 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 14635.118319 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 14621.729214 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 14646.812934 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 14633.888522 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 14658.158072 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 14642.012863 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 14632.139215 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 14658.054061 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 14646.921991 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 14659.559046 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 14659.809251 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 14648.894966 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 14646.459764 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 14656.101820 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 14635.861811 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 14642.002570 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 14614.681536 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 14660.558092 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 14638.697483 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 14628.559063 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 14655.284141 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 14646.977945 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 14650.914473 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 14648.174683 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 14656.328296 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 14653.039872 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 14657.496330 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 14630.232953 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 14633.086328 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 14639.781957 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 14636.344441 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 14636.676662 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 14634.506689 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 14677.604020 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 14642.246734 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 14643.807895 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 14648.563146 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 14637.196247 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 14679.129540 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 14651.376540 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 14658.906553 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 14640.624105 PUPN c1003 c1004 AVER c1091 b99 b100 Count = 5000 Average = 14650. S.D. = 17.390 S.E.M. = 0.24593 ECHO 0 Execution completed -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- MLwiN (version: 3.09) multilevel model (Normal) N min mean max N_complete min_complete mean_complete max_complete sid 19 92 180.78947 290 19 92 180.78947 290 pid 148 1 23.20946 72 148 1 23.20946 72 Estimation algorithm: MCMC Cross-classified Elapsed time : 2.39s Number of obs: 3435 (from total 3435) Number of iter.: 5000 Chains: 1 Burn-in: 500 Bayesian Deviance Information Criterion (DIC) Dbar D(thetabar) pD DIC 14650.481 14575.895 74.585 14725.066 --------------------------------------------------------------------------------------------------- The model formula: attain ~ 1 + vrq + sc + fed + med + choice + school19 + (0 | sid) + (1 | pid) + (1 | pupil) Level 3: sid Level 2: pid Level 1: pupil --------------------------------------------------------------------------------------------------- The fixed part estimates: Coef. Std. Err. z Pr(>|z|) [95% Cred. Interval] ESS Intercept -9.65083 0.28842 -33.46 1.811e-245 *** -10.21938 -9.09109 4014 vrq 0.15478 0.00278 55.63 0 *** 0.14945 0.16025 4211 sc 0.02683 0.00340 7.88 3.166e-15 *** 0.02017 0.03362 4283 fed 0.21623 0.09435 2.29 0.02192 * 0.03011 0.40098 5000 med 0.22358 0.08827 2.53 0.01131 * 0.04847 0.39467 5000 choice -0.12334 0.05473 -2.25 0.02421 * -0.23008 -0.01554 4325 school19 -0.62019 0.24413 -2.54 0.01107 * -1.09211 -0.14045 2397 Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 --------------------------------------------------------------------------------------------------- The random part estimates at the pid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 0.20345 0.04990 0.11724 0.31477 611 --------------------------------------------------------------------------------------------------- The random part estimates at the pupil level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 4.16795 0.10215 3.97439 4.37183 4748 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > # 15.7 Current restrictions for cross-classified models . . . . . . . . .229 > > # Chapter learning outcomes . . . . . . . . . . . . . . . . . . . . . . .128 > > > > > > ############################################################################ > > proc.time() user system elapsed 6.51 0.90 20.31