R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 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 2013-2017 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 v3.05/ 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 for 50 iterations out of 500 -2 * Loglike = 17285.909619 Burning in for 100 iterations out of 500 -2 * Loglike = 17284.270075 Burning in for 150 iterations out of 500 -2 * Loglike = 17285.573612 Burning in for 200 iterations out of 500 -2 * Loglike = 17300.519873 Burning in for 250 iterations out of 500 -2 * Loglike = 17291.925752 Burning in for 300 iterations out of 500 -2 * Loglike = 17294.202626 Burning in for 350 iterations out of 500 -2 * Loglike = 17287.831100 Burning in for 400 iterations out of 500 -2 * Loglike = 17287.578787 Burning in for 450 iterations out of 500 -2 * Loglike = 17287.994403 Burning in for 500 iterations out of 500 -2 * Loglike = 17286.841945 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 = 17290.038757 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 17295.044356 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 17292.418256 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 17303.974614 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 17289.965752 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 17278.065018 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 17295.266499 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 17290.860379 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 17288.636344 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 17298.645817 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 17315.649685 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 17285.657353 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 17297.369024 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 17286.315968 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 17291.938547 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 17293.896478 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 17289.932592 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 17294.282159 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 17288.349655 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 17287.629979 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 17284.887993 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 17291.622455 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 17290.261522 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 17289.561012 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 17291.264359 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 17299.799154 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 17313.578310 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 17292.640901 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 17286.210422 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 17287.836047 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 17288.243406 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 17294.784578 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 17286.911860 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 17292.184510 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 17292.954921 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 17290.139076 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 17296.481733 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 17283.972249 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 17295.954720 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 17293.268081 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 17284.239898 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 17287.627651 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 17287.645570 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 17290.009941 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 17292.873843 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 17292.119300 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 17283.031883 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 17294.650193 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 17296.079133 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 17292.327153 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 17283.827125 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 17288.791944 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 17291.485389 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 17284.324462 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 17287.036180 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 17286.369106 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 17285.360858 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 17296.234774 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 17283.729210 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 17291.999961 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 17293.126226 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 17287.963197 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 17292.010019 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 17280.683174 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 17293.795833 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 17290.619365 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 17300.210213 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 17282.710983 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 17291.448706 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 17290.283155 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 17294.085351 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 17287.813459 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 17296.224165 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 17296.861529 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 17294.595285 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 17291.275412 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 17291.871360 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 17283.739037 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 17297.990227 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 17285.516150 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 17285.117723 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 17296.777949 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 17295.483801 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 17298.626207 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 17297.176748 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 17287.302609 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 17282.765157 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 17293.538320 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 17296.386676 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 17286.570847 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 17296.390096 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 17283.161263 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 17284.314222 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 17296.817965 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 17289.762143 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 17291.583300 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 17294.532601 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 17283.734563 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 17305.113176 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 17290.307013 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: 3.05) 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 : 1.01s 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 17273.632 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 Setting up classifications as categorical variables - may take a while 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 for 50 iterations out of 500 -2 * Loglike = 17123.478483 Burning in for 100 iterations out of 500 -2 * Loglike = 16925.132090 Burning in for 150 iterations out of 500 -2 * Loglike = 16927.319835 Burning in for 200 iterations out of 500 -2 * Loglike = 16965.778183 Burning in for 250 iterations out of 500 -2 * Loglike = 16955.606264 Burning in for 300 iterations out of 500 -2 * Loglike = 16951.951837 Burning in for 350 iterations out of 500 -2 * Loglike = 16945.378353 Burning in for 400 iterations out of 500 -2 * Loglike = 16936.190276 Burning in for 450 iterations out of 500 -2 * Loglike = 16938.670246 Burning in for 500 iterations out of 500 -2 * Loglike = 16944.131253 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 = 16930.772493 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 16958.858172 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 16923.352209 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 16940.009141 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 16914.697421 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 16944.496356 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 16928.528878 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 16943.248935 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 16971.423614 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 16922.090260 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 16935.816614 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 16947.385332 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 16920.685758 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 16928.587528 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 16965.325091 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 16943.473439 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 16919.308622 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 16933.128432 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 16930.758905 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 16957.083527 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 16943.888178 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 16965.964089 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 16921.824473 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 16953.658454 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 16934.451954 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 16951.781793 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 16941.251450 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 16935.745368 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 16955.226196 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 16941.287874 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 16948.896118 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 16945.849702 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 16937.136440 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 16945.958318 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 16974.412435 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 16900.602388 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 16924.854352 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 16937.713157 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 16959.782807 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 16923.766471 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 16976.590398 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 16913.081256 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 16926.910322 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 16990.699816 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 16931.869556 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 16962.784588 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 16946.179309 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 16943.240263 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 16962.278361 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 16920.934579 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 16936.105454 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 16930.768009 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 16932.632200 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 16946.364136 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 16949.664178 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 16927.858517 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 16943.524849 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 16961.762283 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 16948.996892 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 16936.466061 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 16960.544199 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 16935.903308 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 16952.645973 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 16925.194864 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 16949.719926 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 16981.039812 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 16938.904935 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 16931.690563 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 16919.876781 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 16978.709486 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 16943.686121 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 16949.383004 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 16945.389033 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 16978.610197 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 16922.976805 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 16955.136854 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 16937.103010 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 16960.278852 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 16960.759481 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 16927.385163 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 16913.975117 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 16948.521988 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 16923.748271 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 16919.286345 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 16975.125566 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 16961.544364 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 16943.126718 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 16918.061242 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 16945.876480 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 16951.286098 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 16947.170810 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 16952.497601 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 16949.644844 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 16923.183627 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 16941.651907 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 16934.280639 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 16970.783159 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 16919.141601 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 16954.922840 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 16920.466392 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: 3.05) 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 : 2.49s 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 Setting up classifications as categorical variables - may take a while 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 for 50 iterations out of 500 -2 * Loglike = 14750.241560 Burning in for 100 iterations out of 500 -2 * Loglike = 14694.248060 Burning in for 150 iterations out of 500 -2 * Loglike = 14727.035890 Burning in for 200 iterations out of 500 -2 * Loglike = 14741.808216 Burning in for 250 iterations out of 500 -2 * Loglike = 14735.700726 Burning in for 300 iterations out of 500 -2 * Loglike = 14730.688346 Burning in for 350 iterations out of 500 -2 * Loglike = 14723.577810 Burning in for 400 iterations out of 500 -2 * Loglike = 14716.862285 Burning in for 450 iterations out of 500 -2 * Loglike = 14719.935036 Burning in for 500 iterations out of 500 -2 * Loglike = 14713.147241 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 = 14719.161187 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 14753.443470 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 14724.515587 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 14717.527536 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 14684.444549 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 14754.099404 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 14716.822564 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 14718.327716 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 14743.023850 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 14728.745905 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 14710.741183 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 14748.680857 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 14702.322544 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 14723.198117 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 14763.537341 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 14722.157822 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 14707.225998 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 14703.040025 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 14704.818155 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 14735.053464 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 14741.778044 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 14741.867595 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 14713.378221 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 14736.018621 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 14724.682842 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 14745.498219 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 14726.554316 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 14717.280106 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 14737.920580 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 14744.412310 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 14746.066652 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 14715.133821 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 14740.936875 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 14717.969688 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 14731.133698 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 14688.626779 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 14723.229418 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 14716.723823 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 14744.962043 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 14723.759803 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 14750.079767 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 14692.408675 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 14717.307613 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 14772.415783 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 14711.421452 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 14740.805300 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 14731.889286 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 14732.249022 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 14725.183609 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 14709.218525 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 14722.733016 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 14715.351218 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 14708.178392 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 14719.662210 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 14742.280957 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 14722.051788 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 14740.627251 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 14730.235203 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 14731.964063 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 14707.087830 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 14743.560385 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 14714.964404 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 14728.121114 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 14696.421706 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 14728.233892 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 14756.730912 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 14725.503047 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 14712.036141 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 14720.109915 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 14763.221018 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 14714.698793 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 14731.034848 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 14722.792530 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 14755.317849 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 14719.801372 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 14739.033541 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 14739.772896 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 14727.347523 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 14747.980568 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 14712.400613 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 14696.785324 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 14738.048870 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 14719.276540 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 14706.807626 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 14748.271288 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 14761.040203 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 14711.905237 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 14707.175706 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 14732.565714 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 14750.051655 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 14732.341353 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 14720.627695 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 14732.596624 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 14726.924046 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 14707.194710 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 14719.342603 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 14750.334794 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 14703.669434 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 14731.051542 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 14709.931253 PUPN c1003 c1004 AVER c1091 b99 b100 Count = 5000 Average = 14725. S.D. = 17.677 S.E.M. = 0.24999 ECHO 0 Execution completed -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- MLwiN (version: 3.05) 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 : 2.61s 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 14724.549 14643.217 81.332 14805.882 --------------------------------------------------------------------------------------------------- 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 -10.02930 0.28494 -35.20 2.115e-271 *** -10.57939 -9.45871 3249 vrq 0.16005 0.00283 56.52 0 *** 0.15449 0.16555 3462 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 0.01928 0.02175 0.00079 0.07890 321 --------------------------------------------------------------------------------------------------- The random part estimates at the pid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 0.27771 0.06290 0.16898 0.41634 715 --------------------------------------------------------------------------------------------------- The random part estimates at the pupil level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 4.25964 0.10350 4.05843 4.46984 4086 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > (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 Setting up classifications as categorical variables - may take a while 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 for 50 iterations out of 500 -2 * Loglike = 14676.779376 Burning in for 100 iterations out of 500 -2 * Loglike = 14657.409882 Burning in for 150 iterations out of 500 -2 * Loglike = 14657.371993 Burning in for 200 iterations out of 500 -2 * Loglike = 14636.501048 Burning in for 250 iterations out of 500 -2 * Loglike = 14626.108672 Burning in for 300 iterations out of 500 -2 * Loglike = 14617.508670 Burning in for 350 iterations out of 500 -2 * Loglike = 14653.431339 Burning in for 400 iterations out of 500 -2 * Loglike = 14664.460841 Burning in for 450 iterations out of 500 -2 * Loglike = 14625.337900 Burning in for 500 iterations out of 500 -2 * Loglike = 14639.045762 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 = 14664.263372 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 14684.338809 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 14654.727279 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 14668.378023 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 14636.351455 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 14661.661157 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 14646.617554 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 14643.496557 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 14655.090118 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 14624.794526 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 14646.777170 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 14657.732765 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 14670.602650 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 14644.390012 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 14639.220646 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 14649.688959 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 14602.321567 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 14669.837887 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 14625.009182 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 14657.887815 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 14684.691547 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 14661.742185 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 14627.000234 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 14626.090840 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 14675.685923 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 14675.282470 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 14649.365174 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 14689.917680 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 14672.959146 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 14651.938888 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 14655.609455 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 14631.322345 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 14660.826027 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 14672.694768 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 14626.825526 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 14639.047914 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 14687.176756 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 14632.866537 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 14631.550720 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 14641.977156 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 14636.652294 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 14688.048750 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 14651.353674 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 14655.475559 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 14646.058098 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 14654.300137 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 14649.228627 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 14620.217195 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 14639.852652 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 14635.554536 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 14646.352062 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 14656.447605 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 14623.036591 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 14662.583205 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 14663.747846 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 14642.737212 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 14683.996738 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 14627.090198 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 14628.236198 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 14640.340239 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 14641.586459 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 14632.116531 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 14653.911964 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 14632.118804 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 14620.217351 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 14669.094482 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 14662.638162 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 14671.563101 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 14662.243989 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 14625.279259 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 14675.470312 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 14615.103486 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 14678.183377 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 14649.697061 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 14667.342450 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 14654.442691 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 14691.392290 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 14636.447348 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 14638.021426 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 14691.968082 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 14663.297114 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 14655.351998 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 14651.428195 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 14652.941819 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 14668.558477 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 14647.727311 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 14670.241169 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 14658.884938 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 14625.807902 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 14661.451817 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 14635.134848 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 14699.204256 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 14638.605989 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 14639.428086 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 14656.229124 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 14633.419497 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 14625.157429 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 14647.949061 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 14656.463689 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 14648.643350 PUPN c1003 c1004 AVER c1091 b99 b100 Count = 5000 Average = 14651. S.D. = 18.058 S.E.M. = 0.25538 ECHO 0 Execution completed -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- MLwiN (version: 3.05) 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 14650.928 14573.608 77.320 14728.249 --------------------------------------------------------------------------------------------------- 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 -9.71324 0.29161 -33.31 2.885e-243 *** -10.28694 -9.13914 3563 vrq 0.15515 0.00281 55.30 0 *** 0.14972 0.16065 3993 sc 0.02709 0.00338 8.02 1.053e-15 *** 0.02063 0.03370 4038 fed 0.21540 0.09360 2.30 0.02137 * 0.02830 0.39671 5611 med 0.22007 0.08626 2.55 0.01073 * 0.05183 0.39045 5701 choice -0.12182 0.05557 -2.19 0.02837 * -0.22762 -0.01245 5238 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 0.01834 0.00077 0.06662 296 --------------------------------------------------------------------------------------------------- The random part estimates at the pid level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 0.20953 0.05277 0.12014 0.32853 510 --------------------------------------------------------------------------------------------------- The random part estimates at the pupil level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 4.16914 0.10225 3.97291 4.37614 3846 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > 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 Setting up classifications as categorical variables - may take a while 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 for 50 iterations out of 500 -2 * Loglike = 14661.336235 Burning in for 100 iterations out of 500 -2 * Loglike = 14635.979537 Burning in for 150 iterations out of 500 -2 * Loglike = 14669.807757 Burning in for 200 iterations out of 500 -2 * Loglike = 14631.290373 Burning in for 250 iterations out of 500 -2 * Loglike = 14655.069316 Burning in for 300 iterations out of 500 -2 * Loglike = 14666.498665 Burning in for 350 iterations out of 500 -2 * Loglike = 14672.112126 Burning in for 400 iterations out of 500 -2 * Loglike = 14632.793856 Burning in for 450 iterations out of 500 -2 * Loglike = 14651.772821 Burning in for 500 iterations out of 500 -2 * Loglike = 14643.877557 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 = 14654.787638 Actual update 100 of 5000, Stored update 100 of 5000 -2 * Loglike = 14655.674478 Actual update 150 of 5000, Stored update 150 of 5000 -2 * Loglike = 14686.050465 Actual update 200 of 5000, Stored update 200 of 5000 -2 * Loglike = 14629.012641 Actual update 250 of 5000, Stored update 250 of 5000 -2 * Loglike = 14660.517583 Actual update 300 of 5000, Stored update 300 of 5000 -2 * Loglike = 14616.187388 Actual update 350 of 5000, Stored update 350 of 5000 -2 * Loglike = 14659.835784 Actual update 400 of 5000, Stored update 400 of 5000 -2 * Loglike = 14622.972402 Actual update 450 of 5000, Stored update 450 of 5000 -2 * Loglike = 14637.457067 Actual update 500 of 5000, Stored update 500 of 5000 -2 * Loglike = 14635.312516 Actual update 550 of 5000, Stored update 550 of 5000 -2 * Loglike = 14633.066994 Actual update 600 of 5000, Stored update 600 of 5000 -2 * Loglike = 14665.500277 Actual update 650 of 5000, Stored update 650 of 5000 -2 * Loglike = 14652.830949 Actual update 700 of 5000, Stored update 700 of 5000 -2 * Loglike = 14654.765187 Actual update 750 of 5000, Stored update 750 of 5000 -2 * Loglike = 14647.478778 Actual update 800 of 5000, Stored update 800 of 5000 -2 * Loglike = 14661.532704 Actual update 850 of 5000, Stored update 850 of 5000 -2 * Loglike = 14695.160024 Actual update 900 of 5000, Stored update 900 of 5000 -2 * Loglike = 14704.893655 Actual update 950 of 5000, Stored update 950 of 5000 -2 * Loglike = 14652.535479 Actual update 1000 of 5000, Stored update 1000 of 5000 -2 * Loglike = 14659.694759 Actual update 1050 of 5000, Stored update 1050 of 5000 -2 * Loglike = 14676.008600 Actual update 1100 of 5000, Stored update 1100 of 5000 -2 * Loglike = 14662.076410 Actual update 1150 of 5000, Stored update 1150 of 5000 -2 * Loglike = 14624.648833 Actual update 1200 of 5000, Stored update 1200 of 5000 -2 * Loglike = 14645.030363 Actual update 1250 of 5000, Stored update 1250 of 5000 -2 * Loglike = 14649.108993 Actual update 1300 of 5000, Stored update 1300 of 5000 -2 * Loglike = 14636.068398 Actual update 1350 of 5000, Stored update 1350 of 5000 -2 * Loglike = 14654.321966 Actual update 1400 of 5000, Stored update 1400 of 5000 -2 * Loglike = 14639.428110 Actual update 1450 of 5000, Stored update 1450 of 5000 -2 * Loglike = 14659.316076 Actual update 1500 of 5000, Stored update 1500 of 5000 -2 * Loglike = 14638.164084 Actual update 1550 of 5000, Stored update 1550 of 5000 -2 * Loglike = 14648.213558 Actual update 1600 of 5000, Stored update 1600 of 5000 -2 * Loglike = 14655.904918 Actual update 1650 of 5000, Stored update 1650 of 5000 -2 * Loglike = 14655.970770 Actual update 1700 of 5000, Stored update 1700 of 5000 -2 * Loglike = 14677.676745 Actual update 1750 of 5000, Stored update 1750 of 5000 -2 * Loglike = 14666.436405 Actual update 1800 of 5000, Stored update 1800 of 5000 -2 * Loglike = 14663.449347 Actual update 1850 of 5000, Stored update 1850 of 5000 -2 * Loglike = 14638.583134 Actual update 1900 of 5000, Stored update 1900 of 5000 -2 * Loglike = 14680.707632 Actual update 1950 of 5000, Stored update 1950 of 5000 -2 * Loglike = 14638.844893 Actual update 2000 of 5000, Stored update 2000 of 5000 -2 * Loglike = 14662.541449 Actual update 2050 of 5000, Stored update 2050 of 5000 -2 * Loglike = 14649.648885 Actual update 2100 of 5000, Stored update 2100 of 5000 -2 * Loglike = 14680.715763 Actual update 2150 of 5000, Stored update 2150 of 5000 -2 * Loglike = 14678.629878 Actual update 2200 of 5000, Stored update 2200 of 5000 -2 * Loglike = 14637.052519 Actual update 2250 of 5000, Stored update 2250 of 5000 -2 * Loglike = 14650.049936 Actual update 2300 of 5000, Stored update 2300 of 5000 -2 * Loglike = 14646.731061 Actual update 2350 of 5000, Stored update 2350 of 5000 -2 * Loglike = 14644.524710 Actual update 2400 of 5000, Stored update 2400 of 5000 -2 * Loglike = 14655.304284 Actual update 2450 of 5000, Stored update 2450 of 5000 -2 * Loglike = 14627.379524 Actual update 2500 of 5000, Stored update 2500 of 5000 -2 * Loglike = 14633.418384 Actual update 2550 of 5000, Stored update 2550 of 5000 -2 * Loglike = 14627.615458 Actual update 2600 of 5000, Stored update 2600 of 5000 -2 * Loglike = 14636.181147 Actual update 2650 of 5000, Stored update 2650 of 5000 -2 * Loglike = 14644.402181 Actual update 2700 of 5000, Stored update 2700 of 5000 -2 * Loglike = 14631.843648 Actual update 2750 of 5000, Stored update 2750 of 5000 -2 * Loglike = 14635.075359 Actual update 2800 of 5000, Stored update 2800 of 5000 -2 * Loglike = 14658.515106 Actual update 2850 of 5000, Stored update 2850 of 5000 -2 * Loglike = 14677.499063 Actual update 2900 of 5000, Stored update 2900 of 5000 -2 * Loglike = 14631.544869 Actual update 2950 of 5000, Stored update 2950 of 5000 -2 * Loglike = 14677.216347 Actual update 3000 of 5000, Stored update 3000 of 5000 -2 * Loglike = 14648.325214 Actual update 3050 of 5000, Stored update 3050 of 5000 -2 * Loglike = 14659.869479 Actual update 3100 of 5000, Stored update 3100 of 5000 -2 * Loglike = 14656.966110 Actual update 3150 of 5000, Stored update 3150 of 5000 -2 * Loglike = 14634.458733 Actual update 3200 of 5000, Stored update 3200 of 5000 -2 * Loglike = 14672.182665 Actual update 3250 of 5000, Stored update 3250 of 5000 -2 * Loglike = 14666.876308 Actual update 3300 of 5000, Stored update 3300 of 5000 -2 * Loglike = 14648.071070 Actual update 3350 of 5000, Stored update 3350 of 5000 -2 * Loglike = 14630.210364 Actual update 3400 of 5000, Stored update 3400 of 5000 -2 * Loglike = 14638.071233 Actual update 3450 of 5000, Stored update 3450 of 5000 -2 * Loglike = 14630.383815 Actual update 3500 of 5000, Stored update 3500 of 5000 -2 * Loglike = 14665.010825 Actual update 3550 of 5000, Stored update 3550 of 5000 -2 * Loglike = 14644.562202 Actual update 3600 of 5000, Stored update 3600 of 5000 -2 * Loglike = 14655.439399 Actual update 3650 of 5000, Stored update 3650 of 5000 -2 * Loglike = 14645.116172 Actual update 3700 of 5000, Stored update 3700 of 5000 -2 * Loglike = 14655.760037 Actual update 3750 of 5000, Stored update 3750 of 5000 -2 * Loglike = 14651.213281 Actual update 3800 of 5000, Stored update 3800 of 5000 -2 * Loglike = 14671.633678 Actual update 3850 of 5000, Stored update 3850 of 5000 -2 * Loglike = 14651.169244 Actual update 3900 of 5000, Stored update 3900 of 5000 -2 * Loglike = 14675.090322 Actual update 3950 of 5000, Stored update 3950 of 5000 -2 * Loglike = 14666.887144 Actual update 4000 of 5000, Stored update 4000 of 5000 -2 * Loglike = 14685.557666 Actual update 4050 of 5000, Stored update 4050 of 5000 -2 * Loglike = 14639.364781 Actual update 4100 of 5000, Stored update 4100 of 5000 -2 * Loglike = 14660.148266 Actual update 4150 of 5000, Stored update 4150 of 5000 -2 * Loglike = 14664.275727 Actual update 4200 of 5000, Stored update 4200 of 5000 -2 * Loglike = 14654.143370 Actual update 4250 of 5000, Stored update 4250 of 5000 -2 * Loglike = 14655.844335 Actual update 4300 of 5000, Stored update 4300 of 5000 -2 * Loglike = 14668.824187 Actual update 4350 of 5000, Stored update 4350 of 5000 -2 * Loglike = 14636.009191 Actual update 4400 of 5000, Stored update 4400 of 5000 -2 * Loglike = 14640.325848 Actual update 4450 of 5000, Stored update 4450 of 5000 -2 * Loglike = 14651.141788 Actual update 4500 of 5000, Stored update 4500 of 5000 -2 * Loglike = 14632.709842 Actual update 4550 of 5000, Stored update 4550 of 5000 -2 * Loglike = 14648.582003 Actual update 4600 of 5000, Stored update 4600 of 5000 -2 * Loglike = 14667.676416 Actual update 4650 of 5000, Stored update 4650 of 5000 -2 * Loglike = 14629.615091 Actual update 4700 of 5000, Stored update 4700 of 5000 -2 * Loglike = 14643.937254 Actual update 4750 of 5000, Stored update 4750 of 5000 -2 * Loglike = 14657.259210 Actual update 4800 of 5000, Stored update 4800 of 5000 -2 * Loglike = 14648.164860 Actual update 4850 of 5000, Stored update 4850 of 5000 -2 * Loglike = 14712.944131 Actual update 4900 of 5000, Stored update 4900 of 5000 -2 * Loglike = 14661.043883 Actual update 4950 of 5000, Stored update 4950 of 5000 -2 * Loglike = 14656.019673 Actual update 5000 of 5000, Stored update 5000 of 5000 -2 * Loglike = 14641.174568 PUPN c1003 c1004 AVER c1091 b99 b100 Count = 5000 Average = 14651. S.D. = 17.376 S.E.M. = 0.24574 ECHO 0 Execution completed -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- MLwiN (version: 3.05) 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 : 2.54s 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 14650.656 14576.308 74.348 14725.004 --------------------------------------------------------------------------------------------------- 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 -9.64773 0.29410 -32.80 5.209e-236 *** -10.21999 -9.05503 3545 vrq 0.15480 0.00284 54.42 0 *** 0.14912 0.16044 3841 sc 0.02683 0.00341 7.87 3.656e-15 *** 0.02002 0.03345 4585 fed 0.21482 0.09266 2.32 0.02043 * 0.03300 0.40086 5000 med 0.22490 0.08596 2.62 0.008893 ** 0.05447 0.39176 4694 choice -0.12548 0.05567 -2.25 0.0242 * -0.23543 -0.01483 4458 school19 -0.61629 0.24357 -2.53 0.0114 * -1.08583 -0.13685 2630 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 0.20223 0.05130 0.11380 0.31700 623 --------------------------------------------------------------------------------------------------- The random part estimates at the pupil level: Coef. Std. Err. [95% Cred. Interval] ESS var_Intercept 4.16846 0.10364 3.97265 4.37246 3529 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > # 15.7 Current restrictions for cross-classified models . . . . . . . . .229 > > # Chapter learning outcomes . . . . . . . . . . . . . . . . . . . . . . .128 > > > > > > ############################################################################ > > proc.time() user system elapsed 8.71 1.00 22.48