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
> #
> # 18  Multivariate Normal Response Models and Missing Data . . . . . . . 263
> #
> #     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/
> ############################################################################
> 
> # 18.1 GCSE science data with complete records only . . . . . . . . . . .264
> 
> 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="<path to MLwiN>")
> # 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)
> 
> # User's input if necessary
> 
> ## save current par settings
> mypar <- par(no.readonly = TRUE)
> 
> ## Read gcsecomp1 data
> data(gcsecomp1, package="R2MLwiN")
> #summary(gcsecomp1)
> #cor(gcsecomp1[, c("written", "csework")])
> 
> # 18.2 Fitting single level multivariate models . . . . . . . . . . . . .265
> 
> ## IGLS
> (mymodel <- runMLwiN(c(written, csework) ~ 1 + (1 | student), D = "Multivariate Normal", estoptions = list(sort.ignore = TRUE), 
+   data = gcsecomp1))
/nogui option ignored
ECHO    0


Echoing is ON
BATC 1

Batch mode is ON
MAXI 2
STAR
iteration 0
iteration 1

Convergence achieved
TOLE 2
MAXI 20
NEXT
iteration 2

Convergence achieved
ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
Estimation algorithm:  IGLS        Elapsed time : 0.2s 
Number of obs:  1523 (from total 1523)        The model converged after 3 iterations.
Log likelihood:      -12353.1 
Deviance statistic:  24706.2 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(written, csework) ~ 1 + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                       Coef.   Std. Err.        z   Pr(>|z|)         [95% Conf.   Interval] 
Intercept_written   46.93697     0.34562   135.81          0   ***     46.25957    47.61436 
Intercept_csework   73.42902     0.42103   174.40          0   ***     72.60382    74.25423 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                              Coef.   Std. Err. 
var_Intercept_written                     181.92302     6.59254 
cov_Intercept_written_Intercept_csework   105.24772     6.28664 
var_Intercept_csework                     269.97548     9.78339 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> ## MCMC
> (mymodel <- runMLwiN(c(written, csework) ~ 1 + (1 | student), D = "Multivariate Normal", estoptions = list(EstM = 1, 
+   sort.ignore = TRUE), data = gcsecomp1))
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 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 4
Burning in for 50 iterations out of 500
-2 * Loglike = 24715.167725
Burning in for 100 iterations out of 500
-2 * Loglike = 24711.823123
Burning in for 150 iterations out of 500
-2 * Loglike = 24707.853231
Burning in for 200 iterations out of 500
-2 * Loglike = 24710.964703
Burning in for 250 iterations out of 500
-2 * Loglike = 24710.181211
Burning in for 300 iterations out of 500
-2 * Loglike = 24711.623446
Burning in for 350 iterations out of 500
-2 * Loglike = 24715.033589
Burning in for 400 iterations out of 500
-2 * Loglike = 24708.821923
Burning in for 450 iterations out of 500
-2 * Loglike = 24710.342828
Burning in for 500 iterations out of 500
-2 * Loglike = 24717.462188

ERAS G30
LINK 0 G30
ERAS  c1090 c1091

MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 4
Actual update 50 of 5000, Stored update 50 of 5000
-2 * Loglike = 24711.916143
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 24708.255564
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 24710.303449
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 24712.646460
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 24709.495191
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 24717.649037
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 24707.811238
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 24715.700103
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 24713.102917
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 24708.841718
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 24714.562204
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 24708.867475
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 24718.879339
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 24709.338639
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 24712.162045
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 24708.198985
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 24713.491104
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 24715.176980
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 24715.954324
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 24709.913047
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 24708.010160
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 24724.398813
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 24712.825461
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 24706.972368
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 24710.392622
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 24712.014986
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 24712.530155
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 24709.280122
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 24709.631903
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 24711.872015
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 24713.943698
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 24714.056143
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 24712.381865
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 24712.838913
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 24709.235640
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 24712.486862
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 24712.694346
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 24711.862579
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 24707.726977
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 24713.478392
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 24715.475528
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 24707.587885
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 24709.146240
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 24710.481315
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 24711.364867
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 24710.418401
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 24709.525019
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 24708.951447
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 24709.794282
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 24710.278971
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 24709.835629
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 24714.867518
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 24708.827008
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 24707.948611
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 24712.778317
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 24715.693641
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 24709.106106
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 24709.097447
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 24709.985568
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 24716.278663
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 24712.634299
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 24711.849876
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 24712.025412
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 24712.718743
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 24708.064149
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 24711.134952
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 24706.566946
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 24707.149953
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 24710.315491
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 24712.153552
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 24708.943161
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 24710.981859
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 24707.912547
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 24711.339033
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 24707.662198
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 24709.090048
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 24714.224636
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 24710.449901
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 24706.740663
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 24715.555980
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 24714.557692
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 24707.135258
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 24709.043039
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 24709.481746
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 24712.637279
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 24712.057334
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 24711.165538
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 24710.054754
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 24712.493266
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 24708.521703
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 24713.382352
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 24710.547175
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 24714.026718
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 24711.163871
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 24711.246675
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 24713.332209
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 24712.280148
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 24709.281125
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 24713.816069
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 24714.148071
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          24711.
S.D.    =          3.1994
S.E.M.  =        0.045246

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 1.3s 
Number of obs:  1523 (from total 1523)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Bayesian Deviance Information Criterion (DIC)
Dbar      D(thetabar)    pD      DIC
24711.211  24706.245  4.966      24716.177  
--------------------------------------------------------------------------------------------------- 
The model formula:
c(written, csework) ~ 1 + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                       Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_written   46.93472     0.34033  137.91          0  ***    46.27051    47.58569   5438 
Intercept_csework   73.43046     0.42052  174.62          0  ***    72.62514    74.27575   5195 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                              Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_written                     182.41260     6.55904    170.04483   195.75447   4619 
cov_Intercept_written_Intercept_csework   105.39581     6.27642     93.48509   118.33852   5000 
var_Intercept_csework                     270.24990     9.85175    251.83896   290.38533   6031 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> # 18.3 Adding predictor variables . . . . . . . . . . . . . . . . . . . .270
> 
> (mymodel <- runMLwiN(c(written, csework) ~ 1 + female + (1 | student), D = "Multivariate Normal", estoptions = list(EstM = 1, 
+   sort.ignore = TRUE), data = gcsecomp1))
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 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 4
Burning in for 50 iterations out of 500
-2 * Loglike = 24568.281141
Burning in for 100 iterations out of 500
-2 * Loglike = 24562.460647
Burning in for 150 iterations out of 500
-2 * Loglike = 24567.707332
Burning in for 200 iterations out of 500
-2 * Loglike = 24565.383734
Burning in for 250 iterations out of 500
-2 * Loglike = 24564.738855
Burning in for 300 iterations out of 500
-2 * Loglike = 24565.098809
Burning in for 350 iterations out of 500
-2 * Loglike = 24560.587256
Burning in for 400 iterations out of 500
-2 * Loglike = 24569.086918
Burning in for 450 iterations out of 500
-2 * Loglike = 24564.380475
Burning in for 500 iterations out of 500
-2 * Loglike = 24567.110257

ERAS G30
LINK 0 G30
ERAS  c1090 c1091

MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 4
Actual update 50 of 5000, Stored update 50 of 5000
-2 * Loglike = 24565.929103
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 24564.555509
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 24567.508510
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 24567.699686
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 24565.209783
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 24569.022125
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 24563.857577
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 24578.700946
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 24563.821779
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 24566.366078
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 24572.681255
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 24572.049789
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 24564.624809
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 24571.066052
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 24569.727592
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 24568.292872
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 24571.668244
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 24563.039454
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 24563.654067
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 24562.791167
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 24561.121755
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 24564.256578
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 24565.481159
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 24566.213184
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 24572.983116
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 24564.670290
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 24566.253311
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 24570.325158
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 24568.900791
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 24566.335503
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 24567.610260
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 24570.050710
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 24566.370039
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 24564.717643
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 24567.265749
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 24568.335900
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 24569.000708
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 24562.545592
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 24570.583515
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 24566.637525
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 24565.698957
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 24572.760287
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 24560.045256
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 24573.343825
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 24566.701120
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 24565.025201
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 24569.474091
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 24572.645102
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 24570.243171
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 24569.742647
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 24566.253885
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 24568.079904
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 24560.794089
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 24564.010240
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 24562.007227
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 24567.302911
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 24567.179184
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 24565.841911
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 24561.562332
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 24570.907030
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 24570.730242
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 24563.827426
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 24563.520003
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 24570.074754
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 24568.650538
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 24567.183273
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 24569.455763
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 24569.550314
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 24564.310535
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 24562.221421
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 24565.474836
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 24562.858312
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 24582.365794
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 24563.329227
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 24565.187542
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 24564.070298
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 24568.657602
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 24560.877277
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 24564.191339
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 24575.512288
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 24562.358132
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 24562.997834
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 24571.648284
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 24563.124848
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 24564.527684
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 24565.850186
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 24564.104512
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 24562.684209
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 24563.243775
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 24563.369016
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 24562.202109
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 24568.232103
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 24563.580645
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 24573.767377
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 24561.774436
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 24567.335900
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 24573.871363
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 24564.818889
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 24565.111185
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 24565.959848
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          24566.
S.D.    =          3.7625
S.E.M.  =        0.053210

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 1.49s 
Number of obs:  1523 (from total 1523)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Bayesian Deviance Information Criterion (DIC)
Dbar      D(thetabar)    pD      DIC
24566.172  24559.196  6.976      24573.148  
--------------------------------------------------------------------------------------------------- 
The model formula:
c(written, csework) ~ 1 + female + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                          Coef.   Std. Err.       z    Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_written      48.90422     0.53510   91.39           0  ***    47.86913    49.95198   5000 
Intercept_csework      69.74135     0.64421  108.26           0  ***    68.52173    71.03155   5000 
femaleFemale_written   -3.32836     0.69761   -4.77   1.832e-06  ***    -4.68065    -1.97640   5000 
femaleFemale_csework    6.24558     0.83270    7.50   6.363e-14  ***     4.56257     7.87662   5000 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                              Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_written                     179.68092     6.47570    167.59421   193.04257   5000 
cov_Intercept_written_Intercept_csework   110.57329     6.13040     98.64093   122.95368   5258 
var_Intercept_csework                     261.26932     9.55897    243.11617   280.65931   5000 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> # 18.4 A multilevel multivariate model . . . . . . . . . . . . . . . . . 271
> 
> ## Store residual chain at level 3: school
> (mymodel <- runMLwiN(c(written, csework) ~ 1 + female + (1 | school) + (1 | student), D = "Multivariate Normal", estoptions = list(EstM = 1, 
+   resi.store = TRUE, resi.store.levs = 2), data = gcsecomp1))
MLwiN is running, please wait......
/nogui option ignored
ECHO    0


Echoing is ON
BATC 1

Batch mode is ON
MAXI 2
STAR
iteration 0
iteration 1

Convergence not achieved
TOLE 2
MAXI 20
BATC 1

Batch mode is ON
NEXT
iteration 2
iteration 3

Convergence achieved
ECHO 0

Echoing is ON
MCMC   0 500 1 5.8 50 10 G30[1] G30[2]  1 1 1 1 1 4
Burning in for 50 iterations out of 500
-2 * Loglike = 23504.664959
Burning in for 100 iterations out of 500
-2 * Loglike = 23522.842565
Burning in for 150 iterations out of 500
-2 * Loglike = 23524.042444
Burning in for 200 iterations out of 500
-2 * Loglike = 23529.614587
Burning in for 250 iterations out of 500
-2 * Loglike = 23498.056033
Burning in for 300 iterations out of 500
-2 * Loglike = 23507.630834
Burning in for 350 iterations out of 500
-2 * Loglike = 23514.402956
Burning in for 400 iterations out of 500
-2 * Loglike = 23538.690294
Burning in for 450 iterations out of 500
-2 * Loglike = 23558.767641
Burning in for 500 iterations out of 500
-2 * Loglike = 23518.887862

ERAS G30
LINK 0 G30
ERAS  c1090 c1091

MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 4
Actual update 50 of 5000, Stored update 50 of 5000
-2 * Loglike = 23545.220600
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 23480.984113
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 23496.697770
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 23543.692573
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 23553.376526
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 23504.471162
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 23531.881650
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 23522.680656
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 23522.144374
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 23520.323112
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 23513.127071
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 23529.310397
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 23525.952856
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 23525.242768
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 23508.142424
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 23515.886962
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 23574.354958
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 23523.675365
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 23508.244198
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 23528.692061
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 23479.109750
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 23539.095928
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 23559.340910
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 23528.436521
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 23513.485019
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 23530.345199
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 23532.563175
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 23548.213959
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 23511.787110
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 23529.663836
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 23522.942555
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 23506.615530
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 23512.437817
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 23517.175005
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 23517.661747
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 23517.637506
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 23536.410250
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 23515.228640
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 23520.954366
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 23539.206844
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 23548.062536
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 23535.139352
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 23539.459125
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 23496.169121
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 23515.702916
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 23511.837530
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 23507.282220
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 23520.865624
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 23533.749730
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 23521.855871
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 23513.574246
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 23515.772519
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 23528.735462
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 23500.333618
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 23539.357941
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 23536.228166
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 23523.389947
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 23513.924848
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 23559.058151
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 23551.735128
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 23545.320507
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 23535.221430
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 23509.089761
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 23503.073515
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 23531.077661
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 23526.159963
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 23504.877205
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 23516.872656
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 23522.084365
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 23505.054828
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 23503.510120
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 23537.140625
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 23534.437689
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 23549.284190
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 23517.824583
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 23542.382855
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 23544.466631
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 23535.882356
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 23525.809177
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 23546.425247
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 23549.781798
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 23508.665549
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 23512.131338
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 23506.394054
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 23530.379894
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 23518.694346
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 23516.002252
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 23509.660150
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 23512.910539
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 23533.990128
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 23516.233386
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 23516.243563
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 23536.154259
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 23495.994053
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 23528.224452
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 23515.896960
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 23532.486713
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 23532.124859
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 23505.132356
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 23520.762551
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          23524.
S.D.    =          17.695
S.E.M.  =         0.25025

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
        N min     mean max N_complete min_complete mean_complete max_complete
school 73   1 20.86301  83         73            1      20.86301           83
Estimation algorithm:  MCMC      Elapsed time : 3.05s 
Number of obs:  1523 (from total 1523)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Bayesian Deviance Information Criterion (DIC)
Dbar      D(thetabar)    pD      DIC
23523.836  23397.629  126.208    23650.044  
--------------------------------------------------------------------------------------------------- 
The model formula:
c(written, csework) ~ 1 + female + (1 | school) + (1 | student)
Level 2: school     Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                          Coef.   Std. Err.      z    Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_written      49.51727     0.95429  51.89           0  ***    47.61981    51.35287    323 
Intercept_csework      69.68990     1.20742  57.72           0  ***    67.29713    72.03590    280 
femaleFemale_written   -2.43468     0.60530  -4.02   5.764e-05  ***    -3.61457    -1.25755   4684 
femaleFemale_csework    7.00570     0.73927   9.48   2.629e-21  ***     5.60734     8.47061   4331 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the school level: 
                                             Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_written                     52.30344    10.74906     34.90719    76.90354   2568 
cov_Intercept_written_Intercept_csework   29.24192    10.09670     12.12390    50.78904   2688 
var_Intercept_csework                     79.00190    16.13521     52.88268   116.74725   2680 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                              Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_written                     125.33862     4.73379    116.34988   135.27114   4617 
cov_Intercept_written_Intercept_csework    74.45204     4.50973     66.02909    83.75247   4666 
var_Intercept_csework                     184.24917     6.92837    170.93396   198.17814   4621 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> resi <- mymodel@resi.chains$resi_lev2
> label <- 1:ncol(resi)
> 
> ## highlight
> hipos <- rep(0, 6)
> hipos[1] <- which(levels(as.factor(gcsecomp1$school)) == 68137)
> hipos[2] <- which(levels(as.factor(gcsecomp1$school)) == 68201)
> hipos[3] <- which(levels(as.factor(gcsecomp1$school)) == 68711)
> hipos[4] <- which(levels(as.factor(gcsecomp1$school)) == 60427)
> hipos[5] <- which(levels(as.factor(gcsecomp1$school)) == 22710)
> hipos[6] <- which(levels(as.factor(gcsecomp1$school)) == 67105)
> 
> par(mfrow = c(2, 1))
> ## Select u0
> resi0 <- resi[, label[which(label%%2 == 1)]]
> resi0mean <- apply(resi0, 2, mean)
> resi0sd <- apply(resi0, 2, sd)
> rankno0 <- order(resi0mean)
> resi0.lo <- resi0mean - 1.4 * resi0sd
> resi0.hi <- resi0mean + 1.4 * resi0sd
> caterpillar(y = resi0mean[rankno0], x = 1:length(resi0mean), qtlow = resi0.lo[rankno0], qtup = resi0.hi[rankno0], 
+   ylim = c(-24, 21), ylab = "cons.written", xlab = "rank")
> abline(h = 0, lty = "dotted")
> for (i in 1:6) points(x = which(rankno0 == hipos[i]), y = resi0mean[rankno0[which(rankno0 == hipos[i])]], pch = 22, 
+   bg = i + 1)
> 
> ## Select u1
> resi1 <- resi[, label[which(label%%2 == 0)]]
> resi1mean <- apply(resi1, 2, mean)
> resi1sd <- apply(resi1, 2, sd)
> rankno1 <- order(resi1mean)
> resi1.lo <- resi1mean - 1.4 * resi1sd
> resi1.hi <- resi1mean + 1.4 * resi1sd
> caterpillar(y = resi1mean[rankno1], x = 1:length(resi1mean), qtlow = resi1.lo[rankno1], qtup = resi1.hi[rankno1], 
+   ylim = c(-24, 21), ylab = "cons.csework", xlab = "rank")
> abline(h = 0, lty = "dotted")
> for (i in 1:6) points(x = which(rankno1 == hipos[i]), y = resi1mean[rankno1[which(rankno1 == hipos[i])]], pch = 22, 
+   bg = i + 1)
> 
> par(mfrow = c(1, 1))
> plot(resi0mean, resi1mean, pch = 24, bg = "black", xlab = "cons.written", ylab = "cons.csework")
> for (i in 1:6) points(x = resi0mean[rankno0[which(rankno0 == hipos[i])]], y = resi1mean[rankno1[which(rankno1 == hipos[i])]], 
+   pch = 24, bg = i + 1)
> 
> # 18.5 GCSE science data with missing records . . . . . . . . . . . . . .275
> 
> ## Read gcsemv1 data
> data(gcsemv1, package = "R2MLwiN")
> 
> (mymodel <- runMLwiN(c(written, csework) ~ 1 + female + (1 | student), D = "Multivariate Normal", estoptions = list(EstM = 1, 
+   sort.ignore = TRUE), data = gcsemv1))
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 4
Burning in for 50 iterations out of 500
-2 * Loglike = 30651.112963
Burning in for 100 iterations out of 500
-2 * Loglike = 30641.446580
Burning in for 150 iterations out of 500
-2 * Loglike = 30688.758108
Burning in for 200 iterations out of 500
-2 * Loglike = 30680.109943
Burning in for 250 iterations out of 500
-2 * Loglike = 30678.625138
Burning in for 300 iterations out of 500
-2 * Loglike = 30628.520478
Burning in for 350 iterations out of 500
-2 * Loglike = 30677.126225
Burning in for 400 iterations out of 500
-2 * Loglike = 30753.121272
Burning in for 450 iterations out of 500
-2 * Loglike = 30682.105682
Burning in for 500 iterations out of 500
-2 * Loglike = 30687.063692

ERAS G30
LINK 0 G30
ERAS  c1090 c1091

MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 4
Actual update 50 of 5000, Stored update 50 of 5000
-2 * Loglike = 30642.273188
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 30710.780109
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 30656.300474
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 30677.616919
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 30679.653403
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 30695.071091
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 30658.799691
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 30668.603106
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 30754.454416
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 30668.179936
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 30707.232562
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 30670.018877
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 30653.713292
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 30654.738580
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 30709.680185
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 30661.690392
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 30673.263647
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 30717.516670
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 30612.156852
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 30678.685962
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 30717.176571
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 30640.415123
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 30702.054586
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 30687.873549
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 30691.785393
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 30679.630908
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 30670.976400
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 30719.325380
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 30711.175321
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 30628.440846
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 30699.159892
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 30675.841231
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 30705.100004
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 30664.220333
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 30627.797183
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 30706.404538
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 30709.963011
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 30646.435564
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 30697.226873
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 30710.046785
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 30681.622393
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 30668.185411
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 30678.986933
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 30644.207094
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 30682.571877
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 30671.961070
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 30658.549942
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 30706.826613
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 30648.296919
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 30735.506487
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 30697.601543
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 30710.384426
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 30672.998694
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 30659.436194
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 30708.016891
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 30739.995431
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 30649.113080
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 30728.954651
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 30660.876225
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 30737.908639
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 30642.662057
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 30641.395951
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 30650.871348
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 30642.149617
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 30639.422017
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 30655.441018
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 30675.089903
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 30727.908947
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 30634.029609
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 30698.510054
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 30750.410705
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 30681.081580
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 30658.720790
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 30710.244902
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 30717.890515
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 30702.114360
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 30689.722478
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 30658.471710
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 30702.961673
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 30645.691455
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 30691.123355
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 30694.939500
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 30666.021047
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 30718.854279
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 30699.195432
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 30650.999563
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 30698.860349
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 30668.440205
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 30637.186207
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 30676.005536
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 30620.816706
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 30648.521105
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 30703.410137
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 30635.753639
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 30679.936599
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 30652.092603
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 30661.916471
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 30621.786072
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 30691.255284
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 30686.002152
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          30681.
S.D.    =          29.961
S.E.M.  =         0.42372

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 2.22s 
Number of obs:  1905 (from total 1905)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Bayesian Deviance Information Criterion (DIC)
Dbar      D(thetabar)    pD      DIC
30680.758  30292.088  388.670    31069.429  
--------------------------------------------------------------------------------------------------- 
The model formula:
c(written, csework) ~ 1 + female + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                          Coef.   Std. Err.       z    Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_written      48.80068     0.49337   98.91           0  ***    47.81865    49.76957   4359 
Intercept_csework      69.80776     0.60165  116.03           0  ***    68.63450    70.97523   3865 
femaleFemale_written   -3.42845     0.63604   -5.39   7.034e-08  ***    -4.67173    -2.15633   3889 
femaleFemale_csework    5.92975     0.78214    7.58   3.418e-14  ***     4.40694     7.49959   4288 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                              Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_written                     176.66806     6.20849    165.13017   189.42504   4074 
cov_Intercept_written_Intercept_csework   107.93326     5.90549     96.83496   119.81476   3904 
var_Intercept_csework                     257.83095     8.78792    241.11577   275.47575   4109 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> (mymodel <- runMLwiN(c(written, csework) ~ 1 + female + (1 | school) + (1 | student), D = "Multivariate Normal", estoptions = list(EstM = 1, 
+   mcmcMeth = list(dami = 2)), data = gcsemv1))
MLwiN is running, please wait......
/nogui option ignored
ECHO    0


Echoing is ON
BATC 1

Batch mode is ON
MAXI 2
STAR
iteration 0
iteration 1

Convergence not achieved
TOLE 2
MAXI 20
BATC 1

Batch mode is ON
NEXT
iteration 2
iteration 3

Convergence achieved
ECHO 0

Echoing is ON
MCMC   0 500 1 5.8 50 10 G30[1] G30[2]  1 1 1 1 1 4
Burning in for 50 iterations out of 500
-2 * Loglike = 29344.092049
Burning in for 100 iterations out of 500
-2 * Loglike = 29401.578264
Burning in for 150 iterations out of 500
-2 * Loglike = 29415.591400
Burning in for 200 iterations out of 500
-2 * Loglike = 29354.585513
Burning in for 250 iterations out of 500
-2 * Loglike = 29381.781452
Burning in for 300 iterations out of 500
-2 * Loglike = 29405.866082
Burning in for 350 iterations out of 500
-2 * Loglike = 29397.302156
Burning in for 400 iterations out of 500
-2 * Loglike = 29422.558190
Burning in for 450 iterations out of 500
-2 * Loglike = 29367.591939
Burning in for 500 iterations out of 500
-2 * Loglike = 29360.937446

ERAS G30
LINK 0 G30
ERAS  c1090 c1091

MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 4
Actual update 50 of 5000, Stored update 50 of 5000
-2 * Loglike = 29391.141641
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 29334.570345
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 29421.237420
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 29365.855688
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 29351.299066
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 29322.816250
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 29363.037133
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 29394.529273
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 29392.703646
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 29333.789308
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 29370.875517
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 29431.918095
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 29380.929398
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 29372.559301
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 29330.564249
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 29400.067070
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 29417.911304
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 29397.994131
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 29378.519333
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 29365.234060
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 29384.029248
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 29343.739137
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 29358.199793
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 29372.194512
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 29395.009563
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 29367.085651
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 29475.215336
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 29439.357931
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 29405.371043
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 29399.796973
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 29354.958989
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 29374.375253
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 29414.312345
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 29389.289862
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 29351.576955
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 29328.258293
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 29356.803998
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 29362.037378
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 29365.561130
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 29442.950559
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 29383.137793
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 29415.557014
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 29448.221423
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 29425.990340
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 29399.473577
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 29407.574310
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 29434.440078
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 29492.549448
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 29422.780586
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 29412.663806
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 29398.304156
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 29384.891790
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 29382.425594
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 29400.634883
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 29375.928665
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 29294.316512
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 29399.868003
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 29403.852504
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 29386.611403
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 29425.484442
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 29410.035665
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 29402.903853
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 29418.920734
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 29373.509865
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 29342.105343
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 29445.607210
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 29389.173894
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 29359.140503
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 29403.025232
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 29341.426490
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 29478.319653
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 29364.995094
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 29404.363581
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 29347.243246
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 29383.452138
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 29397.985076
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 29360.931755
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 29348.741922
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 29409.959015
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 29372.321578
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 29413.821167
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 29404.678712
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 29407.672468
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 29388.141439
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 29391.706761
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 29390.341535
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 29380.034708
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 29381.163539
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 29431.180648
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 29375.076942
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 29416.458045
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 29412.806474
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 29393.727196
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 29497.511616
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 29355.546432
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 29420.519489
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 29427.436095
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 29365.386649
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 29408.129947
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 29367.944266
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          29389.
S.D.    =          36.134
S.E.M.  =         0.51102

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
        N min     mean max N_complete min_complete mean_complete max_complete
school 73   2 26.09589 104         73            2      26.09589          104
Estimation algorithm:  MCMC      Elapsed time : 3.77s 
Number of obs:  1905 (from total 1905)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Bayesian Deviance Information Criterion (DIC)
Dbar      D(thetabar)    pD      DIC
29389.303  28877.951  511.352    29900.655  
--------------------------------------------------------------------------------------------------- 
The model formula:
c(written, csework) ~ 1 + female + (1 | school) + (1 | student)
Level 2: school     Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                          Coef.   Std. Err.      z    Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_written      49.57791     0.93277  53.15           0  ***    47.69340    51.31091    254 
Intercept_csework      69.72576     1.22424  56.95           0  ***    67.35989    72.16289    204 
femaleFemale_written   -2.50509     0.57450  -4.36   1.298e-05  ***    -3.64086    -1.40406   3537 
femaleFemale_csework    6.73538     0.67492   9.98   1.874e-23  ***     5.46147     8.07613   3541 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the school level: 
                                             Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_written                     49.74115    10.07206     33.67526    72.91785   2586 
cov_Intercept_written_Intercept_csework   26.53397     9.62270      9.61490    47.66072   2775 
var_Intercept_csework                     80.37989    16.02878     53.87081   118.18761   2293 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                              Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_written                     125.01605     4.35738    116.62482   133.94057   3659 
cov_Intercept_written_Intercept_csework    73.19133     4.10512     65.32227    81.21847   3532 
var_Intercept_csework                     180.60366     6.21059    168.76025   192.97747   3810 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> # 18.6 Imputation methods for missing data . . . . . . . . . . . . . . . 280
> 
> # 18.7 Hungarian science exam dataset . . . . . . . . . . . . . . . . . .281
> 
> ## Read hungary1 data
> data(hungary1, package = "R2MLwiN")
> summary(hungary1)
     school         female        es_core         biol_core     
 Min.   : 1018   Male  :1196   Min.   : 0.000   Min.   : 0.000  
 1st Qu.: 4041   Female:1243   1st Qu.: 8.333   1st Qu.: 6.000  
 Median : 8085                 Median : 8.333   Median : 7.000  
 Mean   : 8188                 Mean   : 8.394   Mean   : 7.066  
 3rd Qu.:13016                 3rd Qu.:10.000   3rd Qu.: 8.000  
 Max.   :14015                 Max.   :10.000   Max.   :10.000  
                                                                
    biol_r3          biol_r4         phys_core         phys_r2      
 Min.   : 0.000   Min.   : 0.000   Min.   : 0.000   Min.   : 0.000  
 1st Qu.: 5.000   1st Qu.: 2.500   1st Qu.: 6.000   1st Qu.: 4.286  
 Median : 7.500   Median : 5.000   Median : 7.000   Median : 7.143  
 Mean   : 6.882   Mean   : 5.713   Mean   : 7.212   Mean   : 6.298  
 3rd Qu.: 7.500   3rd Qu.: 7.500   3rd Qu.: 9.000   3rd Qu.: 8.571  
 Max.   :10.000   Max.   :10.000   Max.   :10.000   Max.   :10.000  
 NA's   :1217     NA's   :1233                      NA's   :1213    
      cons      student      
 Min.   :1   Min.   :   1.0  
 1st Qu.:1   1st Qu.: 610.5  
 Median :1   Median :1220.0  
 Mean   :1   Mean   :1220.0  
 3rd Qu.:1   3rd Qu.:1829.5  
 Max.   :1   Max.   :2439.0  
                             
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + female + (1 | school) + (1 | student),
+  D = "Multivariate Normal", data = hungary1))
/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
NEXT
iteration 2
iteration 3

Convergence achieved
ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
        N min     mean max N_complete min_complete mean_complete max_complete
school 99  12 24.63636  34         99           12      24.63636           34
Estimation algorithm:  IGLS        Elapsed time : 11.16s 
Number of obs:  2439 (from total 2439)        The model converged after 4 iterations.
Log likelihood:      -21685.9 
Deviance statistic:  43371.7 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + female + (1 | school) + (1 | student)
Level 2: school     Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                            Coef.   Std. Err.        z     Pr(>|z|)         [95% Conf.   Interval] 
Intercept_es_core         8.37975     0.07668   109.29            0   ***      8.22947     8.53003 
Intercept_biol_core       7.10640     0.09957    71.37            0   ***      6.91124     7.30156 
Intercept_biol_r3         6.84409     0.10909    62.74            0   ***      6.63027     7.05791 
Intercept_biol_r4         5.91266     0.16771    35.26   2.859e-272   ***      5.58395     6.24136 
Intercept_phys_core       7.52045     0.11505    65.37            0   ***      7.29496     7.74594 
Intercept_phys_r2         6.63603     0.12761    52.00            0   ***      6.38591     6.88614 
femaleFemale_es_core     -0.02987     0.05897    -0.51       0.6125           -0.14544     0.08570 
femaleFemale_biol_core   -0.15076     0.06632    -2.27      0.02301   *       -0.28075    -0.02077 
femaleFemale_biol_r3      0.03992     0.12537     0.32       0.7501           -0.20579     0.28564 
femaleFemale_biol_r4     -0.49192     0.13762    -3.57    0.0003508   ***     -0.76164    -0.22219 
femaleFemale_phys_core   -0.69561     0.07291    -9.54    1.427e-21   ***     -0.83852    -0.55270 
femaleFemale_phys_r2     -0.69608     0.11600    -6.00    1.964e-09   ***     -0.92343    -0.46873 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the school level: 
                                                Coef.   Std. Err. 
var_Intercept_es_core                         0.40570     0.06997 
cov_Intercept_es_core_Intercept_biol_core     0.37856     0.07732 
var_Intercept_biol_core                       0.75852     0.12338 
cov_Intercept_es_core_Intercept_biol_r3       0.19676     0.06480 
cov_Intercept_biol_core_Intercept_biol_r3     0.35819     0.08967 
var_Intercept_biol_r3                         0.36706     0.10746 
cov_Intercept_es_core_Intercept_biol_r4       0.40457     0.11506 
cov_Intercept_biol_core_Intercept_biol_r4     0.80206     0.16545 
cov_Intercept_biol_r3_Intercept_biol_r4       0.37398     0.13817 
var_Intercept_biol_r4                         1.83150     0.32650 
cov_Intercept_es_core_Intercept_phys_core     0.37396     0.08641 
cov_Intercept_biol_core_Intercept_phys_core   0.79618     0.13245 
cov_Intercept_biol_r3_Intercept_phys_core     0.46744     0.10631 
cov_Intercept_biol_r4_Intercept_phys_core     0.87168     0.18917 
var_Intercept_phys_core                       1.04069     0.16677 
cov_Intercept_es_core_Intercept_phys_r2       0.34370     0.08796 
cov_Intercept_biol_core_Intercept_phys_r2     0.65881     0.12743 
cov_Intercept_biol_r3_Intercept_phys_r2       0.33522     0.10478 
cov_Intercept_biol_r4_Intercept_phys_r2       0.85667     0.19531 
cov_Intercept_phys_core_Intercept_phys_r2     0.77685     0.14928 
var_Intercept_phys_r2                         0.94509     0.18131 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                                Coef.   Std. Err. 
var_Intercept_es_core                         2.05809     0.06017 
cov_Intercept_es_core_Intercept_biol_core     0.63471     0.04963 
var_Intercept_biol_core                       2.60523     0.07616 
cov_Intercept_es_core_Intercept_biol_r3       0.38653     0.09161 
cov_Intercept_biol_core_Intercept_biol_r3     0.47322     0.10314 
var_Intercept_biol_r3                         4.78296     0.20134 
cov_Intercept_es_core_Intercept_biol_r4       0.47151     0.10011 
cov_Intercept_biol_core_Intercept_biol_r4     1.03747     0.11413 
cov_Intercept_biol_r3_Intercept_biol_r4       1.04231     0.25892 
var_Intercept_biol_r4                         5.84651     0.24665 
cov_Intercept_es_core_Intercept_phys_core     0.65933     0.05431 
cov_Intercept_biol_core_Intercept_phys_core   1.19550     0.06411 
cov_Intercept_biol_r3_Intercept_phys_core     0.41427     0.11310 
cov_Intercept_biol_r4_Intercept_phys_core     1.16200     0.12545 
var_Intercept_phys_core                       3.14312     0.09189 
cov_Intercept_es_core_Intercept_phys_r2       0.66153     0.08516 
cov_Intercept_biol_core_Intercept_phys_r2     1.14354     0.09748 
cov_Intercept_biol_r3_Intercept_phys_r2       0.66092     0.21628 
cov_Intercept_biol_r4_Intercept_phys_r2       1.91150     0.22907 
cov_Intercept_phys_core_Intercept_phys_r2     1.54718     0.10869 
var_Intercept_phys_r2                         4.48816     0.18553 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + female + (1 | school) + (1 | student),
+  D = "Multivariate Normal", estoptions = list(EstM = 1, mcmcMeth = list(dami = c(0, 1000, 2000, 3000, 4000, 
+   5000))), data = hungary1))
MLwiN is running, please wait......
/nogui option ignored
ECHO    0


Echoing is ON
BATC 1

Batch mode is ON
MAXI 2
STAR
iteration 0
iteration 1

Convergence not achieved
TOLE 2
MAXI 20
BATC 1

Batch mode is ON
NEXT
iteration 2
iteration 3

Convergence achieved
ECHO 0

Echoing is ON
MCMC   0 500 1 5.8 50 10 G30[1] G30[2]  1 1 1 1 1 4
Burning in for 50 iterations out of 500
-2 * Loglike = 58696.082742
Burning in for 100 iterations out of 500
-2 * Loglike = 58343.785928
Burning in for 150 iterations out of 500
-2 * Loglike = 58343.453673
Burning in for 200 iterations out of 500
-2 * Loglike = 58540.452250
Burning in for 250 iterations out of 500
-2 * Loglike = 58138.939531
Burning in for 300 iterations out of 500
-2 * Loglike = 58388.394952
Burning in for 350 iterations out of 500
-2 * Loglike = 58506.644027
Burning in for 400 iterations out of 500
-2 * Loglike = 58285.492680
Burning in for 450 iterations out of 500
-2 * Loglike = 58519.825370
Burning in for 500 iterations out of 500
-2 * Loglike = 58230.976054

ERAS G30
LINK 0 G30
ERAS  c1090 c1091

LINK 6 G23
MCMC 1 1000 1 c1090 c1091 c1003 c1004 1 4
Actual update 50 of 5000, Stored update 50 of 5000
-2 * Loglike = 58227.538857
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 58138.588982
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 58633.254751
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 58182.594676
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 58402.654587
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 58367.137314
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 58624.934306
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 58144.295680
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 58557.877094
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 58431.256533
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 58672.200416
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 58225.310468
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 58261.214819
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 58363.172249
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 58401.252639
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 58449.891774
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 58294.344386
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 58384.201194
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 58427.916029
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 58439.283291
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           1000
Average =          58377.
S.D.    =          142.16
S.E.M.  =          4.4954

DAMI 0 G23[1]
NAME G23[1] '_est_1000'
PAUS 1

PAUSed batch file execution
MCMC 1 1000 1 c1090 c1091 c1003 c1004 1 4
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 58391.531909
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 58370.942584
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 58397.265869
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 58445.341255
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 58454.075499
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 58387.242209
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 58377.585653
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 58457.681489
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 58545.796725
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 58448.919548
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 58530.559781
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 58482.861398
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 58278.641602
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 58580.306461
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 58167.729865
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 58270.275447
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 58434.228988
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 58566.123462
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 58582.599986
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 58489.678604
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           2000
Average =          58374.
S.D.    =          142.49
S.E.M.  =          3.1861

DAMI 0 G23[2]
NAME G23[2] '_est_2000'
PAUS 1

PAUSed batch file execution
MCMC 1 1000 1 c1090 c1091 c1003 c1004 1 4
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 58423.817700
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 58457.003397
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 58293.068144
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 58442.502054
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 58456.306300
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 58399.794398
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 58182.224894
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 58444.622054
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 58504.863626
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 58544.916561
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 58494.145994
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 58572.486056
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 58601.152096
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 58352.592421
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 58403.019739
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 58486.875585
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 58130.766778
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 58470.359425
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 58222.911424
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 58286.282611
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           3000
Average =          58377.
S.D.    =          143.13
S.E.M.  =          2.6132

DAMI 0 G23[3]
NAME G23[3] '_est_3000'
PAUS 1

PAUSed batch file execution
MCMC 1 1000 1 c1090 c1091 c1003 c1004 1 4
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 58528.887120
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 58527.595285
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 58459.244578
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 58470.232564
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 58359.600864
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 58429.976589
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 58443.572199
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 58457.875884
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 58266.911768
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 58369.191300
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 58338.263026
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 58225.963688
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 58440.853928
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 58423.724514
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 58451.015175
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 58388.544491
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 58319.853550
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 58314.011581
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 58424.372222
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 58288.613247
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           4000
Average =          58378.
S.D.    =          141.20
S.E.M.  =          2.2325

DAMI 0 G23[4]
NAME G23[4] '_est_4000'
PAUS 1

PAUSed batch file execution
MCMC 1 1000 1 c1090 c1091 c1003 c1004 1 4
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 58188.757117
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 58269.746255
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 58355.577462
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 58427.813616
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 58405.941419
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 58450.550537
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 58117.273135
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 58591.578247
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 58397.768997
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 58350.466371
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 58330.795335
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 58480.360050
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 58022.729573
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 58395.135284
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 58377.143478
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 58499.330294
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 58280.370562
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 58481.450550
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 58464.421551
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 58265.895516
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          58380.
S.D.    =          141.60
S.E.M.  =          2.0025

DAMI 0 G23[5]
NAME G23[5] '_est_5000'
PAUS 1

PAUSed batch file execution
LINK 0 G23
PSTA 'C:/Users/edcmjc/AppData/Local/Temp/Rtmpyg2ViD/MIfile_3c4c111f3adc.dta' '_est_1000' '_est_2000' '_est_3000' '_est_4000' '_est_5000' 'resp_indicator'
ERAS  '_est_1000' '_est_2000' '_est_3000' '_est_4000' '_est_5000'
ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
        N min     mean max N_complete min_complete mean_complete max_complete
school 99  12 24.63636  34         99           12      24.63636           34
Estimation algorithm:  MCMC      Elapsed time : 32.75s 
Number of obs:  2439 (from total 2439)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Bayesian Deviance Information Criterion (DIC)
Dbar      D(thetabar)    pD      DIC
58379.893  54347.315  4032.579   62412.472  
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + female + (1 | school) + (1 | student)
Level 2: school     Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                            Coef.   Std. Err.       z     Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core         8.37294     0.07871  106.38            0  ***     8.22220     8.52807    482 
Intercept_biol_core       7.09322     0.10435   67.97            0  ***     6.88921     7.30053    240 
Intercept_biol_r3         6.83760     0.10940   62.50            0  ***     6.62205     7.04702    897 
Intercept_biol_r4         5.89428     0.17318   34.04   6.427e-254  ***     5.56280     6.24468    328 
Intercept_phys_core       7.50131     0.11819   63.47            0  ***     7.26877     7.73475    243 
Intercept_phys_r2         6.61616     0.13141   50.35            0  ***     6.35607     6.87262    343 
femaleFemale_es_core     -0.03099     0.05991   -0.52        0.605         -0.14707     0.08633   4231 
femaleFemale_biol_core   -0.15139     0.06751   -2.24      0.02493  *      -0.28484    -0.02171   5607 
femaleFemale_biol_r3      0.03542     0.12871    0.28       0.7832         -0.22272     0.28212   1559 
femaleFemale_biol_r4     -0.49575     0.14019   -3.54    0.0004059  ***    -0.77123    -0.22288   1517 
femaleFemale_phys_core   -0.69520     0.07287   -9.54    1.426e-21  ***    -0.83840    -0.55197   4769 
femaleFemale_phys_r2     -0.69466     0.11675   -5.95    2.684e-09  ***    -0.92245    -0.46271   1565 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the school level: 
                                                Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_es_core                         0.43980     0.07479      0.31444     0.60688   2766 
cov_Intercept_es_core_Intercept_biol_core     0.40930     0.08313      0.26683     0.59216   3051 
var_Intercept_biol_core                       0.81671     0.13323      0.59502     1.12616   2987 
cov_Intercept_es_core_Intercept_biol_r3       0.21250     0.06709      0.09379     0.35685    950 
cov_Intercept_biol_core_Intercept_biol_r3     0.38228     0.09131      0.22480     0.57938   1117 
var_Intercept_biol_r3                         0.39071     0.09646      0.23150     0.60621    615 
cov_Intercept_es_core_Intercept_biol_r4       0.43861     0.12416      0.21614     0.70769   2403 
cov_Intercept_biol_core_Intercept_biol_r4     0.86814     0.17985      0.56107     1.26933   2697 
cov_Intercept_biol_r3_Intercept_biol_r4       0.40226     0.13766      0.15112     0.69872    899 
var_Intercept_biol_r4                         1.98600     0.34741      1.40511     2.76820   1875 
cov_Intercept_es_core_Intercept_phys_core     0.40462     0.09189      0.24533     0.59921   2840 
cov_Intercept_biol_core_Intercept_phys_core   0.85803     0.14387      0.62316     1.18384   3522 
cov_Intercept_biol_r3_Intercept_phys_core     0.49868     0.10951      0.30864     0.73652   1269 
cov_Intercept_biol_r4_Intercept_phys_core     0.93814     0.20544      0.59114     1.37903   2557 
var_Intercept_phys_core                       1.12063     0.18030      0.82470     1.51509   3441 
cov_Intercept_es_core_Intercept_phys_r2       0.37183     0.09195      0.21033     0.57192   1784 
cov_Intercept_biol_core_Intercept_phys_r2     0.70912     0.13679      0.47527     1.01685   2263 
cov_Intercept_biol_r3_Intercept_phys_r2       0.35878     0.10557      0.16575     0.58374    891 
cov_Intercept_biol_r4_Intercept_phys_r2       0.92790     0.20902      0.56490     1.40035   2090 
cov_Intercept_phys_core_Intercept_phys_r2     0.83773     0.16017      0.56981     1.19241   2471 
var_Intercept_phys_r2                         1.01802     0.18521      0.70273     1.43662   1614 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                                Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_es_core                         2.06545     0.05992      1.94981     2.18197   4567 
cov_Intercept_es_core_Intercept_biol_core     0.63600     0.04952      0.54409     0.73340   4448 
var_Intercept_biol_core                       2.61459     0.07606      2.46651     2.76556   5186 
cov_Intercept_es_core_Intercept_biol_r3       0.38486     0.09082      0.20697     0.56211   1652 
cov_Intercept_biol_core_Intercept_biol_r3     0.47115     0.10278      0.27449     0.67713   1696 
var_Intercept_biol_r3                         4.83723     0.20314      4.45706     5.24543   1443 
cov_Intercept_es_core_Intercept_biol_r4       0.46979     0.10000      0.27558     0.66570   1384 
cov_Intercept_biol_core_Intercept_biol_r4     1.03875     0.12068      0.79872     1.27913   1285 
cov_Intercept_biol_r3_Intercept_biol_r4       1.04810     0.26777      0.50141     1.57132    400 
var_Intercept_biol_r4                         5.89408     0.25201      5.42073     6.40072   1304 
cov_Intercept_es_core_Intercept_phys_core     0.66155     0.05438      0.55793     0.77011   4626 
cov_Intercept_biol_core_Intercept_phys_core   1.19802     0.06465      1.07600     1.32848   4490 
cov_Intercept_biol_r3_Intercept_phys_core     0.41337     0.11579      0.18247     0.64076   1643 
cov_Intercept_biol_r4_Intercept_phys_core     1.16180     0.12683      0.91504     1.41108   1427 
var_Intercept_phys_core                       3.15537     0.09295      2.97667     3.34705   4709 
cov_Intercept_es_core_Intercept_phys_r2       0.66059     0.08308      0.49663     0.82118   1869 
cov_Intercept_biol_core_Intercept_phys_r2     1.14167     0.09820      0.95217     1.33406   1732 
cov_Intercept_biol_r3_Intercept_phys_r2       0.64444     0.22084      0.21666     1.07607    401 
cov_Intercept_biol_r4_Intercept_phys_r2       1.91384     0.22690      1.46458     2.35945    550 
cov_Intercept_phys_core_Intercept_phys_r2     1.55145     0.10953      1.34497     1.77022   1725 
var_Intercept_phys_r2                         4.52318     0.18159      4.18047     4.89874   1538 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> head(mymodel@data)
  es_core biol_core biol_r3 biol_r4 phys_core phys_r2 school student Intercept
1 10.0000         7    10.0      NA         6  4.2857   1018       1         1
2  6.6667         6      NA     7.5         7 10.0000   1018       2         1
3  8.3333         8    10.0     7.5         5      NA   1018       3         1
4 10.0000         6      NA      NA         8 10.0000   1018       4         1
5  8.3333         7     7.5      NA         7      NA   1018       5         1
6  6.6667         7      NA     5.0         6      NA   1018       6         1
  femaleFemale
1            1
2            0
3            1
4            0
5            1
6            1
> if (!require(mitools)) {
+   warning("mitools package required to use imputationList() function")
+ } else {
+   mi <- imputationList(mymodel@imputations)
+   with(mi, fun=head)
+ }
Loading required package: mitools
$chain1_iteration_1000
  es_core biol_core   biol_r3   biol_r4 phys_core   phys_r2 school student
1 10.0000         7 10.000000  4.724379         6  4.285700   1018       1
2  6.6667         6  5.667503  7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000  7.500000         5  6.044044   1018       3
4 10.0000         6  8.936717  8.232637         8 10.000000   1018       4
5  8.3333         7  7.500000 10.216798         7  6.189163   1018       5
6  6.6667         7  7.023035  5.000000         6  6.052805   1018       6
  Intercept femaleFemale
1         1            1
2         1            0
3         1            1
4         1            0
5         1            1
6         1            1

$chain1_iteration_2000
  es_core biol_core   biol_r3  biol_r4 phys_core   phys_r2 school student
1 10.0000         7 10.000000 5.075112         6  4.285700   1018       1
2  6.6667         6  4.235590 7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000 7.500000         5  2.565862   1018       3
4 10.0000         6  8.824922 6.009976         8 10.000000   1018       4
5  8.3333         7  7.500000 8.780800         7  5.306080   1018       5
6  6.6667         7  9.870448 5.000000         6  3.297573   1018       6
  Intercept femaleFemale
1         1            1
2         1            0
3         1            1
4         1            0
5         1            1
6         1            1

$chain1_iteration_3000
  es_core biol_core   biol_r3  biol_r4 phys_core   phys_r2 school student
1 10.0000         7 10.000000 5.959568         6  4.285700   1018       1
2  6.6667         6  9.268406 7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000 7.500000         5  7.576240   1018       3
4 10.0000         6  8.125290 8.011205         8 10.000000   1018       4
5  8.3333         7  7.500000 6.220782         7  6.198626   1018       5
6  6.6667         7  5.751807 5.000000         6  3.141899   1018       6
  Intercept femaleFemale
1         1            1
2         1            0
3         1            1
4         1            0
5         1            1
6         1            1

$chain1_iteration_4000
  es_core biol_core   biol_r3  biol_r4 phys_core   phys_r2 school student
1 10.0000         7 10.000000 7.993846         6  4.285700   1018       1
2  6.6667         6  8.608494 7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000 7.500000         5  5.701624   1018       3
4 10.0000         6  7.991982 9.678516         8 10.000000   1018       4
5  8.3333         7  7.500000 7.494938         7  6.237312   1018       5
6  6.6667         7  5.851149 5.000000         6  6.310345   1018       6
  Intercept femaleFemale
1         1            1
2         1            0
3         1            1
4         1            0
5         1            1
6         1            1

$chain1_iteration_5000
  es_core biol_core   biol_r3   biol_r4 phys_core   phys_r2 school student
1 10.0000         7 10.000000  6.397553         6  4.285700   1018       1
2  6.6667         6  1.369020  7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000  7.500000         5  5.920979   1018       3
4 10.0000         6  5.496566 10.814918         8 10.000000   1018       4
5  8.3333         7  7.500000  1.850508         7  4.815011   1018       5
6  6.6667         7  5.609484  5.000000         6  1.404587   1018       6
  Intercept femaleFemale
1         1            1
2         1            0
3         1            1
4         1            0
5         1            1
6         1            1

attr(,"call")
with(mi, fun = head)
> 
> # Chapter learning outcomes . . . . . . . . . . . . . . . . . . . . . . .128
> 
> ## reinstate par settings
> par(mypar)
> 
> 
> 
> ############################################################################
> 
> proc.time()
   user  system elapsed 
   7.79    0.98   67.78