R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

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 2013-2024 Zhengzheng Zhang, Christopher M. J. Charlton, Richard M. A. Parker, William J. Browne and George Leckie

Support provided by the Economic and Social Research Council (ESRC)
(Grants RES-149-25-1084, RES-576-25-0032 and ES/K007246/1)

To cite R2MLwiN in publications use:

  Zhengzheng Zhang, Richard M. A. Parker, Christopher M. J. Charlton,
  George Leckie, William J. Browne (2016). R2MLwiN: A Package to Run
  MLwiN from within R. Journal of Statistical Software, 72(10), 1-43.
  doi:10.18637/jss.v072.i10

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{R2MLwiN}: A Package to Run {MLwiN} from within {R}},
    author = {Zhengzheng Zhang and Richard M. A. Parker and Christopher M. J. Charlton and George Leckie and William J. Browne},
    journal = {Journal of Statistical Software},
    year = {2016},
    volume = {72},
    number = {10},
    pages = {1--43},
    doi = {10.18637/jss.v072.i10},
  }

The MLwiN_path option is currently set to C:/Program Files/MLwiN v3.11/
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: 3.11)  multilevel model (Multivariate Normal) 
Estimation algorithm:  IGLS        Elapsed time : 0.22s 
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...
Burning in for 50 iterations out of 500
-2 * Loglike = 24712.761985
Burning in for 100 iterations out of 500
-2 * Loglike = 24712.827164
Burning in for 150 iterations out of 500
-2 * Loglike = 24712.671515
Burning in for 200 iterations out of 500
-2 * Loglike = 24709.265760
Burning in for 250 iterations out of 500
-2 * Loglike = 24709.748955
Burning in for 300 iterations out of 500
-2 * Loglike = 24710.119439
Burning in for 350 iterations out of 500
-2 * Loglike = 24711.763175
Burning in for 400 iterations out of 500
-2 * Loglike = 24711.993138
Burning in for 450 iterations out of 500
-2 * Loglike = 24706.675306
Burning in for 500 iterations out of 500
-2 * Loglike = 24710.497285

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 = 24707.809513
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 24717.455478
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 24709.513195
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 24712.212243
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 24709.963049
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 24708.839905
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 24711.836897
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 24711.187807
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 24709.226189
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 24713.232644
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 24714.150482
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 24711.239913
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 24711.314472
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 24715.376057
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 24715.830198
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 24711.581041
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 24708.425901
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 24712.986972
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 24710.603097
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 24714.875142
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 24718.154447
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 24708.851824
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 24709.998113
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 24709.890677
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 24709.290240
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 24710.014311
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 24716.359053
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 24709.594216
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 24709.429607
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 24715.675608
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 24707.877547
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 24710.146010
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 24713.615539
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 24711.108046
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 24707.245765
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 24711.436871
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 24709.285462
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 24713.312946
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 24708.781266
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 24710.555260
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 24709.476788
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 24709.012963
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 24708.637155
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 24708.548953
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 24708.778156
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 24708.613055
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 24712.910409
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 24711.003002
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 24710.865027
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 24710.067783
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 24708.064205
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 24707.378257
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 24715.167761
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 24707.792922
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 24709.613793
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 24711.950398
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 24711.950282
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 24710.339213
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 24712.922690
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 24711.767735
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 24710.906025
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 24709.669485
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 24713.946617
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 24710.685598
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 24710.054704
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 24709.640552
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 24712.628840
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 24711.267711
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 24709.630018
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 24709.269270
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 24715.381989
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 24708.253988
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 24710.335133
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 24721.629185
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 24711.284693
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 24708.563135
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 24708.332028
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 24711.581025
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 24710.818068
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 24709.237578
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 24707.074358
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 24708.132829
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 24711.192085
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 24728.206116
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 24714.359835
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 24710.067637
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 24714.106760
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 24715.710641
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 24709.429303
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 24709.675076
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 24709.283530
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 24716.419686
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 24716.625441
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 24711.394211
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 24706.896912
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 24708.061037
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 24712.204192
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 24708.730451
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 24707.247809
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 24707.610605
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          24711.
S.D.    =          3.1683
S.E.M.  =        0.044807

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.11)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 1.14s 
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
24711.202  24706.245  4.957      24716.158  
--------------------------------------------------------------------------------------------------- 
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   46.92953     0.34896  134.48          0  ***    46.26110    47.61791   5000 
Intercept_csework   73.42916     0.41586  176.57          0  ***    72.60318    74.23375   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                     182.44520     6.59064    170.13300   196.04102   5000 
cov_Intercept_written_Intercept_csework   105.47374     6.26473     93.45724   117.64518   5278 
var_Intercept_csework                     270.21418     9.65917    251.47894   289.30814   5000 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> # 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...
Burning in for 50 iterations out of 500
-2 * Loglike = 24567.718516
Burning in for 100 iterations out of 500
-2 * Loglike = 24567.044053
Burning in for 150 iterations out of 500
-2 * Loglike = 24572.018209
Burning in for 200 iterations out of 500
-2 * Loglike = 24564.612996
Burning in for 250 iterations out of 500
-2 * Loglike = 24566.572697
Burning in for 300 iterations out of 500
-2 * Loglike = 24563.269828
Burning in for 350 iterations out of 500
-2 * Loglike = 24561.849404
Burning in for 400 iterations out of 500
-2 * Loglike = 24562.399770
Burning in for 450 iterations out of 500
-2 * Loglike = 24571.921662
Burning in for 500 iterations out of 500
-2 * Loglike = 24571.889147

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 = 24563.639862
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 24564.374208
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 24568.079593
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 24563.249613
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 24564.299400
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 24563.246678
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 24563.829818
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 24569.946387
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 24566.209490
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 24566.371750
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 24565.274432
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 24569.721035
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 24567.406906
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 24563.756311
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 24562.740911
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 24564.127781
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 24569.455000
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 24560.558159
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 24567.626609
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 24568.108588
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 24562.300074
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 24568.925395
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 24564.026046
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 24565.989649
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 24562.768297
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 24567.785033
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 24569.532197
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 24564.320173
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 24564.317295
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 24561.677646
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 24569.210464
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 24567.273821
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 24563.721033
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 24569.952308
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 24569.099030
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 24564.472717
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 24563.301852
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 24566.406571
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 24564.920745
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 24566.232300
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 24562.096518
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 24564.366065
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 24564.156437
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 24565.481484
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 24564.533049
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 24561.928832
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 24562.711126
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 24565.340244
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 24565.963406
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 24566.222920
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 24565.804732
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 24563.319451
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 24563.756772
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 24562.557246
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 24568.136169
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 24564.962147
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 24568.563324
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 24561.163991
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 24565.268014
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 24575.976705
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 24571.854292
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 24566.020762
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 24567.582409
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 24561.850883
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 24566.635762
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 24570.644876
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 24568.723586
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 24566.145837
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 24570.375138
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 24567.549690
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 24562.848593
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 24564.419799
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 24566.813369
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 24565.150057
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 24562.026227
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 24571.480125
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 24573.572676
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 24562.433764
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 24565.533476
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 24564.516111
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 24562.370642
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 24568.341832
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 24562.357679
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 24575.248570
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 24567.846368
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 24562.757090
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 24562.805978
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 24562.780030
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 24566.984018
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 24571.960099
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 24574.076517
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 24566.980416
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 24564.366075
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 24564.402447
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 24568.383303
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 24562.536955
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 24565.067532
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 24560.852872
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 24571.760841
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 24563.639889
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          24566.
S.D.    =          3.6787
S.E.M.  =        0.052025

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.11)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 1.41s 
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
24566.152  24559.198  6.954      24573.106  
--------------------------------------------------------------------------------------------------- 
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      48.90698     0.53407   91.57           0  ***    47.87437    49.94766   5741 
Intercept_csework      69.73940     0.64125  108.76           0  ***    68.50809    70.99194   5000 
femaleFemale_written   -3.34052     0.70156   -4.76   1.921e-06  ***    -4.72219    -1.98013   5666 
femaleFemale_csework    6.24260     0.83582    7.47   8.091e-14  ***     4.59801     7.87595   4816 
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                     179.68640     6.54424    167.52565   193.23839   5000 
cov_Intercept_written_Intercept_csework   110.43491     6.28969     98.51269   123.09717   4599 
var_Intercept_csework                     261.12368     9.38071    243.69445   280.43664   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...
Burning in for 50 iterations out of 500
-2 * Loglike = 23518.337586
Burning in for 100 iterations out of 500
-2 * Loglike = 23496.241373
Burning in for 150 iterations out of 500
-2 * Loglike = 23513.367385
Burning in for 200 iterations out of 500
-2 * Loglike = 23533.389402
Burning in for 250 iterations out of 500
-2 * Loglike = 23500.685817
Burning in for 300 iterations out of 500
-2 * Loglike = 23535.204223
Burning in for 350 iterations out of 500
-2 * Loglike = 23506.949106
Burning in for 400 iterations out of 500
-2 * Loglike = 23520.497657
Burning in for 450 iterations out of 500
-2 * Loglike = 23553.905757
Burning in for 500 iterations out of 500
-2 * Loglike = 23561.382655

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 = 23505.451151
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 23533.361167
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 23506.752113
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 23496.287789
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 23516.355384
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 23542.111221
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 23541.522919
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 23539.577406
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 23497.026888
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 23495.372466
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 23539.841345
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 23507.388188
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 23511.025564
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 23515.855340
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 23528.664114
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 23524.520823
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 23523.762951
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 23520.539463
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 23576.192515
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 23525.751990
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 23499.862270
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 23533.618153
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 23536.740711
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 23514.774131
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 23529.166032
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 23515.808994
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 23497.096845
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 23520.124464
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 23506.975254
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 23528.543006
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 23517.035589
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 23542.193505
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 23541.074706
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 23530.885361
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 23500.235021
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 23489.553884
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 23518.667296
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 23521.940540
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 23488.334541
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 23562.747754
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 23528.092866
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 23524.281781
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 23531.623994
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 23542.006286
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 23536.343108
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 23495.154639
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 23500.084408
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 23540.274635
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 23535.588117
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 23508.422165
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 23511.708448
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 23540.072440
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 23500.518295
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 23516.737130
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 23523.847848
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 23533.207426
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 23523.429432
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 23551.127811
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 23510.547879
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 23536.424121
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 23515.489007
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 23503.295158
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 23509.339972
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 23546.523026
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 23525.932989
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 23530.786550
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 23488.185378
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 23507.947982
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 23523.036447
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 23547.058328
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 23531.076926
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 23558.214406
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 23505.136395
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 23504.408086
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 23538.868172
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 23540.344831
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 23519.686898
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 23525.913154
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 23528.771896
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 23511.224909
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 23525.862715
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 23500.362015
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 23516.496746
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 23528.687410
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 23558.412239
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 23526.595460
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 23529.425916
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 23527.276192
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 23556.678637
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 23516.820517
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 23532.439152
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 23513.799531
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 23554.118843
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 23511.771512
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 23533.574337
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 23519.890844
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 23493.642392
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 23512.679313
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 23523.420512
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 23529.820759
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          23525.
S.D.    =          17.633
S.E.M.  =         0.24937

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.11)  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 : 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
23524.533  23397.731  126.802    23651.335  
--------------------------------------------------------------------------------------------------- 
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      49.54661     0.98736  50.18           0  ***    47.53544    51.38876    276 
Intercept_csework      69.74137     1.23505  56.47           0  ***    67.24932    72.07970    251 
femaleFemale_written   -2.44703     0.60321  -4.06   4.978e-05  ***    -3.66714    -1.23090   4488 
femaleFemale_csework    6.98832     0.71803   9.73   2.189e-22  ***     5.57811     8.39508   4468 
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                     52.26476    10.73447     34.59787    76.02030   2444 
cov_Intercept_written_Intercept_csework   29.43397    10.26216     11.68536    51.95842   2464 
var_Intercept_csework                     79.63063    15.78965     54.41638   115.11535   2762 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                              Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_written                     125.30743     4.65047    116.22411   134.48569   4396 
cov_Intercept_written_Intercept_csework    74.28499     4.45052     65.82727    83.28159   4382 
var_Intercept_csework                     184.06718     6.85074    170.79610   198.28880   4610 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> 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...
Burning in for 50 iterations out of 500
-2 * Loglike = 30650.473261
Burning in for 100 iterations out of 500
-2 * Loglike = 30678.224828
Burning in for 150 iterations out of 500
-2 * Loglike = 30688.893993
Burning in for 200 iterations out of 500
-2 * Loglike = 30629.119728
Burning in for 250 iterations out of 500
-2 * Loglike = 30672.167054
Burning in for 300 iterations out of 500
-2 * Loglike = 30664.582320
Burning in for 350 iterations out of 500
-2 * Loglike = 30648.834239
Burning in for 400 iterations out of 500
-2 * Loglike = 30635.826439
Burning in for 450 iterations out of 500
-2 * Loglike = 30685.690289
Burning in for 500 iterations out of 500
-2 * Loglike = 30667.689647

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 = 30646.765233
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 30674.335405
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 30683.828401
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 30721.418470
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 30677.372332
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 30695.636690
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 30721.676946
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 30680.604975
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 30691.810776
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 30653.244011
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 30681.818191
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 30684.552641
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 30685.251660
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 30677.563591
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 30676.683827
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 30675.190371
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 30700.660615
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 30678.117335
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 30662.815336
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 30701.272645
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 30680.303184
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 30659.286515
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 30661.137156
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 30671.704962
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 30677.947274
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 30670.281075
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 30655.760395
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 30669.662076
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 30669.239365
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 30728.360826
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 30728.588734
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 30699.669667
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 30714.569269
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 30648.000459
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 30671.914955
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 30700.076018
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 30680.527511
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 30695.091790
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 30677.178683
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 30682.856575
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 30684.568275
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 30627.483747
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 30698.758249
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 30632.150106
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 30662.254740
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 30749.064118
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 30713.728668
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 30667.354733
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 30636.889802
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 30748.919330
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 30650.142025
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 30681.577165
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 30685.218928
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 30690.988910
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 30688.982363
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 30678.368938
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 30694.225309
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 30616.356085
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 30736.014711
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 30656.828806
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 30677.708688
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 30691.899125
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 30663.636810
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 30672.143090
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 30716.456608
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 30680.227760
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 30696.416920
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 30671.020473
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 30686.819548
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 30635.487121
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 30643.200144
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 30625.264082
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 30721.976553
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 30691.065764
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 30655.038228
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 30662.659161
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 30687.156779
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 30626.185527
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 30693.770783
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 30641.888936
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 30746.279436
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 30679.676974
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 30678.797489
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 30704.906577
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 30677.977882
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 30635.603334
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 30718.035212
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 30699.325768
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 30656.918615
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 30691.333987
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 30677.956397
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 30703.797456
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 30720.342728
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 30693.425487
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 30722.196268
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 30682.447430
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 30602.737628
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 30700.097609
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 30709.236456
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 30649.047208
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          30681.
S.D.    =          29.909
S.E.M.  =         0.42298

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.11)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 1.91s 
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
30680.920  30292.135  388.785    31069.705  
--------------------------------------------------------------------------------------------------- 
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      48.80161     0.49806   97.98           0  ***    47.82918    49.78542   4429 
Intercept_csework      69.83532     0.61048  114.39           0  ***    68.63363    71.01240   4211 
femaleFemale_written   -3.42652     0.65213   -5.25   1.485e-07  ***    -4.68695    -2.12737   4314 
femaleFemale_csework    5.88735     0.79333    7.42   1.162e-13  ***     4.34843     7.42364   4466 
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                     176.64572     5.87232    165.37299   188.30471   4371 
cov_Intercept_written_Intercept_csework   108.02243     5.66291     97.27586   119.30906   4033 
var_Intercept_csework                     258.07835     8.66452    241.39620   275.09566   4173 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> (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...
Burning in for 50 iterations out of 500
-2 * Loglike = 29344.281174
Burning in for 100 iterations out of 500
-2 * Loglike = 29366.494377
Burning in for 150 iterations out of 500
-2 * Loglike = 29413.321660
Burning in for 200 iterations out of 500
-2 * Loglike = 29367.829448
Burning in for 250 iterations out of 500
-2 * Loglike = 29411.000546
Burning in for 300 iterations out of 500
-2 * Loglike = 29378.001450
Burning in for 350 iterations out of 500
-2 * Loglike = 29395.171642
Burning in for 400 iterations out of 500
-2 * Loglike = 29380.177822
Burning in for 450 iterations out of 500
-2 * Loglike = 29423.695203
Burning in for 500 iterations out of 500
-2 * Loglike = 29416.136426

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 = 29440.464074
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 29382.479147
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 29417.987531
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 29438.787231
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 29404.307853
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 29376.739692
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 29373.632375
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 29344.283928
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 29435.696592
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 29363.635290
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 29392.099370
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 29470.452140
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 29351.961052
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 29369.097945
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 29503.943516
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 29351.750135
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 29351.481406
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 29423.189496
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 29394.608243
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 29378.838968
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 29435.913290
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 29431.720691
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 29375.805697
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 29440.092527
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 29433.456945
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 29381.003644
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 29371.167582
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 29338.782511
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 29337.502728
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 29324.386295
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 29388.746006
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 29448.585327
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 29420.532263
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 29379.674029
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 29395.203358
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 29356.619286
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 29321.529115
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 29365.524536
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 29361.350002
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 29393.941322
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 29420.440467
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 29424.625673
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 29381.791621
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 29355.628582
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 29398.251118
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 29319.103551
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 29358.480606
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 29392.597655
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 29418.776871
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 29310.823266
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 29436.073233
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 29420.963872
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 29402.785535
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 29373.615539
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 29340.636021
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 29369.694821
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 29410.910922
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 29406.365410
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 29447.439129
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 29401.949161
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 29425.213466
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 29349.345004
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 29430.062516
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 29398.608834
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 29360.390164
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 29390.529509
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 29406.578385
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 29362.678644
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 29331.190385
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 29357.371720
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 29438.335938
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 29374.507610
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 29363.757250
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 29357.250677
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 29439.942878
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 29394.983895
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 29392.645907
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 29393.618360
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 29444.174352
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 29462.636164
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 29407.667056
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 29359.491920
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 29394.831360
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 29393.973182
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 29355.081174
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 29460.386468
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 29361.586362
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 29411.865114
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 29309.587827
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 29409.961007
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 29379.755173
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 29418.589930
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 29423.454254
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 29408.376016
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 29364.985413
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 29354.395587
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 29417.174804
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 29405.986930
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 29376.049505
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 29329.789163
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          29389.
S.D.    =          35.415
S.E.M.  =         0.50085

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.11)  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 : 3.47s 
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
29388.933  28878.425  510.508    29899.442  
--------------------------------------------------------------------------------------------------- 
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      49.36510     0.96196  51.32           0  ***    47.47247    51.24127    255 
Intercept_csework      69.64355     1.20394  57.85           0  ***    67.26242    71.90673    235 
femaleFemale_written   -2.48806     0.55490  -4.48   7.333e-06  ***    -3.57422    -1.38915   3656 
femaleFemale_csework    6.76583     0.66108  10.23   1.389e-24  ***     5.48019     8.07808   3661 
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                     49.57074    10.11818     33.01899    73.87114   2716 
cov_Intercept_written_Intercept_csework   26.36400     9.61538      9.46633    46.91432   2920 
var_Intercept_csework                     79.75505    15.78038     53.52328   115.39169   2788 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                              Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_written                     125.06278     4.40554    116.77123   134.05452   3648 
cov_Intercept_written_Intercept_csework    73.19540     4.19897     65.43246    81.94018   3620 
var_Intercept_csework                     180.62558     6.33571    168.81559   193.42671   3879 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> # 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: 3.11)  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 : 12.89s 
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...
Burning in for 50 iterations out of 500
-2 * Loglike = 58684.473701
Burning in for 100 iterations out of 500
-2 * Loglike = 58363.350480
Burning in for 150 iterations out of 500
-2 * Loglike = 58415.308613
Burning in for 200 iterations out of 500
-2 * Loglike = 58331.221797
Burning in for 250 iterations out of 500
-2 * Loglike = 58277.187978
Burning in for 300 iterations out of 500
-2 * Loglike = 58309.827112
Burning in for 350 iterations out of 500
-2 * Loglike = 58457.128628
Burning in for 400 iterations out of 500
-2 * Loglike = 58393.432150
Burning in for 450 iterations out of 500
-2 * Loglike = 58123.572620
Burning in for 500 iterations out of 500
-2 * Loglike = 58256.707760

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 = 58461.039378
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 58584.843057
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 58266.276103
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 58285.016543
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 58267.327660
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 58446.442591
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 58426.455924
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 58459.974525
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 58438.382271
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 58091.730342
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 58460.923870
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 58540.001815
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 58339.700082
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 58269.709330
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 58540.947149
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 58497.149654
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 58304.720703
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 58563.191835
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 58430.951889
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 58419.883691
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           1000
Average =          58389.
S.D.    =          133.29
S.E.M.  =          4.2149

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 = 58301.084132
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 58278.147045
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 58472.199145
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 58234.561850
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 58459.341629
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 58017.692409
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 58242.654135
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 58271.072053
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 58470.058247
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 58063.890491
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 58367.314964
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 58527.810695
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 58570.336618
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 58384.522309
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 58165.507213
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 58270.508084
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 58267.010548
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 58624.500752
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 58361.589395
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 58455.251550
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           2000
Average =          58379.
S.D.    =          139.56
S.E.M.  =          3.1206

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 = 58608.210705
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 58248.673304
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 58267.456376
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 58636.755881
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 58239.855677
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 58512.856064
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 58392.965911
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 58321.745510
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 58455.093521
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 58181.344993
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 58466.481574
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 58197.443584
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 58587.326145
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 58346.589729
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 58442.599511
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 58371.015311
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 58164.325362
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 58433.846007
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 58448.840361
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 58567.473335
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           3000
Average =          58377.
S.D.    =          145.56
S.E.M.  =          2.6576

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 = 58464.715229
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 58320.208115
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 58387.516412
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 58381.211969
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 58144.238591
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 58376.205533
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 58329.013052
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 58679.612816
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 58322.651225
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 58452.163490
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 58308.331651
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 58572.594004
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 58387.619283
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 58502.206495
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 58560.004220
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 58396.264804
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 58578.202365
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 58370.495965
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 58196.147649
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 58340.995040
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           4000
Average =          58373.
S.D.    =          143.31
S.E.M.  =          2.2660

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 = 58127.908012
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 58456.645899
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 58345.547504
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 58400.508154
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 58683.533673
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 58551.480112
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 58442.326386
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 58450.727795
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 58389.947324
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 58358.027680
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 58295.877720
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 58415.807499
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 58477.117497
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 58356.940024
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 58135.517382
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 58473.907272
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 58515.967143
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 58080.449766
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 58642.873944
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 58152.081593
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          58373.
S.D.    =          143.66
S.E.M.  =          2.0317

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/RtmpiYRdS7/MIfile_33182d397d.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: 3.11)  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 : 32.41s 
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
58372.560  54340.298  4032.262   62404.822  
--------------------------------------------------------------------------------------------------- 
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         8.37900     0.07986  104.92            0  ***     8.21960     8.53159    413 
Intercept_biol_core       7.10907     0.10208   69.64            0  ***     6.90494     7.29759    255 
Intercept_biol_r3         6.84619     0.11218   61.03            0  ***     6.62460     7.06794    537 
Intercept_biol_r4         5.91972     0.17428   33.97   6.727e-253  ***     5.57955     6.26541    306 
Intercept_phys_core       7.52105     0.12061   62.36            0  ***     7.28389     7.74625    257 
Intercept_phys_r2         6.63456     0.13172   50.37            0  ***     6.38068     6.89431    421 
femaleFemale_es_core     -0.02990     0.05935   -0.50       0.6144         -0.14618     0.08577   4611 
femaleFemale_biol_core   -0.14966     0.06626   -2.26      0.02389  *      -0.28097    -0.01745   5324 
femaleFemale_biol_r3      0.03971     0.12631    0.31       0.7532         -0.20636     0.28295   1718 
femaleFemale_biol_r4     -0.48910     0.13743   -3.56    0.0003722  ***    -0.75416    -0.22000   1489 
femaleFemale_phys_core   -0.69577     0.07440   -9.35     8.61e-21  ***    -0.84020    -0.54998   4554 
femaleFemale_phys_r2     -0.69610     0.11675   -5.96    2.486e-09  ***    -0.92241    -0.46963   1733 
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                         0.43803     0.07487      0.31392     0.60285   3215 
cov_Intercept_es_core_Intercept_biol_core     0.41119     0.08420      0.26763     0.59495   3153 
var_Intercept_biol_core                       0.82125     0.13503      0.59440     1.11741   2981 
cov_Intercept_es_core_Intercept_biol_r3       0.21354     0.06628      0.09381     0.35629   1094 
cov_Intercept_biol_core_Intercept_biol_r3     0.39051     0.09386      0.22772     0.59285   1146 
var_Intercept_biol_r3                         0.39965     0.09553      0.24168     0.61188    695 
cov_Intercept_es_core_Intercept_biol_r4       0.44429     0.12398      0.22369     0.72042   2286 
cov_Intercept_biol_core_Intercept_biol_r4     0.87275     0.18241      0.56171     1.27588   2291 
cov_Intercept_biol_r3_Intercept_biol_r4       0.40669     0.13983      0.15328     0.70131   1175 
var_Intercept_biol_r4                         1.99055     0.34876      1.40703     2.76056   1640 
cov_Intercept_es_core_Intercept_phys_core     0.40597     0.09349      0.24762     0.61380   3249 
cov_Intercept_biol_core_Intercept_phys_core   0.86589     0.14688      0.62175     1.19666   3555 
cov_Intercept_biol_r3_Intercept_phys_core     0.51096     0.11171      0.32308     0.75895   1301 
cov_Intercept_biol_r4_Intercept_phys_core     0.94981     0.20952      0.59408     1.40642   2618 
var_Intercept_phys_core                       1.13454     0.18565      0.82600     1.55653   3189 
cov_Intercept_es_core_Intercept_phys_r2       0.37247     0.09385      0.20894     0.57701   2178 
cov_Intercept_biol_core_Intercept_phys_r2     0.71450     0.13745      0.48448     1.01875   2497 
cov_Intercept_biol_r3_Intercept_phys_r2       0.36151     0.10584      0.17360     0.58532    921 
cov_Intercept_biol_r4_Intercept_phys_r2       0.93004     0.21131      0.57610     1.38649   1689 
cov_Intercept_phys_core_Intercept_phys_r2     0.84364     0.16216      0.56692     1.20425   2758 
var_Intercept_phys_r2                         1.01996     0.18962      0.69666     1.43432   1695 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                                Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_es_core                         2.06730     0.06081      1.95387     2.18963   4700 
cov_Intercept_es_core_Intercept_biol_core     0.63725     0.05019      0.53944     0.73676   4582 
var_Intercept_biol_core                       2.61766     0.07617      2.47231     2.76783   4523 
cov_Intercept_es_core_Intercept_biol_r3       0.38869     0.09107      0.20675     0.56569   1539 
cov_Intercept_biol_core_Intercept_biol_r3     0.47710     0.10031      0.28365     0.67721   1619 
var_Intercept_biol_r3                         4.83774     0.19712      4.46665     5.23799   1482 
cov_Intercept_es_core_Intercept_biol_r4       0.47029     0.09913      0.27304     0.66333   1597 
cov_Intercept_biol_core_Intercept_biol_r4     1.03681     0.12232      0.80025     1.28251   1282 
cov_Intercept_biol_r3_Intercept_biol_r4       1.06760     0.25440      0.55305     1.57484    434 
var_Intercept_biol_r4                         5.89405     0.25385      5.40734     6.41227   1369 
cov_Intercept_es_core_Intercept_phys_core     0.66213     0.05417      0.55752     0.77348   5009 
cov_Intercept_biol_core_Intercept_phys_core   1.19978     0.06485      1.07336     1.33083   4598 
cov_Intercept_biol_r3_Intercept_phys_core     0.41408     0.11126      0.19990     0.63681   1688 
cov_Intercept_biol_r4_Intercept_phys_core     1.16247     0.12604      0.91777     1.41068   1599 
var_Intercept_phys_core                       3.15598     0.09282      2.97850     3.34447   4464 
cov_Intercept_es_core_Intercept_phys_r2       0.66661     0.08404      0.50303     0.83003   1658 
cov_Intercept_biol_core_Intercept_phys_r2     1.15000     0.09710      0.96572     1.34553   1584 
cov_Intercept_biol_r3_Intercept_phys_r2       0.66309     0.21365      0.25330     1.09204    340 
cov_Intercept_biol_r4_Intercept_phys_r2       1.92358     0.21685      1.49658     2.33805    568 
cov_Intercept_phys_core_Intercept_phys_r2     1.55771     0.10891      1.35021     1.77184   1546 
var_Intercept_phys_r2                         4.52838     0.18774      4.17580     4.90464   1533 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> 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 12.123716         6  4.285700   1018       1
2  6.6667         6  7.255589  7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000  7.500000         5  6.242382   1018       3
4 10.0000         6  6.079620  4.421116         8 10.000000   1018       4
5  8.3333         7  7.500000  5.499372         7  8.859745   1018       5
6  6.6667         7  5.263067  5.000000         6  2.714720   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 8.568636         6  4.285700   1018       1
2  6.6667         6  7.799933 7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000 7.500000         5  3.365414   1018       3
4 10.0000         6  6.549963 7.526566         8 10.000000   1018       4
5  8.3333         7  7.500000 4.779687         7  5.743311   1018       5
6  6.6667         7  4.475630 5.000000         6  3.304127   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 7.044004         6  4.285700   1018       1
2  6.6667         6  9.207521 7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000 7.500000         5  7.072733   1018       3
4 10.0000         6 10.462209 8.295353         8 10.000000   1018       4
5  8.3333         7  7.500000 6.464687         7  8.399819   1018       5
6  6.6667         7  8.921084 5.000000         6  6.063890   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 5.568816         6  4.285700   1018       1
2  6.6667         6  6.043774 7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000 7.500000         5  9.141410   1018       3
4 10.0000         6  8.855500 5.286454         8 10.000000   1018       4
5  8.3333         7  7.500000 7.940201         7  7.317906   1018       5
6  6.6667         7  6.428131 5.000000         6  5.479529   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 7.195869         6  4.285700   1018       1
2  6.6667         6  4.548929 7.500000         7 10.000000   1018       2
3  8.3333         8 10.000000 7.500000         5  5.685029   1018       3
4 10.0000         6  8.298112 8.098084         8 10.000000   1018       4
5  8.3333         7  7.500000 6.067368         7  4.489384   1018       5
6  6.6667         7  4.568118 5.000000         6  2.819186   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 
   7.43    1.14   67.68