R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ############################################################################
> #     MLwiN MCMC Manual
> #
> # 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 v3.09/
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: 3.09)  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: 3.09)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 1.13s 
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: 3.09)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 1.42s 
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: 3.09)  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 : 2.98s 
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: 3.09)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 1.89s 
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: 3.09)  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 : 3.48s 
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: 3.09)  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 : 12.71s 
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/Rtmp0CPq9U/MIfile_1e707772517f.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: 3.09)  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 : 30.79s 
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 
   7.35    1.07   65.18