R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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

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

> ############################################################################
> #     MLwiN MCMC Manual
> #
> # 20  Multilevel Factor Analysis Modelling . . . . . . . . . . . . . . . 303
> #
> #     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/
> ############################################################################
> 
> # 20.1 Factor analysis modelling . . . . . . . . . . . . . . . . . . . . 303
> 
> # 20.2 MCMC algorithm . . . . . . . . . . . . . . . . . . . . . . . . . .304
> 
> # 20.3 Hungarian science exam . . . . . . . . . . . . . . . . . . . . . .304
> 
> 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 v3.14/
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
> 
> ## Read hungary1 data
> data(hungary1, package = "R2MLwiN")
> 
> round(colMeans(hungary1[, c("es_core", "biol_core", "phys_core")]), 4)
  es_core biol_core phys_core 
   8.3941    7.0664    7.2120 
> round(apply(hungary1[, c("es_core", "biol_core", "phys_core")], 2, sd), 4)
  es_core biol_core phys_core 
   1.5650    1.8272    2.0627 
> round(cor(hungary1[, c("es_core", "biol_core", "phys_core")]), 4)
          es_core biol_core phys_core
es_core    1.0000    0.3471    0.3128
biol_core  0.3471    1.0000    0.5247
phys_core  0.3128    0.5247    1.0000
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (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: 3.14)  multilevel model (Multivariate Normal) 
Estimation algorithm:  IGLS        Elapsed time : 4.18s 
Number of obs:  2439 (from total 2439)        The model converged after 4 iterations.
Log likelihood:      -22211.8 
Deviance statistic:  44423.6 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.        z   Pr(>|z|)         [95% Conf.   Interval] 
Intercept_es_core     8.39414     0.03168   264.94          0   ***      8.33204     8.45624 
Intercept_biol_core   7.06642     0.03699   191.04          0   ***      6.99392     7.13892 
Intercept_biol_r3     6.89700     0.06379   108.12          0   ***      6.77197     7.02203 
Intercept_biol_r4     5.67445     0.07564    75.02          0   ***      5.52619     5.82270 
Intercept_phys_core   7.21197     0.04176   172.71          0   ***      7.13013     7.29382 
Intercept_phys_r2     6.31601     0.06167   102.42          0   ***      6.19514     6.43687 
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_es_core                         2.44834     0.07011 
cov_Intercept_es_core_Intercept_biol_core     0.99227     0.06127 
var_Intercept_biol_core                       3.33712     0.09556 
cov_Intercept_es_core_Intercept_biol_r3       0.57021     0.10048 
cov_Intercept_biol_core_Intercept_biol_r3     0.81959     0.11771 
var_Intercept_biol_r3                         5.15374     0.20824 
cov_Intercept_es_core_Intercept_biol_r4       0.90490     0.11977 
cov_Intercept_biol_core_Intercept_biol_r4     1.85965     0.14322 
cov_Intercept_biol_r3_Intercept_biol_r4       1.51518     0.28626 
var_Intercept_biol_r4                         7.76196     0.31215 
cov_Intercept_es_core_Intercept_phys_core     1.00938     0.06846 
cov_Intercept_biol_core_Intercept_phys_core   1.97690     0.08615 
cov_Intercept_biol_r3_Intercept_phys_core     0.85576     0.13270 
cov_Intercept_biol_r4_Intercept_phys_core     2.11944     0.16179 
var_Intercept_phys_core                       4.25314     0.12179 
cov_Intercept_es_core_Intercept_phys_r2       0.99492     0.09858 
cov_Intercept_biol_core_Intercept_phys_r2     1.80603     0.11845 
cov_Intercept_biol_r3_Intercept_phys_r2       1.11952     0.23076 
cov_Intercept_biol_r4_Intercept_phys_r2       2.91479     0.26492 
cov_Intercept_phys_core_Intercept_phys_r2     2.40201     0.13617 
var_Intercept_phys_r2                         5.53558     0.21790 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> covM1 <- matrix(, 6, 6)
> colnames(covM1) <- rownames(covM1) <- c("cons.es_core", "cons.biol_core", "cons.biol_r3", "cons.biol_r4", "cons.phys_core", 
+   "cons.phys_r2")
> covM1[upper.tri(covM1, diag = TRUE)] <- mymodel@RP
> # covM1[lower.tri(covM1)] <- t(covM1)[lower.tri(covM1)]
> round(cov2cor(t(covM1)), 3)
               cons.es_core cons.biol_core cons.biol_r3 cons.biol_r4
cons.es_core          1.000             NA           NA           NA
cons.biol_core        0.347          1.000           NA           NA
cons.biol_r3          0.161          0.198        1.000           NA
cons.biol_r4          0.208          0.365        0.240        1.000
cons.phys_core        0.313          0.525        0.183        0.369
cons.phys_r2          0.270          0.420        0.210        0.445
               cons.phys_core cons.phys_r2
cons.es_core               NA           NA
cons.biol_core             NA           NA
cons.biol_r3               NA           NA
cons.biol_r4               NA           NA
cons.phys_core          1.000           NA
cons.phys_r2            0.495            1
> 
> # 20.4 A single factor Bayesian model . . . . . . . . . . . . . . . . . . 307
> 
> nfact <- 1
> lev.fact <- 1
> nfactcor <- 0
> factcor <- NULL
> # see FACT in the MCMC manual
> loading <- matrix(c(1, 0, 0, 0, 0, 0, 1), ncol = 7, nrow = nfact, byrow = TRUE)
> constr <- matrix(c(1, 0, 0, 0, 0, 0, 0), ncol = 7, nrow = nfact, byrow = TRUE)
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (1 | student), D = "Multivariate Normal", 
+   estoptions = list(EstM = 1, fact = list(nfact = nfact, lev.fact = lev.fact, nfactcor = nfactcor, factcor = factcor, 
+     loading = loading, constr = constr)), 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 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 = 63359.391759
Burning in for 100 iterations out of 500
-2 * Loglike = 56692.818665
Burning in for 150 iterations out of 500
-2 * Loglike = 57344.803982
Burning in for 200 iterations out of 500
-2 * Loglike = 56810.614294
Burning in for 250 iterations out of 500
-2 * Loglike = 57175.697941
Burning in for 300 iterations out of 500
-2 * Loglike = 56764.436399
Burning in for 350 iterations out of 500
-2 * Loglike = 56783.691851
Burning in for 400 iterations out of 500
-2 * Loglike = 56902.259944
Burning in for 450 iterations out of 500
-2 * Loglike = 56924.022281
Burning in for 500 iterations out of 500
-2 * Loglike = 56719.502894

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 = 57062.924495
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 56963.946374
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 56963.060949
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 56735.446241
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 56928.529810
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 57230.767480
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 57081.776284
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 56880.332280
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 57048.754523
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 56976.190897
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 56895.837220
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 56972.550127
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 57083.857692
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 56998.729652
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 56715.158757
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 57087.631160
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 57057.605642
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 56985.964988
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 56653.228335
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 57113.240256
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 57094.161184
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 57237.057358
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 56955.348038
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 56956.790393
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 56838.933990
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 56840.409381
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 56801.176295
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 57149.517139
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 56745.023896
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 57064.631971
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 57138.747473
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 56940.120088
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 57020.550727
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 56934.684627
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 56997.104760
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 56905.845270
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 56824.118364
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 56991.390701
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 56837.371813
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 57094.780015
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 57142.228060
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 57240.918932
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 56915.669400
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 56857.781715
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 56664.050946
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 56905.605855
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 56907.639600
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 56734.013120
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 57084.171232
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 57001.242613
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 56912.046955
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 57307.930235
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 56729.765089
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 56824.239802
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 56840.571344
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 56920.865319
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 57259.989094
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 56908.804286
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 57023.444319
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 57278.180005
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 57098.837215
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 56874.803039
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 57007.463294
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 56650.538730
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 56845.665354
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 57031.963381
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 57065.884385
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 57026.126830
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 56792.859073
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 56711.101195
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 57115.447305
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 57273.347935
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 56906.117388
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 57140.799149
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 56975.245144
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 56781.296864
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 56804.769435
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 56996.405490
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 56815.138143
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 56607.834100
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 56884.215505
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 57121.817374
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 56975.616853
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 57121.969087
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 56591.764534
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 56872.880165
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 56841.666325
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 56976.797050
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 56981.614793
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 56823.546473
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 56842.031439
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 56942.503651
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 57034.973677
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 57117.029086
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 57245.089674
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 56666.818347
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 57109.610542
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 57139.033295
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 56902.641869
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 57170.150971
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          56955.
S.D.    =          159.40
S.E.M.  =          2.2542

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.14)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 23.77s 
Number of obs:  2439 (from total 2439)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Deviance statistic:  46362.2 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The estimates of factor 1 loadings:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
load1_es_core     1.00000     0.00000      1.00000     1.00000 
load1_biol_core   1.87685     0.10539      1.67029     2.08341 
load1_biol_r3     0.92789     0.11488      0.70273     1.15305 
load1_biol_r4     2.11146     0.16136      1.79519     2.42772 
load1_phys_core   2.17924     0.12496      1.93432     2.42416 
load1_phys_r2     2.18845     0.14752      1.89931     2.47759 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
              Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1   0.48250     0.04925      0.38597     0.57902 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39480     0.03137  267.60          0  ***     8.33368     8.45845   1893 
Intercept_biol_core   7.06817     0.03619  195.31          0  ***     6.99661     7.13725   1104 
Intercept_biol_r3     6.89535     0.06339  108.78          0  ***     6.77146     7.01642   1612 
Intercept_biol_r4     5.67607     0.07545   75.23          0  ***     5.52643     5.82459   1273 
Intercept_phys_core   7.21437     0.04059  177.75          0  ***     7.13531     7.29267   1017 
Intercept_phys_r2     6.31474     0.06017  104.94          0  ***     6.19753     6.43559   1123 
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_es_core     1.95985     0.06112      1.84247     2.08259   2126 
var_Intercept_biol_core   1.65313     0.07626      1.50357     1.80636    703 
var_Intercept_biol_r3     4.75489     0.20311      4.37593     5.18112   1505 
var_Intercept_biol_r4     5.64647     0.26996      5.12717     6.19806   1028 
var_Intercept_phys_core   1.98247     0.09712      1.79292     2.17602    644 
var_Intercept_phys_r2     3.25402     0.16944      2.93227     3.59242    724 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> ranks <- rank(mymodel@fact.chains$scores)
> plot(x = ranks, mymodel@fact.chains$scores, xlab = "rank", ylab = "factor scores", ylim = c(-2.35, 1.2))
> abline(h = 0, lty = "dotted")
> 
> # 20.5 Adding a second factor to the model . . . . . . . . . . . . . . . .313
> 
> nfact <- 2
> lev.fact <- c(1, 1)
> nfactcor <- 0
> factcor <- NULL
> # see FACT in the MCMC manual
> loading <- matrix(c(1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1), ncol = 7, nrow = nfact, byrow = TRUE)
> constr <- matrix(c(1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0), ncol = 7, nrow = nfact, byrow = TRUE)
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (1 | student), D = "Multivariate Normal", 
+   estoptions = list(EstM = 1, fact = list(nfact = nfact, lev.fact = lev.fact, nfactcor = nfactcor, factcor = factcor, 
+     loading = loading, constr = constr)), 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 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 = 63140.160590
Burning in for 100 iterations out of 500
-2 * Loglike = 56041.564814
Burning in for 150 iterations out of 500
-2 * Loglike = 56213.620237
Burning in for 200 iterations out of 500
-2 * Loglike = 56241.650314
Burning in for 250 iterations out of 500
-2 * Loglike = 56044.102282
Burning in for 300 iterations out of 500
-2 * Loglike = 56242.369590
Burning in for 350 iterations out of 500
-2 * Loglike = 56505.739535
Burning in for 400 iterations out of 500
-2 * Loglike = 56395.431956
Burning in for 450 iterations out of 500
-2 * Loglike = 56552.956722
Burning in for 500 iterations out of 500
-2 * Loglike = 56246.191759

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 = 55770.808161
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 54583.222766
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 55199.487629
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 55394.343840
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 55674.663595
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 55931.098564
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 55467.506777
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 55599.339978
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 55341.420167
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 55134.324168
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 55544.608488
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 55152.256182
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 55404.583916
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 56231.174632
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 55792.833203
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 55923.522114
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 55278.579952
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 55805.429125
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 55737.714773
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 55598.773227
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 55509.930218
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 55510.512922
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 55181.761619
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 54560.182466
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 54360.615468
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 54052.791045
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 54906.925151
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 54643.584427
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 55590.095126
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 55489.387467
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 55414.402700
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 54477.677697
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 54642.345765
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 54104.384612
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 54085.013516
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 54499.626738
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 54754.213387
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 55705.354821
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 55602.410569
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 55262.717823
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 54663.706666
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 54087.313698
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 53655.571922
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 53567.414627
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 54204.382952
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 54638.874304
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 55318.196441
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 55983.580559
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 55175.057795
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 55486.414871
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 55017.028157
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 53820.287291
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 54642.436998
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 54598.902544
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 53731.724470
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 53803.428338
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 54223.798112
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 54425.694333
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 55048.968408
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 54795.183127
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 55037.512710
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 54684.398157
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 55113.172549
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 56326.788369
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 55810.685387
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 55969.660163
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 55792.740345
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 55289.829024
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 55129.935058
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 55399.636742
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 55493.639181
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 55274.219600
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 55268.672335
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 54703.871986
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 54379.691231
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 54203.166778
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 53667.357113
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 52646.665795
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 53482.042063
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 54340.795681
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 54182.826775
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 54235.527490
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 52986.195439
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 53116.956034
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 53357.000574
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 53839.253769
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 53749.260244
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 53751.075590
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 53645.462475
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 53875.720474
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 54111.888130
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 54923.327410
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 54363.976143
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 52842.966223
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 53262.718949
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 53734.481498
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 53049.545135
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 53405.109305
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 54207.845960
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 53224.479317
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          54725.
S.D.    =          885.58
S.E.M.  =          12.524

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.14)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 37.39s 
Number of obs:  2439 (from total 2439)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Deviance statistic:  46362.2 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The estimates of factor 1 loadings:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
load1_es_core     1.00000     0.00000      1.00000     1.00000 
load1_biol_core   1.92063     0.11805      1.68925     2.15201 
load1_biol_r3     0.82567     0.11827      0.59386     1.05749 
load1_biol_r4     1.80013     0.16003      1.48647     2.11379 
load1_phys_core   1.96894     0.10697      1.75928     2.17859 
load1_phys_r2     1.77871     0.13887      1.50652     2.05089 
--------------------------------------------------------------------------------------------------- 
The estimates of factor 2 loadings:
                     Coef.   Std. Err.   [95% Conf.   Interval] 
load2_es_core      0.00000     0.00000      0.00000     0.00000 
load2_biol_core    1.00000     0.00000      1.00000     1.00000 
load2_biol_r3      5.42632     4.32959     -3.05953    13.91216 
load2_biol_r4     16.20362     9.06714     -1.56766    33.97489 
load2_phys_core    7.16403     3.77939     -0.24345    14.57150 
load2_phys_r2     29.10034    16.63477     -3.50321    61.70388 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.51457     0.04829      0.41992     0.60922 
cov_fact2_fact1   0.00000     0.00000      0.00000     0.00000 
var_fact2         0.00985     0.02043     -0.03018     0.04989 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39527     0.03197  262.63          0  ***     8.33235     8.45654   1449 
Intercept_biol_core   7.06820     0.03880  182.17          0  ***     6.99546     7.14509    659 
Intercept_biol_r3     6.89839     0.06448  106.99          0  ***     6.77355     7.02500   1407 
Intercept_biol_r4     5.68077     0.07628   74.47          0  ***     5.53150     5.83365    985 
Intercept_phys_core   7.21567     0.04274  168.84          0  ***     7.13301     7.30125    661 
Intercept_phys_r2     6.31622     0.06097  103.59          0  ***     6.19656     6.43446    453 
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_es_core     1.93026     0.06189      1.81057     2.05103    601 
var_Intercept_biol_core   1.44456     0.10358      1.23608     1.63891    124 
var_Intercept_biol_r3     4.72394     0.19795      4.34219     5.12814   1494 
var_Intercept_biol_r4     5.33740     0.34288      4.61119     5.98369     96 
var_Intercept_phys_core   2.10861     0.09786      1.91442     2.30074    345 
var_Intercept_phys_r2     1.63507     0.59683      0.70458     2.79102     13 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> scores <- mymodel@fact.chains$scores
> plot(scores[, 2], scores[, 1], xlab = "Factor 2", ylab = "Factor 1")
> abline(h = 0, lty = "dotted")
> abline(v = 0, lty = "dotted")
> # 20.6 Examining the chains of the loading estimates . . . . . . . . . . 317
> 
> loads <- mymodel@fact.chains$loadings
> 
> sixway(loads[, "load1_biol_core", drop = FALSE], acf.maxlag = 400, name = "load1.2")
> sixway(loads[, "load2_biol_r3", drop = FALSE], acf.maxlag = 1500, name = "load2.3")
> 
> ## burn-in: 5000, iterations=10,000
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (1 | student), D = "Multivariate Normal", 
+   estoptions = list(EstM = 1, fact = list(nfact = nfact, lev.fact = lev.fact, nfactcor = nfactcor, factcor = factcor, 
+     loading = loading, constr = constr), mcmcMeth = list(burnin = 5000, iterations = 10000)), 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 achieved
TOLE 2
MAXI 20
BATC 1

Batch mode is ON
NEXT
iteration 2

Convergence achieved
ECHO 0

Echoing is ON
MCMC   0 5000 1 5.8 50 10 G30[1] G30[2]  1 1 1 1 1 4
BURNING IN...
Burning in for 50 iterations out of 5000
-2 * Loglike = 63140.160590
Burning in for 100 iterations out of 5000
-2 * Loglike = 56041.564814
Burning in for 150 iterations out of 5000
-2 * Loglike = 56213.620237
Burning in for 200 iterations out of 5000
-2 * Loglike = 56241.650314
Burning in for 250 iterations out of 5000
-2 * Loglike = 56044.102282
Burning in for 300 iterations out of 5000
-2 * Loglike = 56242.369590
Burning in for 350 iterations out of 5000
-2 * Loglike = 56505.739535
Burning in for 400 iterations out of 5000
-2 * Loglike = 56395.431956
Burning in for 450 iterations out of 5000
-2 * Loglike = 56552.956722
Burning in for 500 iterations out of 5000
-2 * Loglike = 56246.191759
Burning in for 550 iterations out of 5000
-2 * Loglike = 56199.167039
Burning in for 600 iterations out of 5000
-2 * Loglike = 55863.300032
Burning in for 650 iterations out of 5000
-2 * Loglike = 54792.975661
Burning in for 700 iterations out of 5000
-2 * Loglike = 55175.650841
Burning in for 750 iterations out of 5000
-2 * Loglike = 55419.435847
Burning in for 800 iterations out of 5000
-2 * Loglike = 55692.964414
Burning in for 850 iterations out of 5000
-2 * Loglike = 55982.599130
Burning in for 900 iterations out of 5000
-2 * Loglike = 55684.755038
Burning in for 950 iterations out of 5000
-2 * Loglike = 55597.659154
Burning in for 1000 iterations out of 5000
-2 * Loglike = 55267.471521
Burning in for 1050 iterations out of 5000
-2 * Loglike = 55198.897834
Burning in for 1100 iterations out of 5000
-2 * Loglike = 55342.284085
Burning in for 1150 iterations out of 5000
-2 * Loglike = 54973.797660
Burning in for 1200 iterations out of 5000
-2 * Loglike = 55270.224271
Burning in for 1250 iterations out of 5000
-2 * Loglike = 56278.027920
Burning in for 1300 iterations out of 5000
-2 * Loglike = 56142.899257
Burning in for 1350 iterations out of 5000
-2 * Loglike = 56092.317539
Burning in for 1400 iterations out of 5000
-2 * Loglike = 55432.807906
Burning in for 1450 iterations out of 5000
-2 * Loglike = 56045.309360
Burning in for 1500 iterations out of 5000
-2 * Loglike = 55718.883963
Burning in for 1550 iterations out of 5000
-2 * Loglike = 55469.823426
Burning in for 1600 iterations out of 5000
-2 * Loglike = 55242.672259
Burning in for 1650 iterations out of 5000
-2 * Loglike = 55421.745653
Burning in for 1700 iterations out of 5000
-2 * Loglike = 55341.654636
Burning in for 1750 iterations out of 5000
-2 * Loglike = 54628.515939
Burning in for 1800 iterations out of 5000
-2 * Loglike = 54341.651160
Burning in for 1850 iterations out of 5000
-2 * Loglike = 54317.892821
Burning in for 1900 iterations out of 5000
-2 * Loglike = 54805.567914
Burning in for 1950 iterations out of 5000
-2 * Loglike = 55049.588905
Burning in for 2000 iterations out of 5000
-2 * Loglike = 55618.390694
Burning in for 2050 iterations out of 5000
-2 * Loglike = 55765.482168
Burning in for 2100 iterations out of 5000
-2 * Loglike = 55538.217749
Burning in for 2150 iterations out of 5000
-2 * Loglike = 54641.990768
Burning in for 2200 iterations out of 5000
-2 * Loglike = 54749.843367
Burning in for 2250 iterations out of 5000
-2 * Loglike = 54262.150368
Burning in for 2300 iterations out of 5000
-2 * Loglike = 54116.636140
Burning in for 2350 iterations out of 5000
-2 * Loglike = 54322.513736
Burning in for 2400 iterations out of 5000
-2 * Loglike = 54774.202301
Burning in for 2450 iterations out of 5000
-2 * Loglike = 55952.660338
Burning in for 2500 iterations out of 5000
-2 * Loglike = 55649.121903
Burning in for 2550 iterations out of 5000
-2 * Loglike = 55227.898994
Burning in for 2600 iterations out of 5000
-2 * Loglike = 54696.205117
Burning in for 2650 iterations out of 5000
-2 * Loglike = 53655.223843
Burning in for 2700 iterations out of 5000
-2 * Loglike = 53672.648352
Burning in for 2750 iterations out of 5000
-2 * Loglike = 53317.370851
Burning in for 2800 iterations out of 5000
-2 * Loglike = 54364.216069
Burning in for 2850 iterations out of 5000
-2 * Loglike = 54462.461825
Burning in for 2900 iterations out of 5000
-2 * Loglike = 55227.454779
Burning in for 2950 iterations out of 5000
-2 * Loglike = 55822.835985
Burning in for 3000 iterations out of 5000
-2 * Loglike = 55083.683174
Burning in for 3050 iterations out of 5000
-2 * Loglike = 55479.244007
Burning in for 3100 iterations out of 5000
-2 * Loglike = 55045.547829
Burning in for 3150 iterations out of 5000
-2 * Loglike = 53979.915844
Burning in for 3200 iterations out of 5000
-2 * Loglike = 54566.144098
Burning in for 3250 iterations out of 5000
-2 * Loglike = 54530.902133
Burning in for 3300 iterations out of 5000
-2 * Loglike = 53634.151532
Burning in for 3350 iterations out of 5000
-2 * Loglike = 53898.065709
Burning in for 3400 iterations out of 5000
-2 * Loglike = 54522.822616
Burning in for 3450 iterations out of 5000
-2 * Loglike = 54204.899134
Burning in for 3500 iterations out of 5000
-2 * Loglike = 55151.341945
Burning in for 3550 iterations out of 5000
-2 * Loglike = 55153.093935
Burning in for 3600 iterations out of 5000
-2 * Loglike = 55413.592983
Burning in for 3650 iterations out of 5000
-2 * Loglike = 54749.367961
Burning in for 3700 iterations out of 5000
-2 * Loglike = 55361.443095
Burning in for 3750 iterations out of 5000
-2 * Loglike = 55973.086738
Burning in for 3800 iterations out of 5000
-2 * Loglike = 55897.642400
Burning in for 3850 iterations out of 5000
-2 * Loglike = 56184.283324
Burning in for 3900 iterations out of 5000
-2 * Loglike = 55634.576484
Burning in for 3950 iterations out of 5000
-2 * Loglike = 55476.000414
Burning in for 4000 iterations out of 5000
-2 * Loglike = 55225.538923
Burning in for 4050 iterations out of 5000
-2 * Loglike = 55392.359291
Burning in for 4100 iterations out of 5000
-2 * Loglike = 55276.059454
Burning in for 4150 iterations out of 5000
-2 * Loglike = 55348.650701
Burning in for 4200 iterations out of 5000
-2 * Loglike = 55410.662845
Burning in for 4250 iterations out of 5000
-2 * Loglike = 54619.328661
Burning in for 4300 iterations out of 5000
-2 * Loglike = 54362.533905
Burning in for 4350 iterations out of 5000
-2 * Loglike = 54302.106499
Burning in for 4400 iterations out of 5000
-2 * Loglike = 53798.112714
Burning in for 4450 iterations out of 5000
-2 * Loglike = 52610.915201
Burning in for 4500 iterations out of 5000
-2 * Loglike = 53756.710380
Burning in for 4550 iterations out of 5000
-2 * Loglike = 54475.441003
Burning in for 4600 iterations out of 5000
-2 * Loglike = 53974.746807
Burning in for 4650 iterations out of 5000
-2 * Loglike = 54108.294906
Burning in for 4700 iterations out of 5000
-2 * Loglike = 53057.013259
Burning in for 4750 iterations out of 5000
-2 * Loglike = 52939.636631
Burning in for 4800 iterations out of 5000
-2 * Loglike = 53398.107314
Burning in for 4850 iterations out of 5000
-2 * Loglike = 53653.996221
Burning in for 4900 iterations out of 5000
-2 * Loglike = 53897.894652
Burning in for 4950 iterations out of 5000
-2 * Loglike = 54132.646167
Burning in for 5000 iterations out of 5000
-2 * Loglike = 53703.229476

ERAS G30
LINK 0 G30
ERAS  c1090 c1091

MCMC 1 10000 1 c1090 c1091 c1003 c1004 1 4
Actual update 50 of 10000, Stored update 50 of 10000
-2 * Loglike = 54111.888130
Actual update 100 of 10000, Stored update 100 of 10000
-2 * Loglike = 54923.327410
Actual update 150 of 10000, Stored update 150 of 10000
-2 * Loglike = 54363.976143
Actual update 200 of 10000, Stored update 200 of 10000
-2 * Loglike = 52842.966223
Actual update 250 of 10000, Stored update 250 of 10000
-2 * Loglike = 53262.718949
Actual update 300 of 10000, Stored update 300 of 10000
-2 * Loglike = 53734.481498
Actual update 350 of 10000, Stored update 350 of 10000
-2 * Loglike = 53049.545135
Actual update 400 of 10000, Stored update 400 of 10000
-2 * Loglike = 53405.109305
Actual update 450 of 10000, Stored update 450 of 10000
-2 * Loglike = 54207.845960
Actual update 500 of 10000, Stored update 500 of 10000
-2 * Loglike = 53224.479317
Actual update 550 of 10000, Stored update 550 of 10000
-2 * Loglike = 53745.151427
Actual update 600 of 10000, Stored update 600 of 10000
-2 * Loglike = 54944.556482
Actual update 650 of 10000, Stored update 650 of 10000
-2 * Loglike = 54641.776044
Actual update 700 of 10000, Stored update 700 of 10000
-2 * Loglike = 54881.265561
Actual update 750 of 10000, Stored update 750 of 10000
-2 * Loglike = 55324.272629
Actual update 800 of 10000, Stored update 800 of 10000
-2 * Loglike = 55660.958360
Actual update 850 of 10000, Stored update 850 of 10000
-2 * Loglike = 55844.272731
Actual update 900 of 10000, Stored update 900 of 10000
-2 * Loglike = 55758.908100
Actual update 950 of 10000, Stored update 950 of 10000
-2 * Loglike = 55396.760654
Actual update 1000 of 10000, Stored update 1000 of 10000
-2 * Loglike = 55757.699938
Actual update 1050 of 10000, Stored update 1050 of 10000
-2 * Loglike = 55223.938494
Actual update 1100 of 10000, Stored update 1100 of 10000
-2 * Loglike = 55343.244713
Actual update 1150 of 10000, Stored update 1150 of 10000
-2 * Loglike = 55324.628403
Actual update 1200 of 10000, Stored update 1200 of 10000
-2 * Loglike = 55024.651418
Actual update 1250 of 10000, Stored update 1250 of 10000
-2 * Loglike = 53632.483114
Actual update 1300 of 10000, Stored update 1300 of 10000
-2 * Loglike = 53468.803866
Actual update 1350 of 10000, Stored update 1350 of 10000
-2 * Loglike = 54564.011307
Actual update 1400 of 10000, Stored update 1400 of 10000
-2 * Loglike = 54153.396933
Actual update 1450 of 10000, Stored update 1450 of 10000
-2 * Loglike = 55064.578197
Actual update 1500 of 10000, Stored update 1500 of 10000
-2 * Loglike = 54192.237287
Actual update 1550 of 10000, Stored update 1550 of 10000
-2 * Loglike = 55114.730732
Actual update 1600 of 10000, Stored update 1600 of 10000
-2 * Loglike = 55577.741749
Actual update 1650 of 10000, Stored update 1650 of 10000
-2 * Loglike = 55019.178405
Actual update 1700 of 10000, Stored update 1700 of 10000
-2 * Loglike = 55179.032391
Actual update 1750 of 10000, Stored update 1750 of 10000
-2 * Loglike = 54622.704249
Actual update 1800 of 10000, Stored update 1800 of 10000
-2 * Loglike = 54509.154418
Actual update 1850 of 10000, Stored update 1850 of 10000
-2 * Loglike = 54362.244915
Actual update 1900 of 10000, Stored update 1900 of 10000
-2 * Loglike = 53187.599754
Actual update 1950 of 10000, Stored update 1950 of 10000
-2 * Loglike = 52986.630948
Actual update 2000 of 10000, Stored update 2000 of 10000
-2 * Loglike = 51593.231271
Actual update 2050 of 10000, Stored update 2050 of 10000
-2 * Loglike = 49887.466444
Actual update 2100 of 10000, Stored update 2100 of 10000
-2 * Loglike = 50474.406736
Actual update 2150 of 10000, Stored update 2150 of 10000
-2 * Loglike = 50845.738094
Actual update 2200 of 10000, Stored update 2200 of 10000
-2 * Loglike = 51322.790524
Actual update 2250 of 10000, Stored update 2250 of 10000
-2 * Loglike = 51014.430974
Actual update 2300 of 10000, Stored update 2300 of 10000
-2 * Loglike = 51882.213014
Actual update 2350 of 10000, Stored update 2350 of 10000
-2 * Loglike = 54332.582728
Actual update 2400 of 10000, Stored update 2400 of 10000
-2 * Loglike = 53810.843884
Actual update 2450 of 10000, Stored update 2450 of 10000
-2 * Loglike = 54831.017082
Actual update 2500 of 10000, Stored update 2500 of 10000
-2 * Loglike = 55405.979457
Actual update 2550 of 10000, Stored update 2550 of 10000
-2 * Loglike = 56223.292644
Actual update 2600 of 10000, Stored update 2600 of 10000
-2 * Loglike = 55733.015624
Actual update 2650 of 10000, Stored update 2650 of 10000
-2 * Loglike = 55385.663933
Actual update 2700 of 10000, Stored update 2700 of 10000
-2 * Loglike = 55744.826300
Actual update 2750 of 10000, Stored update 2750 of 10000
-2 * Loglike = 56257.042957
Actual update 2800 of 10000, Stored update 2800 of 10000
-2 * Loglike = 56172.791316
Actual update 2850 of 10000, Stored update 2850 of 10000
-2 * Loglike = 56020.421022
Actual update 2900 of 10000, Stored update 2900 of 10000
-2 * Loglike = 55276.192261
Actual update 2950 of 10000, Stored update 2950 of 10000
-2 * Loglike = 55865.508352
Actual update 3000 of 10000, Stored update 3000 of 10000
-2 * Loglike = 55858.332925
Actual update 3050 of 10000, Stored update 3050 of 10000
-2 * Loglike = 55622.896185
Actual update 3100 of 10000, Stored update 3100 of 10000
-2 * Loglike = 55669.927002
Actual update 3150 of 10000, Stored update 3150 of 10000
-2 * Loglike = 54359.860745
Actual update 3200 of 10000, Stored update 3200 of 10000
-2 * Loglike = 54582.001420
Actual update 3250 of 10000, Stored update 3250 of 10000
-2 * Loglike = 54103.630422
Actual update 3300 of 10000, Stored update 3300 of 10000
-2 * Loglike = 54592.007815
Actual update 3350 of 10000, Stored update 3350 of 10000
-2 * Loglike = 54457.448978
Actual update 3400 of 10000, Stored update 3400 of 10000
-2 * Loglike = 54362.184012
Actual update 3450 of 10000, Stored update 3450 of 10000
-2 * Loglike = 53906.449672
Actual update 3500 of 10000, Stored update 3500 of 10000
-2 * Loglike = 53037.874875
Actual update 3550 of 10000, Stored update 3550 of 10000
-2 * Loglike = 52221.880802
Actual update 3600 of 10000, Stored update 3600 of 10000
-2 * Loglike = 52551.514481
Actual update 3650 of 10000, Stored update 3650 of 10000
-2 * Loglike = 52848.066540
Actual update 3700 of 10000, Stored update 3700 of 10000
-2 * Loglike = 51567.908993
Actual update 3750 of 10000, Stored update 3750 of 10000
-2 * Loglike = 51413.211473
Actual update 3800 of 10000, Stored update 3800 of 10000
-2 * Loglike = 52130.020629
Actual update 3850 of 10000, Stored update 3850 of 10000
-2 * Loglike = 52276.095093
Actual update 3900 of 10000, Stored update 3900 of 10000
-2 * Loglike = 52683.355019
Actual update 3950 of 10000, Stored update 3950 of 10000
-2 * Loglike = 53962.338646
Actual update 4000 of 10000, Stored update 4000 of 10000
-2 * Loglike = 53990.548844
Actual update 4050 of 10000, Stored update 4050 of 10000
-2 * Loglike = 54334.922176
Actual update 4100 of 10000, Stored update 4100 of 10000
-2 * Loglike = 54235.079531
Actual update 4150 of 10000, Stored update 4150 of 10000
-2 * Loglike = 54063.222213
Actual update 4200 of 10000, Stored update 4200 of 10000
-2 * Loglike = 54949.352938
Actual update 4250 of 10000, Stored update 4250 of 10000
-2 * Loglike = 54319.757408
Actual update 4300 of 10000, Stored update 4300 of 10000
-2 * Loglike = 54522.639188
Actual update 4350 of 10000, Stored update 4350 of 10000
-2 * Loglike = 55364.663271
Actual update 4400 of 10000, Stored update 4400 of 10000
-2 * Loglike = 54921.053068
Actual update 4450 of 10000, Stored update 4450 of 10000
-2 * Loglike = 55881.553731
Actual update 4500 of 10000, Stored update 4500 of 10000
-2 * Loglike = 55415.675166
Actual update 4550 of 10000, Stored update 4550 of 10000
-2 * Loglike = 55405.926681
Actual update 4600 of 10000, Stored update 4600 of 10000
-2 * Loglike = 55458.222882
Actual update 4650 of 10000, Stored update 4650 of 10000
-2 * Loglike = 56152.941151
Actual update 4700 of 10000, Stored update 4700 of 10000
-2 * Loglike = 56073.274579
Actual update 4750 of 10000, Stored update 4750 of 10000
-2 * Loglike = 55543.229005
Actual update 4800 of 10000, Stored update 4800 of 10000
-2 * Loglike = 55844.931467
Actual update 4850 of 10000, Stored update 4850 of 10000
-2 * Loglike = 55475.191638
Actual update 4900 of 10000, Stored update 4900 of 10000
-2 * Loglike = 55732.229831
Actual update 4950 of 10000, Stored update 4950 of 10000
-2 * Loglike = 55335.717367
Actual update 5000 of 10000, Stored update 5000 of 10000
-2 * Loglike = 55236.833058
Actual update 5050 of 10000, Stored update 5050 of 10000
-2 * Loglike = 54879.045222
Actual update 5100 of 10000, Stored update 5100 of 10000
-2 * Loglike = 54402.891858
Actual update 5150 of 10000, Stored update 5150 of 10000
-2 * Loglike = 54528.941710
Actual update 5200 of 10000, Stored update 5200 of 10000
-2 * Loglike = 54049.815402
Actual update 5250 of 10000, Stored update 5250 of 10000
-2 * Loglike = 53163.439351
Actual update 5300 of 10000, Stored update 5300 of 10000
-2 * Loglike = 53642.005146
Actual update 5350 of 10000, Stored update 5350 of 10000
-2 * Loglike = 53925.661194
Actual update 5400 of 10000, Stored update 5400 of 10000
-2 * Loglike = 54142.598404
Actual update 5450 of 10000, Stored update 5450 of 10000
-2 * Loglike = 54224.987520
Actual update 5500 of 10000, Stored update 5500 of 10000
-2 * Loglike = 55281.673072
Actual update 5550 of 10000, Stored update 5550 of 10000
-2 * Loglike = 55141.215821
Actual update 5600 of 10000, Stored update 5600 of 10000
-2 * Loglike = 55205.589973
Actual update 5650 of 10000, Stored update 5650 of 10000
-2 * Loglike = 54625.798581
Actual update 5700 of 10000, Stored update 5700 of 10000
-2 * Loglike = 55062.610357
Actual update 5750 of 10000, Stored update 5750 of 10000
-2 * Loglike = 54649.106278
Actual update 5800 of 10000, Stored update 5800 of 10000
-2 * Loglike = 54892.463597
Actual update 5850 of 10000, Stored update 5850 of 10000
-2 * Loglike = 55773.072104
Actual update 5900 of 10000, Stored update 5900 of 10000
-2 * Loglike = 54600.407250
Actual update 5950 of 10000, Stored update 5950 of 10000
-2 * Loglike = 55524.979912
Actual update 6000 of 10000, Stored update 6000 of 10000
-2 * Loglike = 54683.042960
Actual update 6050 of 10000, Stored update 6050 of 10000
-2 * Loglike = 54050.936477
Actual update 6100 of 10000, Stored update 6100 of 10000
-2 * Loglike = 52883.741299
Actual update 6150 of 10000, Stored update 6150 of 10000
-2 * Loglike = 54404.243729
Actual update 6200 of 10000, Stored update 6200 of 10000
-2 * Loglike = 54509.288467
Actual update 6250 of 10000, Stored update 6250 of 10000
-2 * Loglike = 53671.712403
Actual update 6300 of 10000, Stored update 6300 of 10000
-2 * Loglike = 53223.225079
Actual update 6350 of 10000, Stored update 6350 of 10000
-2 * Loglike = 53073.411346
Actual update 6400 of 10000, Stored update 6400 of 10000
-2 * Loglike = 53313.011518
Actual update 6450 of 10000, Stored update 6450 of 10000
-2 * Loglike = 53758.213956
Actual update 6500 of 10000, Stored update 6500 of 10000
-2 * Loglike = 53479.513096
Actual update 6550 of 10000, Stored update 6550 of 10000
-2 * Loglike = 53288.153955
Actual update 6600 of 10000, Stored update 6600 of 10000
-2 * Loglike = 53104.590020
Actual update 6650 of 10000, Stored update 6650 of 10000
-2 * Loglike = 52942.716015
Actual update 6700 of 10000, Stored update 6700 of 10000
-2 * Loglike = 52291.565717
Actual update 6750 of 10000, Stored update 6750 of 10000
-2 * Loglike = 52960.821696
Actual update 6800 of 10000, Stored update 6800 of 10000
-2 * Loglike = 52267.899061
Actual update 6850 of 10000, Stored update 6850 of 10000
-2 * Loglike = 52441.740709
Actual update 6900 of 10000, Stored update 6900 of 10000
-2 * Loglike = 52992.381497
Actual update 6950 of 10000, Stored update 6950 of 10000
-2 * Loglike = 53470.112851
Actual update 7000 of 10000, Stored update 7000 of 10000
-2 * Loglike = 55100.715310
Actual update 7050 of 10000, Stored update 7050 of 10000
-2 * Loglike = 54776.310024
Actual update 7100 of 10000, Stored update 7100 of 10000
-2 * Loglike = 55274.231195
Actual update 7150 of 10000, Stored update 7150 of 10000
-2 * Loglike = 55285.148907
Actual update 7200 of 10000, Stored update 7200 of 10000
-2 * Loglike = 54822.027694
Actual update 7250 of 10000, Stored update 7250 of 10000
-2 * Loglike = 55259.083292
Actual update 7300 of 10000, Stored update 7300 of 10000
-2 * Loglike = 54882.835420
Actual update 7350 of 10000, Stored update 7350 of 10000
-2 * Loglike = 56036.056266
Actual update 7400 of 10000, Stored update 7400 of 10000
-2 * Loglike = 55287.784479
Actual update 7450 of 10000, Stored update 7450 of 10000
-2 * Loglike = 55569.755071
Actual update 7500 of 10000, Stored update 7500 of 10000
-2 * Loglike = 55912.684812
Actual update 7550 of 10000, Stored update 7550 of 10000
-2 * Loglike = 56002.474421
Actual update 7600 of 10000, Stored update 7600 of 10000
-2 * Loglike = 56411.623671
Actual update 7650 of 10000, Stored update 7650 of 10000
-2 * Loglike = 56510.661518
Actual update 7700 of 10000, Stored update 7700 of 10000
-2 * Loglike = 55778.533186
Actual update 7750 of 10000, Stored update 7750 of 10000
-2 * Loglike = 56008.508466
Actual update 7800 of 10000, Stored update 7800 of 10000
-2 * Loglike = 55466.642310
Actual update 7850 of 10000, Stored update 7850 of 10000
-2 * Loglike = 55369.986838
Actual update 7900 of 10000, Stored update 7900 of 10000
-2 * Loglike = 55707.146839
Actual update 7950 of 10000, Stored update 7950 of 10000
-2 * Loglike = 55774.518986
Actual update 8000 of 10000, Stored update 8000 of 10000
-2 * Loglike = 56227.460867
Actual update 8050 of 10000, Stored update 8050 of 10000
-2 * Loglike = 55384.786536
Actual update 8100 of 10000, Stored update 8100 of 10000
-2 * Loglike = 55514.326896
Actual update 8150 of 10000, Stored update 8150 of 10000
-2 * Loglike = 55609.785166
Actual update 8200 of 10000, Stored update 8200 of 10000
-2 * Loglike = 55777.978677
Actual update 8250 of 10000, Stored update 8250 of 10000
-2 * Loglike = 54928.386387
Actual update 8300 of 10000, Stored update 8300 of 10000
-2 * Loglike = 54309.045496
Actual update 8350 of 10000, Stored update 8350 of 10000
-2 * Loglike = 53846.225038
Actual update 8400 of 10000, Stored update 8400 of 10000
-2 * Loglike = 54954.931978
Actual update 8450 of 10000, Stored update 8450 of 10000
-2 * Loglike = 54994.593360
Actual update 8500 of 10000, Stored update 8500 of 10000
-2 * Loglike = 54436.157704
Actual update 8550 of 10000, Stored update 8550 of 10000
-2 * Loglike = 55441.634706
Actual update 8600 of 10000, Stored update 8600 of 10000
-2 * Loglike = 55450.175712
Actual update 8650 of 10000, Stored update 8650 of 10000
-2 * Loglike = 55241.679109
Actual update 8700 of 10000, Stored update 8700 of 10000
-2 * Loglike = 55040.684119
Actual update 8750 of 10000, Stored update 8750 of 10000
-2 * Loglike = 54661.184468
Actual update 8800 of 10000, Stored update 8800 of 10000
-2 * Loglike = 55295.036661
Actual update 8850 of 10000, Stored update 8850 of 10000
-2 * Loglike = 55706.668116
Actual update 8900 of 10000, Stored update 8900 of 10000
-2 * Loglike = 55903.689681
Actual update 8950 of 10000, Stored update 8950 of 10000
-2 * Loglike = 54956.270848
Actual update 9000 of 10000, Stored update 9000 of 10000
-2 * Loglike = 54739.970897
Actual update 9050 of 10000, Stored update 9050 of 10000
-2 * Loglike = 55618.261136
Actual update 9100 of 10000, Stored update 9100 of 10000
-2 * Loglike = 56094.361188
Actual update 9150 of 10000, Stored update 9150 of 10000
-2 * Loglike = 55590.688768
Actual update 9200 of 10000, Stored update 9200 of 10000
-2 * Loglike = 55026.541343
Actual update 9250 of 10000, Stored update 9250 of 10000
-2 * Loglike = 55671.466696
Actual update 9300 of 10000, Stored update 9300 of 10000
-2 * Loglike = 55472.984713
Actual update 9350 of 10000, Stored update 9350 of 10000
-2 * Loglike = 55975.734717
Actual update 9400 of 10000, Stored update 9400 of 10000
-2 * Loglike = 55910.366769
Actual update 9450 of 10000, Stored update 9450 of 10000
-2 * Loglike = 55295.242722
Actual update 9500 of 10000, Stored update 9500 of 10000
-2 * Loglike = 55510.224549
Actual update 9550 of 10000, Stored update 9550 of 10000
-2 * Loglike = 55532.349297
Actual update 9600 of 10000, Stored update 9600 of 10000
-2 * Loglike = 55391.231320
Actual update 9650 of 10000, Stored update 9650 of 10000
-2 * Loglike = 53863.642316
Actual update 9700 of 10000, Stored update 9700 of 10000
-2 * Loglike = 53313.605619
Actual update 9750 of 10000, Stored update 9750 of 10000
-2 * Loglike = 54179.217626
Actual update 9800 of 10000, Stored update 9800 of 10000
-2 * Loglike = 54049.056565
Actual update 9850 of 10000, Stored update 9850 of 10000
-2 * Loglike = 54175.485189
Actual update 9900 of 10000, Stored update 9900 of 10000
-2 * Loglike = 53280.857093
Actual update 9950 of 10000, Stored update 9950 of 10000
-2 * Loglike = 53638.250683
Actual update 10000 of 10000, Stored update 10000 of 10000
-2 * Loglike = 52907.672043
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =          10000
Average =          54527.
S.D.    =          1235.7
S.E.M.  =          12.357

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.14)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 98.57s 
Number of obs:  2439 (from total 2439)          Number of iter.: 10000  Chains: 1  Burn-in: 5000 
Deviance statistic:  46362.2 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The estimates of factor 1 loadings:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
load1_es_core     1.00000     0.00000      1.00000     1.00000 
load1_biol_core   1.94834     0.11843      1.71622     2.18045 
load1_biol_r3     0.84743     0.11284      0.62628     1.06859 
load1_biol_r4     1.85630     0.15826      1.54611     2.16648 
load1_phys_core   2.00490     0.12364      1.76257     2.24723 
load1_phys_r2     1.85722     0.15841      1.54674     2.16771 
--------------------------------------------------------------------------------------------------- 
The estimates of factor 2 loadings:
                     Coef.   Std. Err.   [95% Conf.   Interval] 
load2_es_core      0.00000     0.00000      0.00000     0.00000 
load2_biol_core    1.00000     0.00000      1.00000     1.00000 
load2_biol_r3     10.70923     6.50366     -2.03771    23.45618 
load2_biol_r4     33.75728    11.52954     11.15980    56.35477 
load2_phys_core   13.62464     4.76901      4.27755    22.97174 
load2_phys_r2     58.51334    20.00860     19.29720    97.72948 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.50614     0.05182      0.40457     0.60771 
cov_fact2_fact1   0.00000     0.00000      0.00000     0.00000 
var_fact2         0.00077     0.00044     -0.00010     0.00163 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39356     0.03178  264.12          0  ***     8.33151     8.45544   2961 
Intercept_biol_core   7.06556     0.03768  187.50          0  ***     6.99152     7.13906   1443 
Intercept_biol_r3     6.89372     0.06463  106.67          0  ***     6.76609     7.02048   2939 
Intercept_biol_r4     5.67547     0.07630   74.38          0  ***     5.52686     5.82745   1873 
Intercept_phys_core   7.21138     0.04260  169.28          0  ***     7.12918     7.29500   1463 
Intercept_phys_r2     6.31341     0.06207  101.71          0  ***     6.19248     6.43369    756 
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_es_core     1.93838     0.06266      1.81948     2.06487   1388 
var_Intercept_biol_core   1.43369     0.10972      1.21607     1.64707    240 
var_Intercept_biol_r3     4.71632     0.20479      4.32101     5.12166   1677 
var_Intercept_biol_r4     5.29591     0.42454      4.17574     5.96141     63 
var_Intercept_phys_core   2.11050     0.10431      1.90169     2.31157    424 
var_Intercept_phys_r2     1.61209     0.72045      0.38473     3.00327     15 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> loads <- mymodel@fact.chains$loadings
> 
> sixway(loads[, "load2_biol_r3", drop = FALSE], acf.maxlag = 500, name = "load2.3")
> 
> # 20.7 Correlated factor . . . . . . . . . . . . . . . . . . . . . . . .319
> 
> nfact <- 2
> lev.fact <- c(1, 1)
> nfactcor <- 1
> factcor <- c(1, 2, 0, 0)
> # see FACT in the MCMC manual
> loading <- matrix(c(1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1), ncol = 7, nrow = nfact, byrow = TRUE)
> constr <- matrix(c(1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0), ncol = 7, nrow = nfact, byrow = TRUE)
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (1 | student), D = "Multivariate Normal", 
+   estoptions = list(EstM = 1, fact = list(nfact = nfact, lev.fact = lev.fact, nfactcor = nfactcor, factcor = factcor, 
+     loading = loading, constr = constr), mcmcMeth = list(burnin = 5000, iterations = 10000)), 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 achieved
TOLE 2
MAXI 20
BATC 1

Batch mode is ON
NEXT
iteration 2

Convergence achieved
ECHO 0

Echoing is ON
MCMC   0 5000 1 5.8 50 10 G30[1] G30[2]  1 1 1 1 1 4
BURNING IN...
Burning in for 50 iterations out of 5000
-2 * Loglike = 63208.332420
Burning in for 100 iterations out of 5000
-2 * Loglike = 56119.640237
Burning in for 150 iterations out of 5000
-2 * Loglike = 55997.445148
Burning in for 200 iterations out of 5000
-2 * Loglike = 56116.230971
Burning in for 250 iterations out of 5000
-2 * Loglike = 56196.417423
Burning in for 300 iterations out of 5000
-2 * Loglike = 55894.803360
Burning in for 350 iterations out of 5000
-2 * Loglike = 56386.488917
Burning in for 400 iterations out of 5000
-2 * Loglike = 56308.187561
Burning in for 450 iterations out of 5000
-2 * Loglike = 56305.785027
Burning in for 500 iterations out of 5000
-2 * Loglike = 56351.414228
Burning in for 550 iterations out of 5000
-2 * Loglike = 56428.416571
Burning in for 600 iterations out of 5000
-2 * Loglike = 56233.669224
Burning in for 650 iterations out of 5000
-2 * Loglike = 55720.684621
Burning in for 700 iterations out of 5000
-2 * Loglike = 56014.577768
Burning in for 750 iterations out of 5000
-2 * Loglike = 56153.851484
Burning in for 800 iterations out of 5000
-2 * Loglike = 56342.670889
Burning in for 850 iterations out of 5000
-2 * Loglike = 56459.484956
Burning in for 900 iterations out of 5000
-2 * Loglike = 56022.585529
Burning in for 950 iterations out of 5000
-2 * Loglike = 56038.935575
Burning in for 1000 iterations out of 5000
-2 * Loglike = 56306.955737
Burning in for 1050 iterations out of 5000
-2 * Loglike = 55953.043113
Burning in for 1100 iterations out of 5000
-2 * Loglike = 56058.251547
Burning in for 1150 iterations out of 5000
-2 * Loglike = 55359.553876
Burning in for 1200 iterations out of 5000
-2 * Loglike = 55984.408773
Burning in for 1250 iterations out of 5000
-2 * Loglike = 55896.850994
Burning in for 1300 iterations out of 5000
-2 * Loglike = 56104.347803
Burning in for 1350 iterations out of 5000
-2 * Loglike = 55872.325498
Burning in for 1400 iterations out of 5000
-2 * Loglike = 56239.705903
Burning in for 1450 iterations out of 5000
-2 * Loglike = 55904.091787
Burning in for 1500 iterations out of 5000
-2 * Loglike = 56307.311335
Burning in for 1550 iterations out of 5000
-2 * Loglike = 56205.909217
Burning in for 1600 iterations out of 5000
-2 * Loglike = 56283.190883
Burning in for 1650 iterations out of 5000
-2 * Loglike = 56055.978291
Burning in for 1700 iterations out of 5000
-2 * Loglike = 56247.188831
Burning in for 1750 iterations out of 5000
-2 * Loglike = 56112.873862
Burning in for 1800 iterations out of 5000
-2 * Loglike = 54896.512751
Burning in for 1850 iterations out of 5000
-2 * Loglike = 55163.654304
Burning in for 1900 iterations out of 5000
-2 * Loglike = 55386.352740
Burning in for 1950 iterations out of 5000
-2 * Loglike = 55105.976032
Burning in for 2000 iterations out of 5000
-2 * Loglike = 56237.686467
Burning in for 2050 iterations out of 5000
-2 * Loglike = 56240.212649
Burning in for 2100 iterations out of 5000
-2 * Loglike = 55919.928398
Burning in for 2150 iterations out of 5000
-2 * Loglike = 55928.201830
Burning in for 2200 iterations out of 5000
-2 * Loglike = 56094.777003
Burning in for 2250 iterations out of 5000
-2 * Loglike = 55926.663181
Burning in for 2300 iterations out of 5000
-2 * Loglike = 55360.491105
Burning in for 2350 iterations out of 5000
-2 * Loglike = 55429.020606
Burning in for 2400 iterations out of 5000
-2 * Loglike = 55333.616885
Burning in for 2450 iterations out of 5000
-2 * Loglike = 55778.138011
Burning in for 2500 iterations out of 5000
-2 * Loglike = 55798.672957
Burning in for 2550 iterations out of 5000
-2 * Loglike = 55781.593522
Burning in for 2600 iterations out of 5000
-2 * Loglike = 55538.712306
Burning in for 2650 iterations out of 5000
-2 * Loglike = 56100.748377
Burning in for 2700 iterations out of 5000
-2 * Loglike = 55275.210748
Burning in for 2750 iterations out of 5000
-2 * Loglike = 55702.921787
Burning in for 2800 iterations out of 5000
-2 * Loglike = 56084.459410
Burning in for 2850 iterations out of 5000
-2 * Loglike = 56321.737427
Burning in for 2900 iterations out of 5000
-2 * Loglike = 55535.679680
Burning in for 2950 iterations out of 5000
-2 * Loglike = 55376.342471
Burning in for 3000 iterations out of 5000
-2 * Loglike = 55312.171305
Burning in for 3050 iterations out of 5000
-2 * Loglike = 55519.809848
Burning in for 3100 iterations out of 5000
-2 * Loglike = 55399.315685
Burning in for 3150 iterations out of 5000
-2 * Loglike = 55935.922826
Burning in for 3200 iterations out of 5000
-2 * Loglike = 55689.605757
Burning in for 3250 iterations out of 5000
-2 * Loglike = 55964.521625
Burning in for 3300 iterations out of 5000
-2 * Loglike = 55906.912589
Burning in for 3350 iterations out of 5000
-2 * Loglike = 56263.292532
Burning in for 3400 iterations out of 5000
-2 * Loglike = 55778.814821
Burning in for 3450 iterations out of 5000
-2 * Loglike = 55596.220412
Burning in for 3500 iterations out of 5000
-2 * Loglike = 55069.353581
Burning in for 3550 iterations out of 5000
-2 * Loglike = 55766.692193
Burning in for 3600 iterations out of 5000
-2 * Loglike = 55985.060789
Burning in for 3650 iterations out of 5000
-2 * Loglike = 55735.208944
Burning in for 3700 iterations out of 5000
-2 * Loglike = 55642.335820
Burning in for 3750 iterations out of 5000
-2 * Loglike = 56402.725591
Burning in for 3800 iterations out of 5000
-2 * Loglike = 55740.850605
Burning in for 3850 iterations out of 5000
-2 * Loglike = 55932.266720
Burning in for 3900 iterations out of 5000
-2 * Loglike = 56215.596563
Burning in for 3950 iterations out of 5000
-2 * Loglike = 55661.811397
Burning in for 4000 iterations out of 5000
-2 * Loglike = 55242.705867
Burning in for 4050 iterations out of 5000
-2 * Loglike = 56013.382512
Burning in for 4100 iterations out of 5000
-2 * Loglike = 56157.148306
Burning in for 4150 iterations out of 5000
-2 * Loglike = 56219.162050
Burning in for 4200 iterations out of 5000
-2 * Loglike = 56046.174900
Burning in for 4250 iterations out of 5000
-2 * Loglike = 55554.559462
Burning in for 4300 iterations out of 5000
-2 * Loglike = 55706.194006
Burning in for 4350 iterations out of 5000
-2 * Loglike = 56264.927638
Burning in for 4400 iterations out of 5000
-2 * Loglike = 55829.284253
Burning in for 4450 iterations out of 5000
-2 * Loglike = 56172.537266
Burning in for 4500 iterations out of 5000
-2 * Loglike = 55706.293257
Burning in for 4550 iterations out of 5000
-2 * Loglike = 55760.512206
Burning in for 4600 iterations out of 5000
-2 * Loglike = 56131.370059
Burning in for 4650 iterations out of 5000
-2 * Loglike = 56044.650540
Burning in for 4700 iterations out of 5000
-2 * Loglike = 56184.557991
Burning in for 4750 iterations out of 5000
-2 * Loglike = 56316.732201
Burning in for 4800 iterations out of 5000
-2 * Loglike = 55877.477408
Burning in for 4850 iterations out of 5000
-2 * Loglike = 56237.716362
Burning in for 4900 iterations out of 5000
-2 * Loglike = 56016.555910
Burning in for 4950 iterations out of 5000
-2 * Loglike = 55742.400590
Burning in for 5000 iterations out of 5000
-2 * Loglike = 56161.291631

ERAS G30
LINK 0 G30
ERAS  c1090 c1091

MCMC 1 10000 1 c1090 c1091 c1003 c1004 1 4
Actual update 50 of 10000, Stored update 50 of 10000
-2 * Loglike = 56377.106035
Actual update 100 of 10000, Stored update 100 of 10000
-2 * Loglike = 55928.729350
Actual update 150 of 10000, Stored update 150 of 10000
-2 * Loglike = 55454.628281
Actual update 200 of 10000, Stored update 200 of 10000
-2 * Loglike = 56110.310739
Actual update 250 of 10000, Stored update 250 of 10000
-2 * Loglike = 56540.413904
Actual update 300 of 10000, Stored update 300 of 10000
-2 * Loglike = 56055.241784
Actual update 350 of 10000, Stored update 350 of 10000
-2 * Loglike = 55796.436922
Actual update 400 of 10000, Stored update 400 of 10000
-2 * Loglike = 55779.313776
Actual update 450 of 10000, Stored update 450 of 10000
-2 * Loglike = 56476.984866
Actual update 500 of 10000, Stored update 500 of 10000
-2 * Loglike = 55790.380812
Actual update 550 of 10000, Stored update 550 of 10000
-2 * Loglike = 55867.868044
Actual update 600 of 10000, Stored update 600 of 10000
-2 * Loglike = 56014.105278
Actual update 650 of 10000, Stored update 650 of 10000
-2 * Loglike = 56373.557844
Actual update 700 of 10000, Stored update 700 of 10000
-2 * Loglike = 55805.535426
Actual update 750 of 10000, Stored update 750 of 10000
-2 * Loglike = 55826.247796
Actual update 800 of 10000, Stored update 800 of 10000
-2 * Loglike = 56486.612463
Actual update 850 of 10000, Stored update 850 of 10000
-2 * Loglike = 56596.183778
Actual update 900 of 10000, Stored update 900 of 10000
-2 * Loglike = 55785.337671
Actual update 950 of 10000, Stored update 950 of 10000
-2 * Loglike = 55794.443852
Actual update 1000 of 10000, Stored update 1000 of 10000
-2 * Loglike = 56105.689815
Actual update 1050 of 10000, Stored update 1050 of 10000
-2 * Loglike = 56048.341369
Actual update 1100 of 10000, Stored update 1100 of 10000
-2 * Loglike = 56130.868282
Actual update 1150 of 10000, Stored update 1150 of 10000
-2 * Loglike = 56043.070899
Actual update 1200 of 10000, Stored update 1200 of 10000
-2 * Loglike = 56088.344621
Actual update 1250 of 10000, Stored update 1250 of 10000
-2 * Loglike = 56077.396151
Actual update 1300 of 10000, Stored update 1300 of 10000
-2 * Loglike = 55642.246087
Actual update 1350 of 10000, Stored update 1350 of 10000
-2 * Loglike = 55417.840157
Actual update 1400 of 10000, Stored update 1400 of 10000
-2 * Loglike = 55605.831715
Actual update 1450 of 10000, Stored update 1450 of 10000
-2 * Loglike = 55551.952134
Actual update 1500 of 10000, Stored update 1500 of 10000
-2 * Loglike = 56067.764620
Actual update 1550 of 10000, Stored update 1550 of 10000
-2 * Loglike = 55314.018790
Actual update 1600 of 10000, Stored update 1600 of 10000
-2 * Loglike = 55216.517969
Actual update 1650 of 10000, Stored update 1650 of 10000
-2 * Loglike = 55262.378418
Actual update 1700 of 10000, Stored update 1700 of 10000
-2 * Loglike = 55515.367122
Actual update 1750 of 10000, Stored update 1750 of 10000
-2 * Loglike = 55088.505397
Actual update 1800 of 10000, Stored update 1800 of 10000
-2 * Loglike = 56316.142646
Actual update 1850 of 10000, Stored update 1850 of 10000
-2 * Loglike = 55754.188482
Actual update 1900 of 10000, Stored update 1900 of 10000
-2 * Loglike = 55778.367123
Actual update 1950 of 10000, Stored update 1950 of 10000
-2 * Loglike = 56008.303537
Actual update 2000 of 10000, Stored update 2000 of 10000
-2 * Loglike = 56099.082633
Actual update 2050 of 10000, Stored update 2050 of 10000
-2 * Loglike = 56331.139515
Actual update 2100 of 10000, Stored update 2100 of 10000
-2 * Loglike = 55552.939510
Actual update 2150 of 10000, Stored update 2150 of 10000
-2 * Loglike = 55699.685170
Actual update 2200 of 10000, Stored update 2200 of 10000
-2 * Loglike = 55451.432681
Actual update 2250 of 10000, Stored update 2250 of 10000
-2 * Loglike = 55255.955125
Actual update 2300 of 10000, Stored update 2300 of 10000
-2 * Loglike = 56352.843356
Actual update 2350 of 10000, Stored update 2350 of 10000
-2 * Loglike = 55977.408421
Actual update 2400 of 10000, Stored update 2400 of 10000
-2 * Loglike = 56157.197495
Actual update 2450 of 10000, Stored update 2450 of 10000
-2 * Loglike = 56339.458297
Actual update 2500 of 10000, Stored update 2500 of 10000
-2 * Loglike = 55872.572171
Actual update 2550 of 10000, Stored update 2550 of 10000
-2 * Loglike = 56105.598055
Actual update 2600 of 10000, Stored update 2600 of 10000
-2 * Loglike = 56470.243854
Actual update 2650 of 10000, Stored update 2650 of 10000
-2 * Loglike = 56283.448739
Actual update 2700 of 10000, Stored update 2700 of 10000
-2 * Loglike = 56555.677064
Actual update 2750 of 10000, Stored update 2750 of 10000
-2 * Loglike = 55932.937894
Actual update 2800 of 10000, Stored update 2800 of 10000
-2 * Loglike = 56325.477689
Actual update 2850 of 10000, Stored update 2850 of 10000
-2 * Loglike = 56409.776171
Actual update 2900 of 10000, Stored update 2900 of 10000
-2 * Loglike = 56067.005506
Actual update 2950 of 10000, Stored update 2950 of 10000
-2 * Loglike = 55748.787836
Actual update 3000 of 10000, Stored update 3000 of 10000
-2 * Loglike = 55763.409314
Actual update 3050 of 10000, Stored update 3050 of 10000
-2 * Loglike = 55706.578464
Actual update 3100 of 10000, Stored update 3100 of 10000
-2 * Loglike = 55923.879893
Actual update 3150 of 10000, Stored update 3150 of 10000
-2 * Loglike = 56516.112367
Actual update 3200 of 10000, Stored update 3200 of 10000
-2 * Loglike = 55878.072860
Actual update 3250 of 10000, Stored update 3250 of 10000
-2 * Loglike = 56340.355200
Actual update 3300 of 10000, Stored update 3300 of 10000
-2 * Loglike = 56493.193609
Actual update 3350 of 10000, Stored update 3350 of 10000
-2 * Loglike = 56380.904771
Actual update 3400 of 10000, Stored update 3400 of 10000
-2 * Loglike = 56225.772097
Actual update 3450 of 10000, Stored update 3450 of 10000
-2 * Loglike = 56029.034234
Actual update 3500 of 10000, Stored update 3500 of 10000
-2 * Loglike = 55946.478362
Actual update 3550 of 10000, Stored update 3550 of 10000
-2 * Loglike = 56451.504700
Actual update 3600 of 10000, Stored update 3600 of 10000
-2 * Loglike = 56386.929134
Actual update 3650 of 10000, Stored update 3650 of 10000
-2 * Loglike = 56159.863422
Actual update 3700 of 10000, Stored update 3700 of 10000
-2 * Loglike = 55212.109492
Actual update 3750 of 10000, Stored update 3750 of 10000
-2 * Loglike = 55690.547846
Actual update 3800 of 10000, Stored update 3800 of 10000
-2 * Loglike = 55302.239324
Actual update 3850 of 10000, Stored update 3850 of 10000
-2 * Loglike = 55609.417248
Actual update 3900 of 10000, Stored update 3900 of 10000
-2 * Loglike = 55985.506836
Actual update 3950 of 10000, Stored update 3950 of 10000
-2 * Loglike = 55293.183130
Actual update 4000 of 10000, Stored update 4000 of 10000
-2 * Loglike = 55282.215109
Actual update 4050 of 10000, Stored update 4050 of 10000
-2 * Loglike = 56356.945005
Actual update 4100 of 10000, Stored update 4100 of 10000
-2 * Loglike = 55328.971657
Actual update 4150 of 10000, Stored update 4150 of 10000
-2 * Loglike = 56120.741571
Actual update 4200 of 10000, Stored update 4200 of 10000
-2 * Loglike = 56761.408399
Actual update 4250 of 10000, Stored update 4250 of 10000
-2 * Loglike = 56136.707712
Actual update 4300 of 10000, Stored update 4300 of 10000
-2 * Loglike = 55576.581074
Actual update 4350 of 10000, Stored update 4350 of 10000
-2 * Loglike = 56173.985537
Actual update 4400 of 10000, Stored update 4400 of 10000
-2 * Loglike = 56283.642418
Actual update 4450 of 10000, Stored update 4450 of 10000
-2 * Loglike = 55725.222524
Actual update 4500 of 10000, Stored update 4500 of 10000
-2 * Loglike = 55701.976996
Actual update 4550 of 10000, Stored update 4550 of 10000
-2 * Loglike = 55531.023478
Actual update 4600 of 10000, Stored update 4600 of 10000
-2 * Loglike = 55313.483011
Actual update 4650 of 10000, Stored update 4650 of 10000
-2 * Loglike = 55794.216505
Actual update 4700 of 10000, Stored update 4700 of 10000
-2 * Loglike = 55480.961093
Actual update 4750 of 10000, Stored update 4750 of 10000
-2 * Loglike = 55663.514240
Actual update 4800 of 10000, Stored update 4800 of 10000
-2 * Loglike = 56436.304043
Actual update 4850 of 10000, Stored update 4850 of 10000
-2 * Loglike = 56179.910734
Actual update 4900 of 10000, Stored update 4900 of 10000
-2 * Loglike = 56676.450235
Actual update 4950 of 10000, Stored update 4950 of 10000
-2 * Loglike = 56017.525415
Actual update 5000 of 10000, Stored update 5000 of 10000
-2 * Loglike = 55766.520696
Actual update 5050 of 10000, Stored update 5050 of 10000
-2 * Loglike = 56141.202813
Actual update 5100 of 10000, Stored update 5100 of 10000
-2 * Loglike = 55736.409252
Actual update 5150 of 10000, Stored update 5150 of 10000
-2 * Loglike = 55619.048665
Actual update 5200 of 10000, Stored update 5200 of 10000
-2 * Loglike = 55603.024842
Actual update 5250 of 10000, Stored update 5250 of 10000
-2 * Loglike = 55432.492196
Actual update 5300 of 10000, Stored update 5300 of 10000
-2 * Loglike = 56194.782115
Actual update 5350 of 10000, Stored update 5350 of 10000
-2 * Loglike = 55879.482258
Actual update 5400 of 10000, Stored update 5400 of 10000
-2 * Loglike = 55831.856894
Actual update 5450 of 10000, Stored update 5450 of 10000
-2 * Loglike = 55361.601402
Actual update 5500 of 10000, Stored update 5500 of 10000
-2 * Loglike = 55092.126714
Actual update 5550 of 10000, Stored update 5550 of 10000
-2 * Loglike = 55985.754959
Actual update 5600 of 10000, Stored update 5600 of 10000
-2 * Loglike = 55754.782077
Actual update 5650 of 10000, Stored update 5650 of 10000
-2 * Loglike = 55477.428555
Actual update 5700 of 10000, Stored update 5700 of 10000
-2 * Loglike = 55237.500345
Actual update 5750 of 10000, Stored update 5750 of 10000
-2 * Loglike = 55018.402377
Actual update 5800 of 10000, Stored update 5800 of 10000
-2 * Loglike = 55350.180591
Actual update 5850 of 10000, Stored update 5850 of 10000
-2 * Loglike = 55738.168845
Actual update 5900 of 10000, Stored update 5900 of 10000
-2 * Loglike = 55284.388728
Actual update 5950 of 10000, Stored update 5950 of 10000
-2 * Loglike = 55879.690534
Actual update 6000 of 10000, Stored update 6000 of 10000
-2 * Loglike = 55375.632878
Actual update 6050 of 10000, Stored update 6050 of 10000
-2 * Loglike = 54481.725757
Actual update 6100 of 10000, Stored update 6100 of 10000
-2 * Loglike = 54771.690781
Actual update 6150 of 10000, Stored update 6150 of 10000
-2 * Loglike = 55271.421439
Actual update 6200 of 10000, Stored update 6200 of 10000
-2 * Loglike = 56141.656130
Actual update 6250 of 10000, Stored update 6250 of 10000
-2 * Loglike = 55956.584460
Actual update 6300 of 10000, Stored update 6300 of 10000
-2 * Loglike = 56344.321253
Actual update 6350 of 10000, Stored update 6350 of 10000
-2 * Loglike = 55841.471837
Actual update 6400 of 10000, Stored update 6400 of 10000
-2 * Loglike = 55495.214874
Actual update 6450 of 10000, Stored update 6450 of 10000
-2 * Loglike = 55374.981800
Actual update 6500 of 10000, Stored update 6500 of 10000
-2 * Loglike = 56167.091347
Actual update 6550 of 10000, Stored update 6550 of 10000
-2 * Loglike = 55305.597583
Actual update 6600 of 10000, Stored update 6600 of 10000
-2 * Loglike = 55818.796052
Actual update 6650 of 10000, Stored update 6650 of 10000
-2 * Loglike = 56060.977601
Actual update 6700 of 10000, Stored update 6700 of 10000
-2 * Loglike = 55727.120815
Actual update 6750 of 10000, Stored update 6750 of 10000
-2 * Loglike = 56052.246146
Actual update 6800 of 10000, Stored update 6800 of 10000
-2 * Loglike = 56262.788326
Actual update 6850 of 10000, Stored update 6850 of 10000
-2 * Loglike = 55720.756676
Actual update 6900 of 10000, Stored update 6900 of 10000
-2 * Loglike = 55849.890968
Actual update 6950 of 10000, Stored update 6950 of 10000
-2 * Loglike = 55981.496066
Actual update 7000 of 10000, Stored update 7000 of 10000
-2 * Loglike = 56349.296438
Actual update 7050 of 10000, Stored update 7050 of 10000
-2 * Loglike = 55895.642068
Actual update 7100 of 10000, Stored update 7100 of 10000
-2 * Loglike = 56005.003169
Actual update 7150 of 10000, Stored update 7150 of 10000
-2 * Loglike = 55586.894906
Actual update 7200 of 10000, Stored update 7200 of 10000
-2 * Loglike = 56047.261043
Actual update 7250 of 10000, Stored update 7250 of 10000
-2 * Loglike = 56134.473712
Actual update 7300 of 10000, Stored update 7300 of 10000
-2 * Loglike = 55770.546577
Actual update 7350 of 10000, Stored update 7350 of 10000
-2 * Loglike = 56462.960732
Actual update 7400 of 10000, Stored update 7400 of 10000
-2 * Loglike = 55916.330448
Actual update 7450 of 10000, Stored update 7450 of 10000
-2 * Loglike = 56033.344211
Actual update 7500 of 10000, Stored update 7500 of 10000
-2 * Loglike = 55666.776871
Actual update 7550 of 10000, Stored update 7550 of 10000
-2 * Loglike = 55959.412894
Actual update 7600 of 10000, Stored update 7600 of 10000
-2 * Loglike = 56280.815170
Actual update 7650 of 10000, Stored update 7650 of 10000
-2 * Loglike = 55852.238794
Actual update 7700 of 10000, Stored update 7700 of 10000
-2 * Loglike = 56253.521268
Actual update 7750 of 10000, Stored update 7750 of 10000
-2 * Loglike = 56309.376909
Actual update 7800 of 10000, Stored update 7800 of 10000
-2 * Loglike = 56028.063920
Actual update 7850 of 10000, Stored update 7850 of 10000
-2 * Loglike = 55863.697157
Actual update 7900 of 10000, Stored update 7900 of 10000
-2 * Loglike = 55692.577735
Actual update 7950 of 10000, Stored update 7950 of 10000
-2 * Loglike = 56370.509916
Actual update 8000 of 10000, Stored update 8000 of 10000
-2 * Loglike = 56518.473379
Actual update 8050 of 10000, Stored update 8050 of 10000
-2 * Loglike = 55828.694122
Actual update 8100 of 10000, Stored update 8100 of 10000
-2 * Loglike = 55636.507028
Actual update 8150 of 10000, Stored update 8150 of 10000
-2 * Loglike = 55521.139970
Actual update 8200 of 10000, Stored update 8200 of 10000
-2 * Loglike = 55632.769076
Actual update 8250 of 10000, Stored update 8250 of 10000
-2 * Loglike = 56094.418269
Actual update 8300 of 10000, Stored update 8300 of 10000
-2 * Loglike = 55832.199992
Actual update 8350 of 10000, Stored update 8350 of 10000
-2 * Loglike = 55333.537679
Actual update 8400 of 10000, Stored update 8400 of 10000
-2 * Loglike = 55778.141282
Actual update 8450 of 10000, Stored update 8450 of 10000
-2 * Loglike = 56002.502841
Actual update 8500 of 10000, Stored update 8500 of 10000
-2 * Loglike = 55928.997085
Actual update 8550 of 10000, Stored update 8550 of 10000
-2 * Loglike = 56223.417583
Actual update 8600 of 10000, Stored update 8600 of 10000
-2 * Loglike = 55810.864159
Actual update 8650 of 10000, Stored update 8650 of 10000
-2 * Loglike = 56030.182552
Actual update 8700 of 10000, Stored update 8700 of 10000
-2 * Loglike = 55981.790221
Actual update 8750 of 10000, Stored update 8750 of 10000
-2 * Loglike = 55947.649278
Actual update 8800 of 10000, Stored update 8800 of 10000
-2 * Loglike = 55211.458588
Actual update 8850 of 10000, Stored update 8850 of 10000
-2 * Loglike = 56211.239418
Actual update 8900 of 10000, Stored update 8900 of 10000
-2 * Loglike = 55551.264124
Actual update 8950 of 10000, Stored update 8950 of 10000
-2 * Loglike = 56093.548237
Actual update 9000 of 10000, Stored update 9000 of 10000
-2 * Loglike = 55959.514175
Actual update 9050 of 10000, Stored update 9050 of 10000
-2 * Loglike = 56250.002393
Actual update 9100 of 10000, Stored update 9100 of 10000
-2 * Loglike = 55971.579328
Actual update 9150 of 10000, Stored update 9150 of 10000
-2 * Loglike = 56221.140768
Actual update 9200 of 10000, Stored update 9200 of 10000
-2 * Loglike = 56259.495824
Actual update 9250 of 10000, Stored update 9250 of 10000
-2 * Loglike = 55962.128978
Actual update 9300 of 10000, Stored update 9300 of 10000
-2 * Loglike = 55734.854160
Actual update 9350 of 10000, Stored update 9350 of 10000
-2 * Loglike = 56216.644596
Actual update 9400 of 10000, Stored update 9400 of 10000
-2 * Loglike = 55517.622084
Actual update 9450 of 10000, Stored update 9450 of 10000
-2 * Loglike = 56298.031052
Actual update 9500 of 10000, Stored update 9500 of 10000
-2 * Loglike = 56023.636625
Actual update 9550 of 10000, Stored update 9550 of 10000
-2 * Loglike = 56058.069200
Actual update 9600 of 10000, Stored update 9600 of 10000
-2 * Loglike = 56358.417369
Actual update 9650 of 10000, Stored update 9650 of 10000
-2 * Loglike = 55982.168762
Actual update 9700 of 10000, Stored update 9700 of 10000
-2 * Loglike = 55775.470095
Actual update 9750 of 10000, Stored update 9750 of 10000
-2 * Loglike = 55694.793840
Actual update 9800 of 10000, Stored update 9800 of 10000
-2 * Loglike = 56255.568072
Actual update 9850 of 10000, Stored update 9850 of 10000
-2 * Loglike = 56474.455259
Actual update 9900 of 10000, Stored update 9900 of 10000
-2 * Loglike = 56353.110112
Actual update 9950 of 10000, Stored update 9950 of 10000
-2 * Loglike = 56114.813251
Actual update 10000 of 10000, Stored update 10000 of 10000
-2 * Loglike = 55667.877960
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =          10000
Average =          55882.
S.D.    =          378.72
S.E.M.  =          3.7872

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.14)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 177.08s 
Number of obs:  2439 (from total 2439)          Number of iter.: 10000  Chains: 1  Burn-in: 5000 
Deviance statistic:  46362.2 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The estimates of factor 1 loadings:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
load1_es_core     1.00000     0.00000      1.00000     1.00000 
load1_biol_core   1.67388     0.21067      1.26097     2.08678 
load1_biol_r3     0.74860     0.20917      0.33864     1.15856 
load1_biol_r4     1.46045     0.57983      0.32400     2.59689 
load1_phys_core   1.79818     0.32088      1.16925     2.42710 
load1_phys_r2     1.60400     0.57457      0.47785     2.73014 
--------------------------------------------------------------------------------------------------- 
The estimates of factor 2 loadings:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
load2_es_core     0.00000     0.00000      0.00000     0.00000 
load2_biol_core   1.00000     0.00000      1.00000     1.00000 
load2_biol_r3     0.91956     0.52256     -0.10464     1.94375 
load2_biol_r4     3.33418     0.99818      1.37778     5.29058 
load2_phys_core   1.64690     0.30744      1.04433     2.24946 
load2_phys_r2     3.23337     0.77184      1.72058     4.74616 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                     Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1          0.59541     0.07291      0.45252     0.73831 
cov_fact2_fact1   -0.01411     0.09245     -0.19531     0.16710 
var_fact2          0.17422     0.05496      0.06650     0.28193 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39368     0.03196  262.60          0  ***     8.33139     8.45611   3649 
Intercept_biol_core   7.06610     0.03688  191.59          0  ***     6.99442     7.13834   1701 
Intercept_biol_r3     6.89290     0.06394  107.80          0  ***     6.76869     7.01924   3046 
Intercept_biol_r4     5.68087     0.07552   75.22          0  ***     5.53329     5.82763   1975 
Intercept_phys_core   7.21150     0.04242  169.99          0  ***     7.12888     7.29508   1654 
Intercept_phys_r2     6.30850     0.06288  100.32          0  ***     6.18351     6.43269   1422 
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_es_core     1.85257     0.07507      1.70746     2.00088    167 
var_Intercept_biol_core   1.59030     0.08877      1.41039     1.75897    504 
var_Intercept_biol_r3     4.71033     0.20363      4.32454     5.11721   1428 
var_Intercept_biol_r4     4.93848     0.62529      3.32788     5.86304     59 
var_Intercept_phys_core   2.02418     0.10436      1.81408     2.22412    416 
var_Intercept_phys_r2     2.65787     0.38388      1.75470     3.29141     73 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> # 20.8 Multilevel factor analysis . . . . . . . . . . . . . . . . . . . 320
> 
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (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: 3.14)  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 : 12.58s 
Number of obs:  2439 (from total 2439)        The model converged after 4 iterations.
Log likelihood:      -21741.7 
Deviance statistic:  43483.4 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + (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     8.36456     0.07048   118.68            0   ***      8.22642     8.50270 
Intercept_biol_core   7.02963     0.09329    75.36            0   ***      6.84679     7.21246 
Intercept_biol_r3     6.86631     0.08714    78.80            0   ***      6.69553     7.03710 
Intercept_biol_r4     5.66255     0.15125    37.44   8.995e-307   ***      5.36611     5.95899 
Intercept_phys_core   7.16598     0.10749    66.67            0   ***      6.95530     7.37666 
Intercept_phys_r2     6.28462     0.11193    56.15            0   ***      6.06524     6.50400 
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                         0.40499     0.06988 
cov_Intercept_es_core_Intercept_biol_core     0.37601     0.07694 
var_Intercept_biol_core                       0.75147     0.12242 
cov_Intercept_es_core_Intercept_biol_r3       0.19670     0.06474 
cov_Intercept_biol_core_Intercept_biol_r3     0.35625     0.08928 
var_Intercept_biol_r3                         0.36644     0.10740 
cov_Intercept_es_core_Intercept_biol_r4       0.39488     0.11394 
cov_Intercept_biol_core_Intercept_biol_r4     0.78180     0.16313 
cov_Intercept_biol_r3_Intercept_biol_r4       0.37116     0.13716 
var_Intercept_biol_r4                         1.79652     0.32194 
cov_Intercept_es_core_Intercept_phys_core     0.36433     0.08507 
cov_Intercept_biol_core_Intercept_phys_core   0.77631     0.12995 
cov_Intercept_biol_r3_Intercept_phys_core     0.46260     0.10498 
cov_Intercept_biol_r4_Intercept_phys_core     0.83050     0.18451 
var_Intercept_phys_core                       1.00595     0.16256 
cov_Intercept_es_core_Intercept_phys_r2       0.33301     0.08651 
cov_Intercept_biol_core_Intercept_phys_r2     0.63796     0.12483 
cov_Intercept_biol_r3_Intercept_phys_r2       0.33224     0.10346 
cov_Intercept_biol_r4_Intercept_phys_r2       0.81288     0.19035 
cov_Intercept_phys_core_Intercept_phys_r2     0.73583     0.14464 
var_Intercept_phys_r2                         0.90416     0.17651 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                                Coef.   Std. Err. 
var_Intercept_es_core                         2.05838     0.06017 
cov_Intercept_es_core_Intercept_biol_core     0.63604     0.04970 
var_Intercept_biol_core                       2.61148     0.07634 
cov_Intercept_es_core_Intercept_biol_r3       0.38635     0.09164 
cov_Intercept_biol_core_Intercept_biol_r3     0.47310     0.10329 
var_Intercept_biol_r3                         4.78515     0.20143 
cov_Intercept_es_core_Intercept_biol_r4       0.47453     0.10043 
cov_Intercept_biol_core_Intercept_biol_r4     1.06113     0.11470 
cov_Intercept_biol_r3_Intercept_biol_r4       1.02731     0.25994 
var_Intercept_biol_r4                         5.90951     0.24913 
cov_Intercept_es_core_Intercept_phys_core     0.66538     0.05534 
cov_Intercept_biol_core_Intercept_phys_core   1.22339     0.06546 
cov_Intercept_biol_r3_Intercept_phys_core     0.40789     0.11532 
cov_Intercept_biol_r4_Intercept_phys_core     1.25367     0.12857 
var_Intercept_phys_core                       3.26710     0.09551 
cov_Intercept_es_core_Intercept_phys_r2       0.67298     0.08608 
cov_Intercept_biol_core_Intercept_phys_r2     1.17334     0.09871 
cov_Intercept_biol_r3_Intercept_phys_r2       0.70362     0.21817 
cov_Intercept_biol_r4_Intercept_phys_r2       2.01961     0.23157 
cov_Intercept_phys_core_Intercept_phys_r2     1.68011     0.11252 
var_Intercept_phys_r2                         4.62657     0.19082 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> covM1 <- matrix(, 6, 6)
> colnames(covM1) <- rownames(covM1) <- c("cons.es_core", "cons.biol_core", "cons.biol_r3", "cons.biol_r4", "cons.phys_core", 
+   "cons.phys_r2")
> covM1[upper.tri(covM1, diag = TRUE)] <- mymodel@RP[22:42]
> # covM1[lower.tri(covM1)] <- t(covM1)[lower.tri(covM1)]
> round(cov2cor(t(covM1)), 3)
               cons.es_core cons.biol_core cons.biol_r3 cons.biol_r4
cons.es_core          1.000             NA           NA           NA
cons.biol_core        0.274          1.000           NA           NA
cons.biol_r3          0.123          0.134        1.000           NA
cons.biol_r4          0.136          0.270        0.193        1.000
cons.phys_core        0.257          0.419        0.103        0.285
cons.phys_r2          0.218          0.338        0.150        0.386
               cons.phys_core cons.phys_r2
cons.es_core               NA           NA
cons.biol_core             NA           NA
cons.biol_r3               NA           NA
cons.biol_r4               NA           NA
cons.phys_core          1.000           NA
cons.phys_r2            0.432            1
> 
> covM2 <- matrix(, 6, 6)
> colnames(covM2) <- rownames(covM2) <- c("cons.es_core", "cons.biol_core", "cons.biol_r3", "cons.biol_r4", "cons.phys_core", 
+   "cons.phys_r2")
> covM2[upper.tri(covM2, diag = TRUE)] <- mymodel@RP[1:21]
> # covM2[lower.tri(covM2)] <- t(covM2)[lower.tri(covM2)]
> round(cov2cor(t(covM2)), 3)
               cons.es_core cons.biol_core cons.biol_r3 cons.biol_r4
cons.es_core          1.000             NA           NA           NA
cons.biol_core        0.682          1.000           NA           NA
cons.biol_r3          0.511          0.679        1.000           NA
cons.biol_r4          0.463          0.673        0.457        1.000
cons.phys_core        0.571          0.893        0.762        0.618
cons.phys_r2          0.550          0.774        0.577        0.638
               cons.phys_core cons.phys_r2
cons.es_core               NA           NA
cons.biol_core             NA           NA
cons.biol_r3               NA           NA
cons.biol_r4               NA           NA
cons.phys_core          1.000           NA
cons.phys_r2            0.772            1
> 
> # 20.9 Two level factor model . . . . . . . . . . . . . . . . . . . . . 321
> 
> nfact <- 2
> lev.fact <- c(1, 2)
> nfactcor <- 0
> factcor <- NULL
> # see FACT in the MCMC manual
> loading <- matrix(c(1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1), ncol = 7, nrow = nfact, byrow = TRUE)
> constr <- matrix(c(1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0), ncol = 7, nrow = nfact, byrow = TRUE)
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (1 | school) + (1 | student), 
+   D = "Multivariate Normal", estoptions = list(EstM = 1, fact = list(nfact = nfact, lev.fact = lev.fact, nfactcor = nfactcor, 
+     factcor = factcor, loading = loading, constr = constr)), 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

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 = 60675.468202
Burning in for 100 iterations out of 500
-2 * Loglike = 55727.960965
Burning in for 150 iterations out of 500
-2 * Loglike = 55890.112291
Burning in for 200 iterations out of 500
-2 * Loglike = 55232.168692
Burning in for 250 iterations out of 500
-2 * Loglike = 55661.913058
Burning in for 300 iterations out of 500
-2 * Loglike = 55520.262335
Burning in for 350 iterations out of 500
-2 * Loglike = 55349.415318
Burning in for 400 iterations out of 500
-2 * Loglike = 55486.948524
Burning in for 450 iterations out of 500
-2 * Loglike = 55628.251506
Burning in for 500 iterations out of 500
-2 * Loglike = 55887.364045

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 = 55750.109844
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 55860.913486
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 55385.722941
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 55767.119836
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 55460.916386
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 55544.267169
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 55701.705673
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 55503.433055
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 55408.092975
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 55417.139171
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 55836.255873
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 55408.785736
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 55435.550659
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 55366.402691
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 55955.354166
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 55789.511246
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 55393.228829
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 55625.012081
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 55458.911568
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 55674.012229
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 55633.057091
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 55743.059688
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 55793.899743
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 55566.772600
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 55509.218663
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 55710.510652
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 55938.825386
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 55460.073364
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 55485.615842
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 55505.991826
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 55390.392269
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 55498.672262
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 55777.595265
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 55622.089191
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 55721.824332
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 55438.632389
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 55530.362167
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 55526.455393
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 55814.581065
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 55824.469271
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 55693.540171
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 55600.664701
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 55899.227255
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 55657.231321
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 55501.314919
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 55687.420916
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 55414.768838
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 55315.550573
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 55487.525697
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 55927.040646
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 55983.766001
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 55652.682387
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 55747.756514
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 55888.611150
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 55714.339833
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 55937.228944
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 55328.091086
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 55678.633578
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 55433.372266
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 55889.612260
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 55537.340411
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 55182.528638
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 55937.700650
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 55942.924692
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 55581.412564
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 55640.314110
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 55608.945843
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 55699.748589
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 55568.764974
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 55650.230515
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 55422.943680
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 55819.536956
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 55445.401432
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 55330.461586
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 55732.017077
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 55420.295579
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 55299.928063
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 55137.096080
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 55691.055908
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 55496.674632
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 55494.604132
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 55097.396304
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 55899.953532
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 55708.699243
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 55105.196001
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 55657.841525
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 55755.209354
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 55825.858341
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 55558.340015
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 55526.638050
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 55561.675093
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 55717.775844
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 55969.788450
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 55721.954929
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 55616.795762
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 55647.263466
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 55995.407379
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 55771.385436
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 55782.247106
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 55406.776873
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          55620.
S.D.    =          179.67
S.E.M.  =          2.5409

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.14)  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 : 46.5s 
Number of obs:  2439 (from total 2439)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Deviance statistic:  44980 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + (1 | school) + (1 | student)
Level 2: school     Level 1: student      
--------------------------------------------------------------------------------------------------- 
The estimates of factor 1 loadings:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
load1_es_core     1.00000     0.00000      1.00000     1.00000 
load1_biol_core   1.78423     0.14740      1.49534     2.07312 
load1_biol_r3     0.84370     0.15412      0.54163     1.14577 
load1_biol_r4     1.95149     0.21814      1.52394     2.37904 
load1_phys_core   2.16391     0.18953      1.79244     2.53538 
load1_phys_r2     2.31999     0.22692      1.87523     2.76475 
--------------------------------------------------------------------------------------------------- 
The estimates of factor 2 loadings:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
load2_es_core     1.00000     0.00000      1.00000     1.00000 
load2_biol_core   2.50862     0.68946      1.15731     3.85993 
load2_biol_r3     1.32258     0.45905      0.42285     2.22230 
load2_biol_r4     2.71949     0.85386      1.04596     4.39301 
load2_phys_core   2.81659     0.85166      1.14736     4.48581 
load2_phys_r2     2.33076     0.69263      0.97323     3.68828 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.31904     0.04659      0.22774     0.41035 
cov_fact2_fact1   0.00000     0.00000      0.00000     0.00000 
var_fact2         0.13794     0.06961      0.00150     0.27437 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z     Pr(>|z|)       [95% Cred.   Interval]   ESS 
Intercept_es_core     8.36484     0.06970  120.02            0  ***     8.22129     8.49820   198 
Intercept_biol_core   7.02485     0.09413   74.63            0  ***     6.85122     7.20475    80 
Intercept_biol_r3     6.86416     0.08882   77.29            0  ***     6.69350     7.04089   311 
Intercept_biol_r4     5.65312     0.15244   37.08   4.921e-301  ***     5.37394     5.97195   204 
Intercept_phys_core   7.15882     0.11142   64.25            0  ***     6.93721     7.37609    93 
Intercept_phys_r2     6.28034     0.11428   54.95            0  ***     6.06057     6.50888   129 
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     0.24216     0.05059      0.15673     0.35182   288 
var_Intercept_biol_core   0.05200     0.04121      0.00160     0.14772    43 
var_Intercept_biol_r3     0.17752     0.08250      0.04440     0.36316   192 
var_Intercept_biol_r4     0.98824     0.22502      0.60425     1.50247   701 
var_Intercept_phys_core   0.14754     0.06541      0.00717     0.27026    67 
var_Intercept_phys_r2     0.31880     0.10095      0.14176     0.53782   305 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                            Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_es_core     1.73862     0.05797      1.62924     1.85587    876 
var_Intercept_biol_core   1.61776     0.07385      1.47518     1.76166    622 
var_Intercept_biol_r3     4.59336     0.19853      4.22434     5.00516   1408 
var_Intercept_biol_r4     4.74314     0.23632      4.30141     5.20892    902 
var_Intercept_phys_core   1.80342     0.09538      1.61057     1.98539    526 
var_Intercept_phys_r2     2.94426     0.17280      2.61454     3.29549    600 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> ranks <- rank(na.omit(mymodel@fact.chains$scores[, 2]))
> plot(x = ranks, y = na.omit(mymodel@fact.chains$scores[, 2]), xlab = "rank", ylab = "factor scores", ylim = c(-1, 
+   1))
> abline(h = 0, lty = "dotted")
> 
> # 20.10 Extensions and some warnings . . . . . . . . . . . . . . . . . . 324
> 
> # Chapter learning outcomes . . . . . . . . . . . . . . . . . . . . . . .325
> 
> 
> 
> 
> 
> ############################################################################
> 
> proc.time()
   user  system elapsed 
   7.21    3.68  413.17