R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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  Natural language support but running in an English locale

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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
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> ############################################################################
> #     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 2013-2017 Zhengzheng Zhang, Christopher M. J. Charlton, Richard M. A. Parker, William J. Browne and George Leckie

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

To cite R2MLwiN in publications use:

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

A BibTeX entry for LaTeX users is

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

The MLwiN_path option is currently set to C:/Program Files/MLwiN v3.05/
To change this use: options(MLwiN_path="<path to MLwiN>")
> # MLwiN folder
> mlwin <- getOption("MLwiN_path")
> while (!file.access(mlwin, mode = 1) == 0) {
+   cat("Please specify the root MLwiN folder or the full path to the MLwiN executable:\n")
+   mlwin <- scan(what = character(0), sep = "\n")
+   mlwin <- gsub("\\", "/", mlwin, fixed = TRUE)
+ }
> options(MLwiN_path = mlwin)
> 
> # User's input if necessary
> 
> ## 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: 3.05)  multilevel model (Multivariate Normal) 
Estimation algorithm:  IGLS        Elapsed time : 3.44s 
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 for 50 iterations out of 500
-2 * Loglike = 63322.422618
Burning in for 100 iterations out of 500
-2 * Loglike = 56911.749329
Burning in for 150 iterations out of 500
-2 * Loglike = 56877.866618
Burning in for 200 iterations out of 500
-2 * Loglike = 57189.151900
Burning in for 250 iterations out of 500
-2 * Loglike = 57213.839430
Burning in for 300 iterations out of 500
-2 * Loglike = 56919.996588
Burning in for 350 iterations out of 500
-2 * Loglike = 56769.305229
Burning in for 400 iterations out of 500
-2 * Loglike = 56722.338373
Burning in for 450 iterations out of 500
-2 * Loglike = 57170.470560
Burning in for 500 iterations out of 500
-2 * Loglike = 56953.639622

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 = 57074.664800
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 57043.068920
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 56761.829256
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 56949.888600
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 56958.572235
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 57303.333054
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 57088.680271
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 56658.424629
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 57138.698396
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 56715.988067
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 56735.320447
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 56912.796731
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 56700.641063
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 56982.989269
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 56984.598672
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 56565.418194
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 56948.946434
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 57048.462255
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 57170.098439
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 56801.661623
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 56920.753104
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 56988.825550
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 56963.926785
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 56907.423080
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 56833.599297
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 57140.058255
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 57093.808737
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 57013.884231
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 56907.978649
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 56947.893421
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 56994.264829
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 56903.282768
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 56768.281411
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 56827.337545
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 56675.513664
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 56871.951853
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 57121.637976
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 57164.837809
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 56970.707476
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 57048.288435
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 57271.720691
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 56641.735315
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 56978.905380
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 56857.050241
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 57226.793662
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 56866.302306
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 57008.555854
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 56835.661491
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 57114.810611
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 56891.361918
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 56515.611155
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 57025.951289
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 57191.725672
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 56964.822428
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 57092.649835
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 57072.348422
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 56774.951475
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 57115.429794
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 56730.591647
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 57145.148579
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 56927.855817
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 56837.839552
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 56965.885474
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 56918.739970
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 56963.686532
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 56913.656925
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 56705.749404
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 56745.274223
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 56756.700477
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 57082.841023
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 57008.452260
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 57110.881907
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 56992.909849
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 56914.251473
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 56561.890325
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 56885.327156
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 56904.419048
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 56958.551223
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 57144.301355
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 57076.164160
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 57110.410423
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 56823.004537
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 57076.522322
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 56779.192534
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 56965.005147
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 56710.688435
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 57056.349784
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 56844.341769
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 56746.899714
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 57132.147085
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 56978.607498
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 56807.099716
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 56691.433296
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 57190.245220
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 57159.416244
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 56881.978964
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 56935.531866
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 56893.192836
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 57094.878189
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 57006.304539
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          56951.
S.D.    =          160.33
S.E.M.  =          2.2674

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 26.53s 
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   1.89387     0.10016      1.69756     2.09018 
load1_biol_r3     0.93400     0.11530      0.70800     1.15999 
load1_biol_r4     2.12954     0.15814      1.81958     2.43949 
load1_phys_core   2.19554     0.11795      1.96437     2.42672 
load1_phys_r2     2.21037     0.14071      1.93458     2.48616 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
              Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1   0.47464     0.04553      0.38540     0.56389 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39393     0.03213  261.28          0  ***     8.33049     8.45598   1645 
Intercept_biol_core   7.06609     0.03748  188.52          0  ***     6.99349     7.14040    738 
Intercept_biol_r3     6.89300     0.06411  107.53          0  ***     6.76406     7.01854   1581 
Intercept_biol_r4     5.67387     0.07651   74.16          0  ***     5.52505     5.82296   1173 
Intercept_phys_core   7.21148     0.04250  169.68          0  ***     7.12832     7.29446    895 
Intercept_phys_r2     6.30911     0.06221  101.41          0  ***     6.18729     6.42915    811 
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     1.96392     0.06089      1.84792     2.08646   2014 
var_Intercept_biol_core   1.65090     0.07569      1.50354     1.79715    791 
var_Intercept_biol_r3     4.74443     0.19581      4.37201     5.14168   1534 
var_Intercept_biol_r4     5.65481     0.26245      5.14877     6.18949   1053 
var_Intercept_phys_core   1.98407     0.09603      1.79746     2.17664    710 
var_Intercept_phys_r2     3.24706     0.16900      2.92497     3.59522    838 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> 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
Adapting finished and took 100 iterations
Adapting took 100 iterations
Burning in for 50 iterations out of 500
-2 * Loglike = 56252.961416
Burning in for 100 iterations out of 500
-2 * Loglike = 56416.761477
Burning in for 150 iterations out of 500
-2 * Loglike = 55920.488161
Burning in for 200 iterations out of 500
-2 * Loglike = 56274.666970
Burning in for 250 iterations out of 500
-2 * Loglike = 56298.379105
Burning in for 300 iterations out of 500
-2 * Loglike = 56058.129863
Burning in for 350 iterations out of 500
-2 * Loglike = 56469.419695
Burning in for 400 iterations out of 500
-2 * Loglike = 56214.381798
Burning in for 450 iterations out of 500
-2 * Loglike = 56061.084457
Burning in for 500 iterations out of 500
-2 * Loglike = 56159.187499

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 = 56193.788119
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 56252.875422
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 56657.476054
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 56413.277217
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 56406.975900
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 55982.414401
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 56125.492984
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 56207.013615
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 56015.581237
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 55764.987458
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 56473.877130
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 55766.641263
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 56088.588860
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 55920.126227
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 55703.455964
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 55921.220266
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 55393.838219
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 55925.602564
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 55763.421174
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 55730.360727
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 55919.101793
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 56318.495337
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 56028.858108
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 55446.260101
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 55519.923804
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 55240.401729
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 55792.504831
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 55757.982084
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 55901.642128
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 55569.283589
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 55627.244941
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 55817.685435
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 55922.836043
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 55964.311836
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 55525.751146
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 55753.847350
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 56147.873381
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 55976.817281
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 55586.654586
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 55659.572529
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 55130.944653
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 55958.263001
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 55748.546877
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 54540.935957
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 55352.992691
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 54894.869229
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 55395.814787
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 55196.325830
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 53978.381729
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 53804.593695
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 53548.830821
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 54907.123460
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 54854.988292
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 53744.855127
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 55127.247301
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 54980.347563
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 55642.347154
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 55310.004454
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 55128.284681
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 55632.967338
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 55487.003626
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 55568.005504
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 54402.249190
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 54681.602199
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 53982.032473
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 54197.506578
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 54076.259241
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 53727.978403
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 54672.412817
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 54082.710197
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 54341.344254
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 53873.940154
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 54149.957516
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 53341.293155
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 53144.762836
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 52679.761129
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 53523.665498
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 55364.983042
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 55947.087994
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 55868.025568
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 55570.472686
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 55398.567204
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 55074.538551
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 54698.045485
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 54923.424217
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 55395.540044
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 55483.883118
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 55066.756445
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 55722.080385
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 55803.578954
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 55939.234584
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 55588.078243
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 55039.082458
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 54384.772843
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 54513.322324
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 55002.634627
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 55206.640739
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 55876.159005
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 55354.522034
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 56132.065354
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          55292.
S.D.    =          815.71
S.E.M.  =          11.536

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 38.06s 
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   1.88461     0.16464      1.56192     2.20730 
load1_biol_r3     0.80912     0.12560      0.56295     1.05528 
load1_biol_r4     1.73636     0.21778      1.30953     2.16319 
load1_phys_core   1.94328     0.15687      1.63581     2.25075 
load1_phys_r2     1.76612     0.17772      1.41779     2.11445 
--------------------------------------------------------------------------------------------------- 
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      5.07759     4.77481     -4.28086    14.43604 
load2_biol_r4     16.30910    11.67452     -6.57254    39.19074 
load2_phys_core    6.99641     4.96061     -2.72620    16.71903 
load2_phys_r2     25.18344    18.82405    -11.71101    62.07789 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.52472     0.06403      0.39923     0.65021 
cov_fact2_fact1   0.00000     0.00000      0.00000     0.00000 
var_fact2         0.03175     0.06056     -0.08694     0.15044 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39454     0.03167  265.05          0  ***     8.33140     8.45683   1850 
Intercept_biol_core   7.06641     0.03648  193.72          0  ***     6.99541     7.13662    802 
Intercept_biol_r3     6.89077     0.06442  106.97          0  ***     6.76697     7.01738   1386 
Intercept_biol_r4     5.67489     0.07463   76.04          0  ***     5.52678     5.82276   1095 
Intercept_phys_core   7.21043     0.04031  178.87          0  ***     7.13168     7.28868    862 
Intercept_phys_r2     6.31550     0.06114  103.29          0  ***     6.19470     6.43390    604 
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     1.91981     0.07315      1.76238     2.05743    95 
var_Intercept_biol_core   1.46565     0.12535      1.19573     1.69263    95 
var_Intercept_biol_r3     4.71060     0.21029      4.30914     5.12963   963 
var_Intercept_biol_r4     5.18013     0.44436      4.17056     5.89920    64 
var_Intercept_phys_core   2.08461     0.10555      1.87272     2.29242   316 
var_Intercept_phys_r2     2.11520     0.65273      0.81772     3.15318    12 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> 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
Adapting finished and took 100 iterations
Adapting took 100 iterations
Burning in for 50 iterations out of 5000
-2 * Loglike = 56252.961416
Burning in for 100 iterations out of 5000
-2 * Loglike = 56416.761477
Burning in for 150 iterations out of 5000
-2 * Loglike = 55920.488161
Burning in for 200 iterations out of 5000
-2 * Loglike = 56274.666970
Burning in for 250 iterations out of 5000
-2 * Loglike = 56298.379105
Burning in for 300 iterations out of 5000
-2 * Loglike = 56058.129863
Burning in for 350 iterations out of 5000
-2 * Loglike = 56469.419695
Burning in for 400 iterations out of 5000
-2 * Loglike = 56214.381798
Burning in for 450 iterations out of 5000
-2 * Loglike = 56061.084457
Burning in for 500 iterations out of 5000
-2 * Loglike = 56159.187499
Burning in for 550 iterations out of 5000
-2 * Loglike = 56092.673805
Burning in for 600 iterations out of 5000
-2 * Loglike = 56407.516590
Burning in for 650 iterations out of 5000
-2 * Loglike = 56344.890838
Burning in for 700 iterations out of 5000
-2 * Loglike = 56643.599406
Burning in for 750 iterations out of 5000
-2 * Loglike = 56355.985126
Burning in for 800 iterations out of 5000
-2 * Loglike = 56212.390458
Burning in for 850 iterations out of 5000
-2 * Loglike = 55770.992438
Burning in for 900 iterations out of 5000
-2 * Loglike = 56125.934955
Burning in for 950 iterations out of 5000
-2 * Loglike = 56288.321338
Burning in for 1000 iterations out of 5000
-2 * Loglike = 55829.923644
Burning in for 1050 iterations out of 5000
-2 * Loglike = 55682.523743
Burning in for 1100 iterations out of 5000
-2 * Loglike = 56166.894485
Burning in for 1150 iterations out of 5000
-2 * Loglike = 55884.091210
Burning in for 1200 iterations out of 5000
-2 * Loglike = 56341.642039
Burning in for 1250 iterations out of 5000
-2 * Loglike = 55892.113814
Burning in for 1300 iterations out of 5000
-2 * Loglike = 55561.870330
Burning in for 1350 iterations out of 5000
-2 * Loglike = 55883.740849
Burning in for 1400 iterations out of 5000
-2 * Loglike = 55302.363275
Burning in for 1450 iterations out of 5000
-2 * Loglike = 56132.410162
Burning in for 1500 iterations out of 5000
-2 * Loglike = 55918.393048
Burning in for 1550 iterations out of 5000
-2 * Loglike = 55829.194743
Burning in for 1600 iterations out of 5000
-2 * Loglike = 55837.672729
Burning in for 1650 iterations out of 5000
-2 * Loglike = 56252.254583
Burning in for 1700 iterations out of 5000
-2 * Loglike = 56128.542404
Burning in for 1750 iterations out of 5000
-2 * Loglike = 55579.238691
Burning in for 1800 iterations out of 5000
-2 * Loglike = 55671.191473
Burning in for 1850 iterations out of 5000
-2 * Loglike = 55546.070750
Burning in for 1900 iterations out of 5000
-2 * Loglike = 55867.901876
Burning in for 1950 iterations out of 5000
-2 * Loglike = 55557.704560
Burning in for 2000 iterations out of 5000
-2 * Loglike = 55652.922188
Burning in for 2050 iterations out of 5000
-2 * Loglike = 55485.537759
Burning in for 2100 iterations out of 5000
-2 * Loglike = 55480.862126
Burning in for 2150 iterations out of 5000
-2 * Loglike = 56010.584676
Burning in for 2200 iterations out of 5000
-2 * Loglike = 56017.306328
Burning in for 2250 iterations out of 5000
-2 * Loglike = 56250.821354
Burning in for 2300 iterations out of 5000
-2 * Loglike = 55314.193872
Burning in for 2350 iterations out of 5000
-2 * Loglike = 55882.696043
Burning in for 2400 iterations out of 5000
-2 * Loglike = 56089.509667
Burning in for 2450 iterations out of 5000
-2 * Loglike = 56086.442479
Burning in for 2500 iterations out of 5000
-2 * Loglike = 55492.880920
Burning in for 2550 iterations out of 5000
-2 * Loglike = 55806.834832
Burning in for 2600 iterations out of 5000
-2 * Loglike = 54928.438368
Burning in for 2650 iterations out of 5000
-2 * Loglike = 56003.882427
Burning in for 2700 iterations out of 5000
-2 * Loglike = 55822.676849
Burning in for 2750 iterations out of 5000
-2 * Loglike = 54745.065155
Burning in for 2800 iterations out of 5000
-2 * Loglike = 55433.693322
Burning in for 2850 iterations out of 5000
-2 * Loglike = 54965.937645
Burning in for 2900 iterations out of 5000
-2 * Loglike = 55559.048900
Burning in for 2950 iterations out of 5000
-2 * Loglike = 55130.753312
Burning in for 3000 iterations out of 5000
-2 * Loglike = 53899.805993
Burning in for 3050 iterations out of 5000
-2 * Loglike = 53327.592342
Burning in for 3100 iterations out of 5000
-2 * Loglike = 53793.116225
Burning in for 3150 iterations out of 5000
-2 * Loglike = 55118.205917
Burning in for 3200 iterations out of 5000
-2 * Loglike = 54808.377830
Burning in for 3250 iterations out of 5000
-2 * Loglike = 54057.154655
Burning in for 3300 iterations out of 5000
-2 * Loglike = 54940.536361
Burning in for 3350 iterations out of 5000
-2 * Loglike = 55226.072775
Burning in for 3400 iterations out of 5000
-2 * Loglike = 55707.191984
Burning in for 3450 iterations out of 5000
-2 * Loglike = 55349.863606
Burning in for 3500 iterations out of 5000
-2 * Loglike = 55340.597227
Burning in for 3550 iterations out of 5000
-2 * Loglike = 55367.242979
Burning in for 3600 iterations out of 5000
-2 * Loglike = 55673.109332
Burning in for 3650 iterations out of 5000
-2 * Loglike = 55598.987890
Burning in for 3700 iterations out of 5000
-2 * Loglike = 54794.970755
Burning in for 3750 iterations out of 5000
-2 * Loglike = 54729.854357
Burning in for 3800 iterations out of 5000
-2 * Loglike = 54024.017228
Burning in for 3850 iterations out of 5000
-2 * Loglike = 54422.993595
Burning in for 3900 iterations out of 5000
-2 * Loglike = 54341.203755
Burning in for 3950 iterations out of 5000
-2 * Loglike = 53671.314087
Burning in for 4000 iterations out of 5000
-2 * Loglike = 55101.764877
Burning in for 4050 iterations out of 5000
-2 * Loglike = 54413.626169
Burning in for 4100 iterations out of 5000
-2 * Loglike = 54519.182254
Burning in for 4150 iterations out of 5000
-2 * Loglike = 53714.503578
Burning in for 4200 iterations out of 5000
-2 * Loglike = 54189.960543
Burning in for 4250 iterations out of 5000
-2 * Loglike = 53118.394601
Burning in for 4300 iterations out of 5000
-2 * Loglike = 52821.672373
Burning in for 4350 iterations out of 5000
-2 * Loglike = 52964.860530
Burning in for 4400 iterations out of 5000
-2 * Loglike = 53613.465790
Burning in for 4450 iterations out of 5000
-2 * Loglike = 55506.326896
Burning in for 4500 iterations out of 5000
-2 * Loglike = 55975.312877
Burning in for 4550 iterations out of 5000
-2 * Loglike = 55881.411022
Burning in for 4600 iterations out of 5000
-2 * Loglike = 55294.745119
Burning in for 4650 iterations out of 5000
-2 * Loglike = 55287.872237
Burning in for 4700 iterations out of 5000
-2 * Loglike = 55117.707263
Burning in for 4750 iterations out of 5000
-2 * Loglike = 54839.030497
Burning in for 4800 iterations out of 5000
-2 * Loglike = 55069.443451
Burning in for 4850 iterations out of 5000
-2 * Loglike = 55541.610235
Burning in for 4900 iterations out of 5000
-2 * Loglike = 55431.433553
Burning in for 4950 iterations out of 5000
-2 * Loglike = 55019.736630
Burning in for 5000 iterations out of 5000
-2 * Loglike = 55577.814350

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 = 55939.234584
Actual update 100 of 10000, Stored update 100 of 10000
-2 * Loglike = 55588.078243
Actual update 150 of 10000, Stored update 150 of 10000
-2 * Loglike = 55039.082458
Actual update 200 of 10000, Stored update 200 of 10000
-2 * Loglike = 54384.772843
Actual update 250 of 10000, Stored update 250 of 10000
-2 * Loglike = 54513.322324
Actual update 300 of 10000, Stored update 300 of 10000
-2 * Loglike = 55002.634627
Actual update 350 of 10000, Stored update 350 of 10000
-2 * Loglike = 55206.640739
Actual update 400 of 10000, Stored update 400 of 10000
-2 * Loglike = 55876.159005
Actual update 450 of 10000, Stored update 450 of 10000
-2 * Loglike = 55354.522034
Actual update 500 of 10000, Stored update 500 of 10000
-2 * Loglike = 56132.065354
Actual update 550 of 10000, Stored update 550 of 10000
-2 * Loglike = 55418.028741
Actual update 600 of 10000, Stored update 600 of 10000
-2 * Loglike = 54501.759682
Actual update 650 of 10000, Stored update 650 of 10000
-2 * Loglike = 55567.591795
Actual update 700 of 10000, Stored update 700 of 10000
-2 * Loglike = 55870.603503
Actual update 750 of 10000, Stored update 750 of 10000
-2 * Loglike = 56035.545799
Actual update 800 of 10000, Stored update 800 of 10000
-2 * Loglike = 55685.372069
Actual update 850 of 10000, Stored update 850 of 10000
-2 * Loglike = 55257.133026
Actual update 900 of 10000, Stored update 900 of 10000
-2 * Loglike = 55251.167336
Actual update 950 of 10000, Stored update 950 of 10000
-2 * Loglike = 55962.552130
Actual update 1000 of 10000, Stored update 1000 of 10000
-2 * Loglike = 55286.342832
Actual update 1050 of 10000, Stored update 1050 of 10000
-2 * Loglike = 55127.630886
Actual update 1100 of 10000, Stored update 1100 of 10000
-2 * Loglike = 55939.943210
Actual update 1150 of 10000, Stored update 1150 of 10000
-2 * Loglike = 55337.596555
Actual update 1200 of 10000, Stored update 1200 of 10000
-2 * Loglike = 55656.393957
Actual update 1250 of 10000, Stored update 1250 of 10000
-2 * Loglike = 56233.786558
Actual update 1300 of 10000, Stored update 1300 of 10000
-2 * Loglike = 55591.698534
Actual update 1350 of 10000, Stored update 1350 of 10000
-2 * Loglike = 55796.039454
Actual update 1400 of 10000, Stored update 1400 of 10000
-2 * Loglike = 55408.338888
Actual update 1450 of 10000, Stored update 1450 of 10000
-2 * Loglike = 55114.405958
Actual update 1500 of 10000, Stored update 1500 of 10000
-2 * Loglike = 55991.391717
Actual update 1550 of 10000, Stored update 1550 of 10000
-2 * Loglike = 55710.224094
Actual update 1600 of 10000, Stored update 1600 of 10000
-2 * Loglike = 55304.642123
Actual update 1650 of 10000, Stored update 1650 of 10000
-2 * Loglike = 55771.014198
Actual update 1700 of 10000, Stored update 1700 of 10000
-2 * Loglike = 55693.033302
Actual update 1750 of 10000, Stored update 1750 of 10000
-2 * Loglike = 56638.175140
Actual update 1800 of 10000, Stored update 1800 of 10000
-2 * Loglike = 55947.176362
Actual update 1850 of 10000, Stored update 1850 of 10000
-2 * Loglike = 56221.411656
Actual update 1900 of 10000, Stored update 1900 of 10000
-2 * Loglike = 55780.899471
Actual update 1950 of 10000, Stored update 1950 of 10000
-2 * Loglike = 55492.075442
Actual update 2000 of 10000, Stored update 2000 of 10000
-2 * Loglike = 55504.668442
Actual update 2050 of 10000, Stored update 2050 of 10000
-2 * Loglike = 55504.041162
Actual update 2100 of 10000, Stored update 2100 of 10000
-2 * Loglike = 56233.446755
Actual update 2150 of 10000, Stored update 2150 of 10000
-2 * Loglike = 54643.701244
Actual update 2200 of 10000, Stored update 2200 of 10000
-2 * Loglike = 55677.906442
Actual update 2250 of 10000, Stored update 2250 of 10000
-2 * Loglike = 55165.061734
Actual update 2300 of 10000, Stored update 2300 of 10000
-2 * Loglike = 55595.684754
Actual update 2350 of 10000, Stored update 2350 of 10000
-2 * Loglike = 55924.525179
Actual update 2400 of 10000, Stored update 2400 of 10000
-2 * Loglike = 55344.381203
Actual update 2450 of 10000, Stored update 2450 of 10000
-2 * Loglike = 55475.430128
Actual update 2500 of 10000, Stored update 2500 of 10000
-2 * Loglike = 55569.235901
Actual update 2550 of 10000, Stored update 2550 of 10000
-2 * Loglike = 55763.620746
Actual update 2600 of 10000, Stored update 2600 of 10000
-2 * Loglike = 54971.386560
Actual update 2650 of 10000, Stored update 2650 of 10000
-2 * Loglike = 54938.814674
Actual update 2700 of 10000, Stored update 2700 of 10000
-2 * Loglike = 55859.459059
Actual update 2750 of 10000, Stored update 2750 of 10000
-2 * Loglike = 55438.800371
Actual update 2800 of 10000, Stored update 2800 of 10000
-2 * Loglike = 55787.240549
Actual update 2850 of 10000, Stored update 2850 of 10000
-2 * Loglike = 55602.626539
Actual update 2900 of 10000, Stored update 2900 of 10000
-2 * Loglike = 55601.526946
Actual update 2950 of 10000, Stored update 2950 of 10000
-2 * Loglike = 55234.178661
Actual update 3000 of 10000, Stored update 3000 of 10000
-2 * Loglike = 56379.004469
Actual update 3050 of 10000, Stored update 3050 of 10000
-2 * Loglike = 55614.278711
Actual update 3100 of 10000, Stored update 3100 of 10000
-2 * Loglike = 55086.803103
Actual update 3150 of 10000, Stored update 3150 of 10000
-2 * Loglike = 55355.548515
Actual update 3200 of 10000, Stored update 3200 of 10000
-2 * Loglike = 54637.472769
Actual update 3250 of 10000, Stored update 3250 of 10000
-2 * Loglike = 54543.392238
Actual update 3300 of 10000, Stored update 3300 of 10000
-2 * Loglike = 55276.688357
Actual update 3350 of 10000, Stored update 3350 of 10000
-2 * Loglike = 55120.180495
Actual update 3400 of 10000, Stored update 3400 of 10000
-2 * Loglike = 55268.025015
Actual update 3450 of 10000, Stored update 3450 of 10000
-2 * Loglike = 54881.659149
Actual update 3500 of 10000, Stored update 3500 of 10000
-2 * Loglike = 55384.870650
Actual update 3550 of 10000, Stored update 3550 of 10000
-2 * Loglike = 55021.340703
Actual update 3600 of 10000, Stored update 3600 of 10000
-2 * Loglike = 54405.907268
Actual update 3650 of 10000, Stored update 3650 of 10000
-2 * Loglike = 55019.968680
Actual update 3700 of 10000, Stored update 3700 of 10000
-2 * Loglike = 54158.655117
Actual update 3750 of 10000, Stored update 3750 of 10000
-2 * Loglike = 54511.533916
Actual update 3800 of 10000, Stored update 3800 of 10000
-2 * Loglike = 54111.899176
Actual update 3850 of 10000, Stored update 3850 of 10000
-2 * Loglike = 53873.619074
Actual update 3900 of 10000, Stored update 3900 of 10000
-2 * Loglike = 53730.136182
Actual update 3950 of 10000, Stored update 3950 of 10000
-2 * Loglike = 53610.318596
Actual update 4000 of 10000, Stored update 4000 of 10000
-2 * Loglike = 54919.133652
Actual update 4050 of 10000, Stored update 4050 of 10000
-2 * Loglike = 53824.073232
Actual update 4100 of 10000, Stored update 4100 of 10000
-2 * Loglike = 54732.361197
Actual update 4150 of 10000, Stored update 4150 of 10000
-2 * Loglike = 55029.760167
Actual update 4200 of 10000, Stored update 4200 of 10000
-2 * Loglike = 54816.068329
Actual update 4250 of 10000, Stored update 4250 of 10000
-2 * Loglike = 54816.654254
Actual update 4300 of 10000, Stored update 4300 of 10000
-2 * Loglike = 54093.803506
Actual update 4350 of 10000, Stored update 4350 of 10000
-2 * Loglike = 54561.506402
Actual update 4400 of 10000, Stored update 4400 of 10000
-2 * Loglike = 54201.505392
Actual update 4450 of 10000, Stored update 4450 of 10000
-2 * Loglike = 53534.459427
Actual update 4500 of 10000, Stored update 4500 of 10000
-2 * Loglike = 52629.329555
Actual update 4550 of 10000, Stored update 4550 of 10000
-2 * Loglike = 51658.484105
Actual update 4600 of 10000, Stored update 4600 of 10000
-2 * Loglike = 52131.318406
Actual update 4650 of 10000, Stored update 4650 of 10000
-2 * Loglike = 52927.171789
Actual update 4700 of 10000, Stored update 4700 of 10000
-2 * Loglike = 51945.308721
Actual update 4750 of 10000, Stored update 4750 of 10000
-2 * Loglike = 51798.491601
Actual update 4800 of 10000, Stored update 4800 of 10000
-2 * Loglike = 50633.377708
Actual update 4850 of 10000, Stored update 4850 of 10000
-2 * Loglike = 50826.594882
Actual update 4900 of 10000, Stored update 4900 of 10000
-2 * Loglike = 49951.419690
Actual update 4950 of 10000, Stored update 4950 of 10000
-2 * Loglike = 50058.109831
Actual update 5000 of 10000, Stored update 5000 of 10000
-2 * Loglike = 50809.038564
Actual update 5050 of 10000, Stored update 5050 of 10000
-2 * Loglike = 51147.917195
Actual update 5100 of 10000, Stored update 5100 of 10000
-2 * Loglike = 50744.867894
Actual update 5150 of 10000, Stored update 5150 of 10000
-2 * Loglike = 50668.346574
Actual update 5200 of 10000, Stored update 5200 of 10000
-2 * Loglike = 50916.990958
Actual update 5250 of 10000, Stored update 5250 of 10000
-2 * Loglike = 51368.445926
Actual update 5300 of 10000, Stored update 5300 of 10000
-2 * Loglike = 51904.009955
Actual update 5350 of 10000, Stored update 5350 of 10000
-2 * Loglike = 51893.519769
Actual update 5400 of 10000, Stored update 5400 of 10000
-2 * Loglike = 51561.251634
Actual update 5450 of 10000, Stored update 5450 of 10000
-2 * Loglike = 51678.029941
Actual update 5500 of 10000, Stored update 5500 of 10000
-2 * Loglike = 51445.191720
Actual update 5550 of 10000, Stored update 5550 of 10000
-2 * Loglike = 51198.451094
Actual update 5600 of 10000, Stored update 5600 of 10000
-2 * Loglike = 51427.766033
Actual update 5650 of 10000, Stored update 5650 of 10000
-2 * Loglike = 51482.206983
Actual update 5700 of 10000, Stored update 5700 of 10000
-2 * Loglike = 50833.729809
Actual update 5750 of 10000, Stored update 5750 of 10000
-2 * Loglike = 51699.824724
Actual update 5800 of 10000, Stored update 5800 of 10000
-2 * Loglike = 50606.305966
Actual update 5850 of 10000, Stored update 5850 of 10000
-2 * Loglike = 49953.167819
Actual update 5900 of 10000, Stored update 5900 of 10000
-2 * Loglike = 49303.744163
Actual update 5950 of 10000, Stored update 5950 of 10000
-2 * Loglike = 49186.631917
Actual update 6000 of 10000, Stored update 6000 of 10000
-2 * Loglike = 49549.008305
Actual update 6050 of 10000, Stored update 6050 of 10000
-2 * Loglike = 49244.604603
Actual update 6100 of 10000, Stored update 6100 of 10000
-2 * Loglike = 48923.250353
Actual update 6150 of 10000, Stored update 6150 of 10000
-2 * Loglike = 49397.937525
Actual update 6200 of 10000, Stored update 6200 of 10000
-2 * Loglike = 48579.065193
Actual update 6250 of 10000, Stored update 6250 of 10000
-2 * Loglike = 47623.995754
Actual update 6300 of 10000, Stored update 6300 of 10000
-2 * Loglike = 48286.927772
Actual update 6350 of 10000, Stored update 6350 of 10000
-2 * Loglike = 49013.918248
Actual update 6400 of 10000, Stored update 6400 of 10000
-2 * Loglike = 47617.771992
Actual update 6450 of 10000, Stored update 6450 of 10000
-2 * Loglike = 47048.960311
Actual update 6500 of 10000, Stored update 6500 of 10000
-2 * Loglike = 47633.419682
Actual update 6550 of 10000, Stored update 6550 of 10000
-2 * Loglike = 47240.976744
Actual update 6600 of 10000, Stored update 6600 of 10000
-2 * Loglike = 45719.372368
Actual update 6650 of 10000, Stored update 6650 of 10000
-2 * Loglike = 45116.817667
Actual update 6700 of 10000, Stored update 6700 of 10000
-2 * Loglike = 45722.571977
Actual update 6750 of 10000, Stored update 6750 of 10000
-2 * Loglike = 44792.937802
Actual update 6800 of 10000, Stored update 6800 of 10000
-2 * Loglike = 45925.469053
Actual update 6850 of 10000, Stored update 6850 of 10000
-2 * Loglike = 46101.114407
Actual update 6900 of 10000, Stored update 6900 of 10000
-2 * Loglike = 46457.425207
Actual update 6950 of 10000, Stored update 6950 of 10000
-2 * Loglike = 45992.739517
Actual update 7000 of 10000, Stored update 7000 of 10000
-2 * Loglike = 45041.161523
Actual update 7050 of 10000, Stored update 7050 of 10000
-2 * Loglike = 45295.351211
Actual update 7100 of 10000, Stored update 7100 of 10000
-2 * Loglike = 46331.737446
Actual update 7150 of 10000, Stored update 7150 of 10000
-2 * Loglike = 45531.507588
Actual update 7200 of 10000, Stored update 7200 of 10000
-2 * Loglike = 46212.389407
Actual update 7250 of 10000, Stored update 7250 of 10000
-2 * Loglike = 46337.379671
Actual update 7300 of 10000, Stored update 7300 of 10000
-2 * Loglike = 46245.976193
Actual update 7350 of 10000, Stored update 7350 of 10000
-2 * Loglike = 46801.946425
Actual update 7400 of 10000, Stored update 7400 of 10000
-2 * Loglike = 47076.767709
Actual update 7450 of 10000, Stored update 7450 of 10000
-2 * Loglike = 46019.564029
Actual update 7500 of 10000, Stored update 7500 of 10000
-2 * Loglike = 46462.478143
Actual update 7550 of 10000, Stored update 7550 of 10000
-2 * Loglike = 46451.414252
Actual update 7600 of 10000, Stored update 7600 of 10000
-2 * Loglike = 47291.541405
Actual update 7650 of 10000, Stored update 7650 of 10000
-2 * Loglike = 48347.718188
Actual update 7700 of 10000, Stored update 7700 of 10000
-2 * Loglike = 48741.053291
Actual update 7750 of 10000, Stored update 7750 of 10000
-2 * Loglike = 48525.346918
Actual update 7800 of 10000, Stored update 7800 of 10000
-2 * Loglike = 48644.791373
Actual update 7850 of 10000, Stored update 7850 of 10000
-2 * Loglike = 49227.066433
Actual update 7900 of 10000, Stored update 7900 of 10000
-2 * Loglike = 49104.767794
Actual update 7950 of 10000, Stored update 7950 of 10000
-2 * Loglike = 49696.609790
Actual update 8000 of 10000, Stored update 8000 of 10000
-2 * Loglike = 49627.399078
Actual update 8050 of 10000, Stored update 8050 of 10000
-2 * Loglike = 49643.404442
Actual update 8100 of 10000, Stored update 8100 of 10000
-2 * Loglike = 50066.770848
Actual update 8150 of 10000, Stored update 8150 of 10000
-2 * Loglike = 50797.596322
Actual update 8200 of 10000, Stored update 8200 of 10000
-2 * Loglike = 49328.144604
Actual update 8250 of 10000, Stored update 8250 of 10000
-2 * Loglike = 49863.675392
Actual update 8300 of 10000, Stored update 8300 of 10000
-2 * Loglike = 49821.604885
Actual update 8350 of 10000, Stored update 8350 of 10000
-2 * Loglike = 50735.812267
Actual update 8400 of 10000, Stored update 8400 of 10000
-2 * Loglike = 51338.383379
Actual update 8450 of 10000, Stored update 8450 of 10000
-2 * Loglike = 51191.262792
Actual update 8500 of 10000, Stored update 8500 of 10000
-2 * Loglike = 51011.046923
Actual update 8550 of 10000, Stored update 8550 of 10000
-2 * Loglike = 51135.088814
Actual update 8600 of 10000, Stored update 8600 of 10000
-2 * Loglike = 51210.431187
Actual update 8650 of 10000, Stored update 8650 of 10000
-2 * Loglike = 50880.833364
Actual update 8700 of 10000, Stored update 8700 of 10000
-2 * Loglike = 51267.406850
Actual update 8750 of 10000, Stored update 8750 of 10000
-2 * Loglike = 51759.244871
Actual update 8800 of 10000, Stored update 8800 of 10000
-2 * Loglike = 51539.959116
Actual update 8850 of 10000, Stored update 8850 of 10000
-2 * Loglike = 50655.473261
Actual update 8900 of 10000, Stored update 8900 of 10000
-2 * Loglike = 51778.828907
Actual update 8950 of 10000, Stored update 8950 of 10000
-2 * Loglike = 50177.176511
Actual update 9000 of 10000, Stored update 9000 of 10000
-2 * Loglike = 50348.660692
Actual update 9050 of 10000, Stored update 9050 of 10000
-2 * Loglike = 50282.797465
Actual update 9100 of 10000, Stored update 9100 of 10000
-2 * Loglike = 49994.312656
Actual update 9150 of 10000, Stored update 9150 of 10000
-2 * Loglike = 51217.721860
Actual update 9200 of 10000, Stored update 9200 of 10000
-2 * Loglike = 50962.879204
Actual update 9250 of 10000, Stored update 9250 of 10000
-2 * Loglike = 52075.612745
Actual update 9300 of 10000, Stored update 9300 of 10000
-2 * Loglike = 50937.068379
Actual update 9350 of 10000, Stored update 9350 of 10000
-2 * Loglike = 50405.424494
Actual update 9400 of 10000, Stored update 9400 of 10000
-2 * Loglike = 51290.997130
Actual update 9450 of 10000, Stored update 9450 of 10000
-2 * Loglike = 50667.822685
Actual update 9500 of 10000, Stored update 9500 of 10000
-2 * Loglike = 51818.945936
Actual update 9550 of 10000, Stored update 9550 of 10000
-2 * Loglike = 51553.037858
Actual update 9600 of 10000, Stored update 9600 of 10000
-2 * Loglike = 50994.349207
Actual update 9650 of 10000, Stored update 9650 of 10000
-2 * Loglike = 51216.804077
Actual update 9700 of 10000, Stored update 9700 of 10000
-2 * Loglike = 51371.275791
Actual update 9750 of 10000, Stored update 9750 of 10000
-2 * Loglike = 51489.208542
Actual update 9800 of 10000, Stored update 9800 of 10000
-2 * Loglike = 50941.927454
Actual update 9850 of 10000, Stored update 9850 of 10000
-2 * Loglike = 51482.832189
Actual update 9900 of 10000, Stored update 9900 of 10000
-2 * Loglike = 52838.447247
Actual update 9950 of 10000, Stored update 9950 of 10000
-2 * Loglike = 52389.562487
Actual update 10000 of 10000, Stored update 10000 of 10000
-2 * Loglike = 52820.509222
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =          10000
Average =          52170.
S.D.    =          3244.3
S.E.M.  =          32.443

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 100.63s 
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   1.90808     0.11938      1.67411     2.14205 
load1_biol_r3     0.84387     0.11571      0.61708     1.07066 
load1_biol_r4     1.83808     0.16308      1.51845     2.15772 
load1_phys_core   1.98907     0.12945      1.73534     2.24279 
load1_phys_r2     1.78071     0.17222      1.44317     2.11825 
--------------------------------------------------------------------------------------------------- 
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      5.81090     6.35694     -6.64847    18.27027 
load2_biol_r4     17.63520    13.67583     -9.16894    44.43935 
load2_phys_core    7.22332     5.00200     -2.58041    17.02706 
load2_phys_r2     31.18321    12.48619      6.71073    55.65570 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.51748     0.05478      0.41011     0.62485 
cov_fact2_fact1   0.00000     0.00000      0.00000     0.00000 
var_fact2         0.00441     0.00293     -0.00134     0.01016 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39534     0.03134  267.88          0  ***     8.33445     8.45858   2351 
Intercept_biol_core   7.06843     0.03658  193.23          0  ***     6.99707     7.13982   1083 
Intercept_biol_r3     6.89545     0.06454  106.83          0  ***     6.77098     7.02418   3015 
Intercept_biol_r4     5.67712     0.07603   74.67          0  ***     5.52715     5.82591   1590 
Intercept_phys_core   7.21353     0.04089  176.43          0  ***     7.13378     7.29295    907 
Intercept_phys_r2     6.32058     0.06810   92.81          0  ***     6.18546     6.44918    135 
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     1.93173     0.06255      1.81342     2.05612    792 
var_Intercept_biol_core   1.46836     0.09910      1.26942     1.66048    224 
var_Intercept_biol_r3     4.73570     0.20695      4.33710     5.15451   1612 
var_Intercept_biol_r4     5.40338     0.36197      4.56660     6.01766    109 
var_Intercept_phys_core   2.10705     0.09878      1.90991     2.30009    408 
var_Intercept_phys_r2     1.04447     0.97185      0.03310     2.83699      3 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> 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
Adapting finished and took 100 iterations
Adapting took 100 iterations
Burning in for 50 iterations out of 5000
-2 * Loglike = 56477.347763
Burning in for 100 iterations out of 5000
-2 * Loglike = 56085.763854
Burning in for 150 iterations out of 5000
-2 * Loglike = 56277.681504
Burning in for 200 iterations out of 5000
-2 * Loglike = 56431.572446
Burning in for 250 iterations out of 5000
-2 * Loglike = 56485.210602
Burning in for 300 iterations out of 5000
-2 * Loglike = 56233.962152
Burning in for 350 iterations out of 5000
-2 * Loglike = 56642.551652
Burning in for 400 iterations out of 5000
-2 * Loglike = 56067.297298
Burning in for 450 iterations out of 5000
-2 * Loglike = 56323.873639
Burning in for 500 iterations out of 5000
-2 * Loglike = 56623.186107
Burning in for 550 iterations out of 5000
-2 * Loglike = 56571.307280
Burning in for 600 iterations out of 5000
-2 * Loglike = 56513.146728
Burning in for 650 iterations out of 5000
-2 * Loglike = 56139.667705
Burning in for 700 iterations out of 5000
-2 * Loglike = 56213.655798
Burning in for 750 iterations out of 5000
-2 * Loglike = 56113.365272
Burning in for 800 iterations out of 5000
-2 * Loglike = 56223.053582
Burning in for 850 iterations out of 5000
-2 * Loglike = 55782.763386
Burning in for 900 iterations out of 5000
-2 * Loglike = 56143.669795
Burning in for 950 iterations out of 5000
-2 * Loglike = 56339.831224
Burning in for 1000 iterations out of 5000
-2 * Loglike = 56367.346043
Burning in for 1050 iterations out of 5000
-2 * Loglike = 56402.754470
Burning in for 1100 iterations out of 5000
-2 * Loglike = 56359.691181
Burning in for 1150 iterations out of 5000
-2 * Loglike = 56252.779680
Burning in for 1200 iterations out of 5000
-2 * Loglike = 56433.965312
Burning in for 1250 iterations out of 5000
-2 * Loglike = 56246.668852
Burning in for 1300 iterations out of 5000
-2 * Loglike = 56527.255417
Burning in for 1350 iterations out of 5000
-2 * Loglike = 56568.070509
Burning in for 1400 iterations out of 5000
-2 * Loglike = 56807.812509
Burning in for 1450 iterations out of 5000
-2 * Loglike = 56530.013088
Burning in for 1500 iterations out of 5000
-2 * Loglike = 56184.475930
Burning in for 1550 iterations out of 5000
-2 * Loglike = 56024.271102
Burning in for 1600 iterations out of 5000
-2 * Loglike = 56026.152059
Burning in for 1650 iterations out of 5000
-2 * Loglike = 56388.506312
Burning in for 1700 iterations out of 5000
-2 * Loglike = 56188.023424
Burning in for 1750 iterations out of 5000
-2 * Loglike = 55245.427864
Burning in for 1800 iterations out of 5000
-2 * Loglike = 55749.183921
Burning in for 1850 iterations out of 5000
-2 * Loglike = 56049.932354
Burning in for 1900 iterations out of 5000
-2 * Loglike = 56088.359475
Burning in for 1950 iterations out of 5000
-2 * Loglike = 56773.811556
Burning in for 2000 iterations out of 5000
-2 * Loglike = 56624.001367
Burning in for 2050 iterations out of 5000
-2 * Loglike = 55810.109258
Burning in for 2100 iterations out of 5000
-2 * Loglike = 56221.489646
Burning in for 2150 iterations out of 5000
-2 * Loglike = 56183.039524
Burning in for 2200 iterations out of 5000
-2 * Loglike = 55960.127955
Burning in for 2250 iterations out of 5000
-2 * Loglike = 55708.784171
Burning in for 2300 iterations out of 5000
-2 * Loglike = 56101.408174
Burning in for 2350 iterations out of 5000
-2 * Loglike = 56247.080232
Burning in for 2400 iterations out of 5000
-2 * Loglike = 56052.666555
Burning in for 2450 iterations out of 5000
-2 * Loglike = 56465.396446
Burning in for 2500 iterations out of 5000
-2 * Loglike = 56261.138410
Burning in for 2550 iterations out of 5000
-2 * Loglike = 55623.908856
Burning in for 2600 iterations out of 5000
-2 * Loglike = 55786.803782
Burning in for 2650 iterations out of 5000
-2 * Loglike = 55473.354003
Burning in for 2700 iterations out of 5000
-2 * Loglike = 55814.930279
Burning in for 2750 iterations out of 5000
-2 * Loglike = 56034.165211
Burning in for 2800 iterations out of 5000
-2 * Loglike = 56191.303749
Burning in for 2850 iterations out of 5000
-2 * Loglike = 56237.107835
Burning in for 2900 iterations out of 5000
-2 * Loglike = 56128.518419
Burning in for 2950 iterations out of 5000
-2 * Loglike = 55953.817731
Burning in for 3000 iterations out of 5000
-2 * Loglike = 56075.103996
Burning in for 3050 iterations out of 5000
-2 * Loglike = 55391.277803
Burning in for 3100 iterations out of 5000
-2 * Loglike = 55839.610278
Burning in for 3150 iterations out of 5000
-2 * Loglike = 56663.707862
Burning in for 3200 iterations out of 5000
-2 * Loglike = 56150.845960
Burning in for 3250 iterations out of 5000
-2 * Loglike = 56088.722978
Burning in for 3300 iterations out of 5000
-2 * Loglike = 55861.843877
Burning in for 3350 iterations out of 5000
-2 * Loglike = 55566.123812
Burning in for 3400 iterations out of 5000
-2 * Loglike = 55415.676137
Burning in for 3450 iterations out of 5000
-2 * Loglike = 55563.757915
Burning in for 3500 iterations out of 5000
-2 * Loglike = 56179.931894
Burning in for 3550 iterations out of 5000
-2 * Loglike = 56182.282278
Burning in for 3600 iterations out of 5000
-2 * Loglike = 56032.896643
Burning in for 3650 iterations out of 5000
-2 * Loglike = 56109.867181
Burning in for 3700 iterations out of 5000
-2 * Loglike = 56306.496422
Burning in for 3750 iterations out of 5000
-2 * Loglike = 56050.776761
Burning in for 3800 iterations out of 5000
-2 * Loglike = 56115.816900
Burning in for 3850 iterations out of 5000
-2 * Loglike = 55323.823904
Burning in for 3900 iterations out of 5000
-2 * Loglike = 56243.519460
Burning in for 3950 iterations out of 5000
-2 * Loglike = 56215.326843
Burning in for 4000 iterations out of 5000
-2 * Loglike = 56212.086368
Burning in for 4050 iterations out of 5000
-2 * Loglike = 55551.237051
Burning in for 4100 iterations out of 5000
-2 * Loglike = 55546.964817
Burning in for 4150 iterations out of 5000
-2 * Loglike = 56411.155546
Burning in for 4200 iterations out of 5000
-2 * Loglike = 56542.922088
Burning in for 4250 iterations out of 5000
-2 * Loglike = 56133.915373
Burning in for 4300 iterations out of 5000
-2 * Loglike = 55957.594967
Burning in for 4350 iterations out of 5000
-2 * Loglike = 56143.211073
Burning in for 4400 iterations out of 5000
-2 * Loglike = 55847.343888
Burning in for 4450 iterations out of 5000
-2 * Loglike = 55703.911763
Burning in for 4500 iterations out of 5000
-2 * Loglike = 55404.383194
Burning in for 4550 iterations out of 5000
-2 * Loglike = 56072.480968
Burning in for 4600 iterations out of 5000
-2 * Loglike = 55905.491810
Burning in for 4650 iterations out of 5000
-2 * Loglike = 55823.900455
Burning in for 4700 iterations out of 5000
-2 * Loglike = 55688.932585
Burning in for 4750 iterations out of 5000
-2 * Loglike = 55791.300612
Burning in for 4800 iterations out of 5000
-2 * Loglike = 55953.576240
Burning in for 4850 iterations out of 5000
-2 * Loglike = 56320.362389
Burning in for 4900 iterations out of 5000
-2 * Loglike = 56089.064014
Burning in for 4950 iterations out of 5000
-2 * Loglike = 56225.690796
Burning in for 5000 iterations out of 5000
-2 * Loglike = 56227.821563

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 = 56019.420711
Actual update 100 of 10000, Stored update 100 of 10000
-2 * Loglike = 56606.455811
Actual update 150 of 10000, Stored update 150 of 10000
-2 * Loglike = 56061.022773
Actual update 200 of 10000, Stored update 200 of 10000
-2 * Loglike = 55919.826071
Actual update 250 of 10000, Stored update 250 of 10000
-2 * Loglike = 56172.781383
Actual update 300 of 10000, Stored update 300 of 10000
-2 * Loglike = 56411.038931
Actual update 350 of 10000, Stored update 350 of 10000
-2 * Loglike = 56069.689400
Actual update 400 of 10000, Stored update 400 of 10000
-2 * Loglike = 55475.656565
Actual update 450 of 10000, Stored update 450 of 10000
-2 * Loglike = 56188.009986
Actual update 500 of 10000, Stored update 500 of 10000
-2 * Loglike = 55835.414103
Actual update 550 of 10000, Stored update 550 of 10000
-2 * Loglike = 55852.719092
Actual update 600 of 10000, Stored update 600 of 10000
-2 * Loglike = 55834.171978
Actual update 650 of 10000, Stored update 650 of 10000
-2 * Loglike = 55903.829077
Actual update 700 of 10000, Stored update 700 of 10000
-2 * Loglike = 56299.649303
Actual update 750 of 10000, Stored update 750 of 10000
-2 * Loglike = 56301.054194
Actual update 800 of 10000, Stored update 800 of 10000
-2 * Loglike = 56044.104395
Actual update 850 of 10000, Stored update 850 of 10000
-2 * Loglike = 56319.053234
Actual update 900 of 10000, Stored update 900 of 10000
-2 * Loglike = 56097.673975
Actual update 950 of 10000, Stored update 950 of 10000
-2 * Loglike = 56156.417012
Actual update 1000 of 10000, Stored update 1000 of 10000
-2 * Loglike = 56069.527689
Actual update 1050 of 10000, Stored update 1050 of 10000
-2 * Loglike = 56359.886379
Actual update 1100 of 10000, Stored update 1100 of 10000
-2 * Loglike = 55868.064076
Actual update 1150 of 10000, Stored update 1150 of 10000
-2 * Loglike = 56109.040136
Actual update 1200 of 10000, Stored update 1200 of 10000
-2 * Loglike = 55790.137889
Actual update 1250 of 10000, Stored update 1250 of 10000
-2 * Loglike = 55516.857830
Actual update 1300 of 10000, Stored update 1300 of 10000
-2 * Loglike = 56084.444600
Actual update 1350 of 10000, Stored update 1350 of 10000
-2 * Loglike = 55772.659164
Actual update 1400 of 10000, Stored update 1400 of 10000
-2 * Loglike = 56123.612720
Actual update 1450 of 10000, Stored update 1450 of 10000
-2 * Loglike = 56107.873815
Actual update 1500 of 10000, Stored update 1500 of 10000
-2 * Loglike = 55711.303421
Actual update 1550 of 10000, Stored update 1550 of 10000
-2 * Loglike = 56105.740979
Actual update 1600 of 10000, Stored update 1600 of 10000
-2 * Loglike = 55912.975724
Actual update 1650 of 10000, Stored update 1650 of 10000
-2 * Loglike = 56079.507756
Actual update 1700 of 10000, Stored update 1700 of 10000
-2 * Loglike = 55443.998351
Actual update 1750 of 10000, Stored update 1750 of 10000
-2 * Loglike = 55855.756456
Actual update 1800 of 10000, Stored update 1800 of 10000
-2 * Loglike = 56093.426713
Actual update 1850 of 10000, Stored update 1850 of 10000
-2 * Loglike = 56502.966924
Actual update 1900 of 10000, Stored update 1900 of 10000
-2 * Loglike = 56136.752606
Actual update 1950 of 10000, Stored update 1950 of 10000
-2 * Loglike = 56114.574091
Actual update 2000 of 10000, Stored update 2000 of 10000
-2 * Loglike = 56164.191867
Actual update 2050 of 10000, Stored update 2050 of 10000
-2 * Loglike = 55938.769845
Actual update 2100 of 10000, Stored update 2100 of 10000
-2 * Loglike = 56413.290263
Actual update 2150 of 10000, Stored update 2150 of 10000
-2 * Loglike = 55942.868423
Actual update 2200 of 10000, Stored update 2200 of 10000
-2 * Loglike = 55653.340765
Actual update 2250 of 10000, Stored update 2250 of 10000
-2 * Loglike = 55644.260328
Actual update 2300 of 10000, Stored update 2300 of 10000
-2 * Loglike = 56141.078405
Actual update 2350 of 10000, Stored update 2350 of 10000
-2 * Loglike = 55599.577631
Actual update 2400 of 10000, Stored update 2400 of 10000
-2 * Loglike = 55667.437347
Actual update 2450 of 10000, Stored update 2450 of 10000
-2 * Loglike = 55817.539157
Actual update 2500 of 10000, Stored update 2500 of 10000
-2 * Loglike = 55771.028691
Actual update 2550 of 10000, Stored update 2550 of 10000
-2 * Loglike = 56339.068356
Actual update 2600 of 10000, Stored update 2600 of 10000
-2 * Loglike = 56198.571223
Actual update 2650 of 10000, Stored update 2650 of 10000
-2 * Loglike = 56132.990601
Actual update 2700 of 10000, Stored update 2700 of 10000
-2 * Loglike = 55975.057315
Actual update 2750 of 10000, Stored update 2750 of 10000
-2 * Loglike = 55836.416667
Actual update 2800 of 10000, Stored update 2800 of 10000
-2 * Loglike = 55874.425969
Actual update 2850 of 10000, Stored update 2850 of 10000
-2 * Loglike = 55821.423525
Actual update 2900 of 10000, Stored update 2900 of 10000
-2 * Loglike = 55997.750608
Actual update 2950 of 10000, Stored update 2950 of 10000
-2 * Loglike = 55907.452220
Actual update 3000 of 10000, Stored update 3000 of 10000
-2 * Loglike = 56299.938927
Actual update 3050 of 10000, Stored update 3050 of 10000
-2 * Loglike = 55856.731558
Actual update 3100 of 10000, Stored update 3100 of 10000
-2 * Loglike = 56074.858867
Actual update 3150 of 10000, Stored update 3150 of 10000
-2 * Loglike = 56235.545770
Actual update 3200 of 10000, Stored update 3200 of 10000
-2 * Loglike = 55961.678341
Actual update 3250 of 10000, Stored update 3250 of 10000
-2 * Loglike = 56012.064222
Actual update 3300 of 10000, Stored update 3300 of 10000
-2 * Loglike = 55920.820502
Actual update 3350 of 10000, Stored update 3350 of 10000
-2 * Loglike = 56128.560007
Actual update 3400 of 10000, Stored update 3400 of 10000
-2 * Loglike = 56279.272089
Actual update 3450 of 10000, Stored update 3450 of 10000
-2 * Loglike = 55940.281588
Actual update 3500 of 10000, Stored update 3500 of 10000
-2 * Loglike = 56153.358296
Actual update 3550 of 10000, Stored update 3550 of 10000
-2 * Loglike = 56505.409433
Actual update 3600 of 10000, Stored update 3600 of 10000
-2 * Loglike = 55976.075363
Actual update 3650 of 10000, Stored update 3650 of 10000
-2 * Loglike = 55669.867245
Actual update 3700 of 10000, Stored update 3700 of 10000
-2 * Loglike = 56025.181217
Actual update 3750 of 10000, Stored update 3750 of 10000
-2 * Loglike = 55822.254589
Actual update 3800 of 10000, Stored update 3800 of 10000
-2 * Loglike = 55738.205344
Actual update 3850 of 10000, Stored update 3850 of 10000
-2 * Loglike = 56412.499625
Actual update 3900 of 10000, Stored update 3900 of 10000
-2 * Loglike = 56324.169760
Actual update 3950 of 10000, Stored update 3950 of 10000
-2 * Loglike = 56550.826833
Actual update 4000 of 10000, Stored update 4000 of 10000
-2 * Loglike = 56137.752927
Actual update 4050 of 10000, Stored update 4050 of 10000
-2 * Loglike = 55548.506956
Actual update 4100 of 10000, Stored update 4100 of 10000
-2 * Loglike = 56126.479915
Actual update 4150 of 10000, Stored update 4150 of 10000
-2 * Loglike = 55845.262550
Actual update 4200 of 10000, Stored update 4200 of 10000
-2 * Loglike = 56428.873090
Actual update 4250 of 10000, Stored update 4250 of 10000
-2 * Loglike = 55769.371764
Actual update 4300 of 10000, Stored update 4300 of 10000
-2 * Loglike = 55455.841581
Actual update 4350 of 10000, Stored update 4350 of 10000
-2 * Loglike = 56060.551812
Actual update 4400 of 10000, Stored update 4400 of 10000
-2 * Loglike = 56087.193163
Actual update 4450 of 10000, Stored update 4450 of 10000
-2 * Loglike = 55293.735133
Actual update 4500 of 10000, Stored update 4500 of 10000
-2 * Loglike = 55656.953072
Actual update 4550 of 10000, Stored update 4550 of 10000
-2 * Loglike = 55452.588447
Actual update 4600 of 10000, Stored update 4600 of 10000
-2 * Loglike = 56349.249999
Actual update 4650 of 10000, Stored update 4650 of 10000
-2 * Loglike = 55671.309042
Actual update 4700 of 10000, Stored update 4700 of 10000
-2 * Loglike = 55844.262162
Actual update 4750 of 10000, Stored update 4750 of 10000
-2 * Loglike = 55831.712315
Actual update 4800 of 10000, Stored update 4800 of 10000
-2 * Loglike = 55736.562585
Actual update 4850 of 10000, Stored update 4850 of 10000
-2 * Loglike = 55689.357925
Actual update 4900 of 10000, Stored update 4900 of 10000
-2 * Loglike = 55311.524143
Actual update 4950 of 10000, Stored update 4950 of 10000
-2 * Loglike = 56160.468205
Actual update 5000 of 10000, Stored update 5000 of 10000
-2 * Loglike = 55424.981879
Actual update 5050 of 10000, Stored update 5050 of 10000
-2 * Loglike = 56132.699556
Actual update 5100 of 10000, Stored update 5100 of 10000
-2 * Loglike = 55947.293035
Actual update 5150 of 10000, Stored update 5150 of 10000
-2 * Loglike = 55505.009113
Actual update 5200 of 10000, Stored update 5200 of 10000
-2 * Loglike = 56260.773739
Actual update 5250 of 10000, Stored update 5250 of 10000
-2 * Loglike = 55903.493350
Actual update 5300 of 10000, Stored update 5300 of 10000
-2 * Loglike = 56212.317442
Actual update 5350 of 10000, Stored update 5350 of 10000
-2 * Loglike = 55959.769715
Actual update 5400 of 10000, Stored update 5400 of 10000
-2 * Loglike = 55550.275091
Actual update 5450 of 10000, Stored update 5450 of 10000
-2 * Loglike = 55964.952425
Actual update 5500 of 10000, Stored update 5500 of 10000
-2 * Loglike = 55998.102921
Actual update 5550 of 10000, Stored update 5550 of 10000
-2 * Loglike = 56029.269068
Actual update 5600 of 10000, Stored update 5600 of 10000
-2 * Loglike = 55505.086700
Actual update 5650 of 10000, Stored update 5650 of 10000
-2 * Loglike = 56035.943812
Actual update 5700 of 10000, Stored update 5700 of 10000
-2 * Loglike = 56539.383696
Actual update 5750 of 10000, Stored update 5750 of 10000
-2 * Loglike = 56355.078421
Actual update 5800 of 10000, Stored update 5800 of 10000
-2 * Loglike = 56007.128747
Actual update 5850 of 10000, Stored update 5850 of 10000
-2 * Loglike = 56375.795153
Actual update 5900 of 10000, Stored update 5900 of 10000
-2 * Loglike = 56348.937517
Actual update 5950 of 10000, Stored update 5950 of 10000
-2 * Loglike = 56265.868291
Actual update 6000 of 10000, Stored update 6000 of 10000
-2 * Loglike = 56192.266315
Actual update 6050 of 10000, Stored update 6050 of 10000
-2 * Loglike = 56620.841010
Actual update 6100 of 10000, Stored update 6100 of 10000
-2 * Loglike = 55932.522712
Actual update 6150 of 10000, Stored update 6150 of 10000
-2 * Loglike = 56132.528871
Actual update 6200 of 10000, Stored update 6200 of 10000
-2 * Loglike = 56329.742587
Actual update 6250 of 10000, Stored update 6250 of 10000
-2 * Loglike = 56199.548199
Actual update 6300 of 10000, Stored update 6300 of 10000
-2 * Loglike = 56587.865267
Actual update 6350 of 10000, Stored update 6350 of 10000
-2 * Loglike = 56433.603457
Actual update 6400 of 10000, Stored update 6400 of 10000
-2 * Loglike = 56422.119394
Actual update 6450 of 10000, Stored update 6450 of 10000
-2 * Loglike = 55986.962785
Actual update 6500 of 10000, Stored update 6500 of 10000
-2 * Loglike = 56101.997721
Actual update 6550 of 10000, Stored update 6550 of 10000
-2 * Loglike = 56258.213303
Actual update 6600 of 10000, Stored update 6600 of 10000
-2 * Loglike = 55602.029242
Actual update 6650 of 10000, Stored update 6650 of 10000
-2 * Loglike = 56147.502525
Actual update 6700 of 10000, Stored update 6700 of 10000
-2 * Loglike = 56154.123280
Actual update 6750 of 10000, Stored update 6750 of 10000
-2 * Loglike = 56103.948842
Actual update 6800 of 10000, Stored update 6800 of 10000
-2 * Loglike = 56188.611424
Actual update 6850 of 10000, Stored update 6850 of 10000
-2 * Loglike = 56381.473881
Actual update 6900 of 10000, Stored update 6900 of 10000
-2 * Loglike = 56177.356217
Actual update 6950 of 10000, Stored update 6950 of 10000
-2 * Loglike = 56260.904795
Actual update 7000 of 10000, Stored update 7000 of 10000
-2 * Loglike = 56721.831251
Actual update 7050 of 10000, Stored update 7050 of 10000
-2 * Loglike = 56000.699740
Actual update 7100 of 10000, Stored update 7100 of 10000
-2 * Loglike = 56358.533416
Actual update 7150 of 10000, Stored update 7150 of 10000
-2 * Loglike = 56148.648768
Actual update 7200 of 10000, Stored update 7200 of 10000
-2 * Loglike = 56457.717582
Actual update 7250 of 10000, Stored update 7250 of 10000
-2 * Loglike = 56516.186320
Actual update 7300 of 10000, Stored update 7300 of 10000
-2 * Loglike = 56468.565834
Actual update 7350 of 10000, Stored update 7350 of 10000
-2 * Loglike = 56470.438957
Actual update 7400 of 10000, Stored update 7400 of 10000
-2 * Loglike = 56670.424164
Actual update 7450 of 10000, Stored update 7450 of 10000
-2 * Loglike = 56422.480374
Actual update 7500 of 10000, Stored update 7500 of 10000
-2 * Loglike = 56413.121202
Actual update 7550 of 10000, Stored update 7550 of 10000
-2 * Loglike = 56323.040817
Actual update 7600 of 10000, Stored update 7600 of 10000
-2 * Loglike = 56295.542293
Actual update 7650 of 10000, Stored update 7650 of 10000
-2 * Loglike = 56331.882587
Actual update 7700 of 10000, Stored update 7700 of 10000
-2 * Loglike = 56249.498654
Actual update 7750 of 10000, Stored update 7750 of 10000
-2 * Loglike = 56099.840977
Actual update 7800 of 10000, Stored update 7800 of 10000
-2 * Loglike = 56055.214903
Actual update 7850 of 10000, Stored update 7850 of 10000
-2 * Loglike = 56330.971586
Actual update 7900 of 10000, Stored update 7900 of 10000
-2 * Loglike = 56710.694773
Actual update 7950 of 10000, Stored update 7950 of 10000
-2 * Loglike = 56599.735350
Actual update 8000 of 10000, Stored update 8000 of 10000
-2 * Loglike = 56143.318387
Actual update 8050 of 10000, Stored update 8050 of 10000
-2 * Loglike = 56055.472221
Actual update 8100 of 10000, Stored update 8100 of 10000
-2 * Loglike = 55992.624370
Actual update 8150 of 10000, Stored update 8150 of 10000
-2 * Loglike = 56251.102115
Actual update 8200 of 10000, Stored update 8200 of 10000
-2 * Loglike = 56270.052381
Actual update 8250 of 10000, Stored update 8250 of 10000
-2 * Loglike = 55391.796869
Actual update 8300 of 10000, Stored update 8300 of 10000
-2 * Loglike = 56175.290295
Actual update 8350 of 10000, Stored update 8350 of 10000
-2 * Loglike = 56294.102855
Actual update 8400 of 10000, Stored update 8400 of 10000
-2 * Loglike = 56051.802938
Actual update 8450 of 10000, Stored update 8450 of 10000
-2 * Loglike = 56249.553916
Actual update 8500 of 10000, Stored update 8500 of 10000
-2 * Loglike = 55834.036411
Actual update 8550 of 10000, Stored update 8550 of 10000
-2 * Loglike = 56013.817951
Actual update 8600 of 10000, Stored update 8600 of 10000
-2 * Loglike = 55778.250983
Actual update 8650 of 10000, Stored update 8650 of 10000
-2 * Loglike = 55537.692283
Actual update 8700 of 10000, Stored update 8700 of 10000
-2 * Loglike = 56060.451313
Actual update 8750 of 10000, Stored update 8750 of 10000
-2 * Loglike = 55409.260049
Actual update 8800 of 10000, Stored update 8800 of 10000
-2 * Loglike = 55402.517775
Actual update 8850 of 10000, Stored update 8850 of 10000
-2 * Loglike = 55897.217967
Actual update 8900 of 10000, Stored update 8900 of 10000
-2 * Loglike = 55619.522680
Actual update 8950 of 10000, Stored update 8950 of 10000
-2 * Loglike = 55774.385540
Actual update 9000 of 10000, Stored update 9000 of 10000
-2 * Loglike = 55538.048799
Actual update 9050 of 10000, Stored update 9050 of 10000
-2 * Loglike = 55725.400278
Actual update 9100 of 10000, Stored update 9100 of 10000
-2 * Loglike = 55401.483694
Actual update 9150 of 10000, Stored update 9150 of 10000
-2 * Loglike = 55952.299498
Actual update 9200 of 10000, Stored update 9200 of 10000
-2 * Loglike = 55906.759537
Actual update 9250 of 10000, Stored update 9250 of 10000
-2 * Loglike = 55736.389088
Actual update 9300 of 10000, Stored update 9300 of 10000
-2 * Loglike = 55686.051177
Actual update 9350 of 10000, Stored update 9350 of 10000
-2 * Loglike = 56361.933104
Actual update 9400 of 10000, Stored update 9400 of 10000
-2 * Loglike = 56022.029572
Actual update 9450 of 10000, Stored update 9450 of 10000
-2 * Loglike = 55611.485770
Actual update 9500 of 10000, Stored update 9500 of 10000
-2 * Loglike = 55819.565212
Actual update 9550 of 10000, Stored update 9550 of 10000
-2 * Loglike = 56097.148521
Actual update 9600 of 10000, Stored update 9600 of 10000
-2 * Loglike = 56214.266525
Actual update 9650 of 10000, Stored update 9650 of 10000
-2 * Loglike = 55338.750967
Actual update 9700 of 10000, Stored update 9700 of 10000
-2 * Loglike = 55495.723644
Actual update 9750 of 10000, Stored update 9750 of 10000
-2 * Loglike = 55868.929209
Actual update 9800 of 10000, Stored update 9800 of 10000
-2 * Loglike = 56044.520540
Actual update 9850 of 10000, Stored update 9850 of 10000
-2 * Loglike = 56024.632070
Actual update 9900 of 10000, Stored update 9900 of 10000
-2 * Loglike = 55877.738358
Actual update 9950 of 10000, Stored update 9950 of 10000
-2 * Loglike = 55860.284219
Actual update 10000 of 10000, Stored update 10000 of 10000
-2 * Loglike = 55941.433256
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =          10000
Average =          56039.
S.D.    =          314.49
S.E.M.  =          3.1449

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 168.88s 
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   1.50252     0.30035      0.91385     2.09118 
load1_biol_r3     0.63403     0.28806      0.06943     1.19862 
load1_biol_r4     1.06387     0.89471     -0.68974     2.81747 
load1_phys_core   1.54630     0.48551      0.59471     2.49789 
load1_phys_r2     1.19428     0.85449     -0.48049     2.86905 
--------------------------------------------------------------------------------------------------- 
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     0.76924     0.43220     -0.07785     1.61633 
load2_biol_r4     2.89391     0.83827      1.25092     4.53689 
load2_phys_core   1.62017     0.26394      1.10286     2.13748 
load2_phys_r2     2.86555     0.73692      1.42122     4.30988 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.63194     0.09030      0.45496     0.80893 
cov_fact2_fact1   0.03420     0.21199     -0.38129     0.44969 
var_fact2         0.27891     0.16246     -0.03951     0.59733 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39364     0.03172  264.64          0  ***     8.33158     8.45515   3550 
Intercept_biol_core   7.06626     0.03657  193.24          0  ***     6.99268     7.13694   1727 
Intercept_biol_r3     6.89389     0.06413  107.51          0  ***     6.76893     7.01660   2696 
Intercept_biol_r4     5.68273     0.07527   75.50          0  ***     5.53445     5.83000   2102 
Intercept_phys_core   7.21148     0.04146  173.95          0  ***     7.12880     7.29212   1716 
Intercept_phys_r2     6.31084     0.06183  102.06          0  ***     6.19036     6.43098   1514 
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     1.81735     0.09375      1.57804     1.97482     48 
var_Intercept_biol_core   1.60518     0.08761      1.43255     1.77271    545 
var_Intercept_biol_r3     4.71662     0.20417      4.32683     5.12589   2660 
var_Intercept_biol_r4     5.10554     0.46319      4.05858     5.90819     93 
var_Intercept_phys_core   2.01016     0.11411      1.76018     2.21508    285 
var_Intercept_phys_r2     2.76022     0.32436      2.09589     3.35190     91 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> # 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: 3.05)  multilevel model (Multivariate Normal) 
        N min     mean max N_complete min_complete mean_complete max_complete
school 99  12 24.63636  34         99           12      24.63636           34
Estimation algorithm:  IGLS        Elapsed time : 11.69s 
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
Adapting finished and took 100 iterations
Adapting took 100 iterations
Burning in for 50 iterations out of 500
-2 * Loglike = 55718.916398
Burning in for 100 iterations out of 500
-2 * Loglike = 55527.204981
Burning in for 150 iterations out of 500
-2 * Loglike = 55407.076101
Burning in for 200 iterations out of 500
-2 * Loglike = 55524.466026
Burning in for 250 iterations out of 500
-2 * Loglike = 55769.259619
Burning in for 300 iterations out of 500
-2 * Loglike = 55674.408104
Burning in for 350 iterations out of 500
-2 * Loglike = 55370.421399
Burning in for 400 iterations out of 500
-2 * Loglike = 55698.799480
Burning in for 450 iterations out of 500
-2 * Loglike = 55749.093597
Burning in for 500 iterations out of 500
-2 * Loglike = 55686.529795

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 = 55572.038205
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 55634.669751
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 55460.194765
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 55927.763079
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 55845.390486
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 55443.819532
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 55480.502079
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 55692.908595
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 55991.838762
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 55785.687209
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 55623.098096
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 55613.796349
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 55751.507935
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 55470.014049
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 55608.393333
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 55798.812642
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 55567.722600
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 55856.907345
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 55764.801232
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 55816.710225
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 55827.498157
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 55501.994026
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 55480.720435
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 55279.769244
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 55616.952581
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 55452.912754
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 55470.728714
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 55376.704894
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 55738.516750
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 55557.856155
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 55477.963045
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 55677.189568
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 55828.381896
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 55506.082750
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 55584.678909
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 55504.370330
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 55755.727657
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 55616.306484
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 55884.923638
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 55284.844638
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 55689.420934
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 55541.614446
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 55629.471828
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 55513.291040
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 55598.034498
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 55437.783140
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 55471.894432
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 55513.563597
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 55638.659380
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 55818.129636
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 55423.403421
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 55586.057164
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 55775.684111
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 55234.461266
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 55426.165028
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 55382.031873
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 55477.713600
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 55407.262074
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 55389.202026
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 55813.329900
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 55459.073948
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 55580.044880
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 55891.030316
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 55646.942705
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 55854.739040
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 55690.205528
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 55756.650751
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 55539.383312
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 55265.738949
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 55442.908454
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 55674.879902
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 55908.389091
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 55585.032650
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 55786.599919
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 55462.661428
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 55482.942618
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 55746.751672
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 55642.135074
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 55130.176856
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 55585.905652
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 55594.048851
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 55675.945813
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 55627.532753
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 55741.786779
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 55609.475553
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 55775.514221
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 55608.190032
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 55952.320889
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 55395.479753
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 55588.084962
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 55647.429300
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 55440.463578
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 55662.824722
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 55654.552008
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 55616.137402
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 55817.643773
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 55838.967215
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 55578.783627
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 55576.983202
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 55519.342359
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          55618.
S.D.    =          182.63
S.E.M.  =          2.5828

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.05)  multilevel model (Multivariate Normal) 
        N min     mean max N_complete min_complete mean_complete max_complete
school 99  12 24.63636  34         99           12      24.63636           34
Estimation algorithm:  MCMC      Elapsed time : 43.91s 
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   1.79986     0.12672      1.55149     2.04823 
load1_biol_r3     0.84120     0.15026      0.54671     1.13570 
load1_biol_r4     1.97750     0.18942      1.60623     2.34876 
load1_phys_core   2.18940     0.15650      1.88266     2.49614 
load1_phys_r2     2.34812     0.18360      1.98827     2.70798 
--------------------------------------------------------------------------------------------------- 
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   2.28523     0.40200      1.49733     3.07314 
load2_biol_r3     1.18528     0.30558      0.58635     1.78421 
load2_biol_r4     2.46895     0.54491      1.40095     3.53695 
load2_phys_core   2.50422     0.45933      1.60395     3.40448 
load2_phys_r2     2.12060     0.43416      1.26966     2.97154 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.31094     0.03659      0.23922     0.38267 
cov_fact2_fact1   0.00000     0.00000      0.00000     0.00000 
var_fact2         0.15206     0.05733      0.03970     0.26443 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z    Pr(>|z|)       [95% Cred.   Interval]   ESS 
Intercept_es_core     8.36622     0.06950  120.38           0  ***     8.22776     8.49975   184 
Intercept_biol_core   7.03362     0.09276   75.83           0  ***     6.84877     7.22125    72 
Intercept_biol_r3     6.87138     0.08692   79.05           0  ***     6.69930     7.04368   282 
Intercept_biol_r4     5.66842     0.16010   35.41   1.37e-274  ***     5.35884     5.99703   127 
Intercept_phys_core   7.16698     0.10845   66.08           0  ***     6.94502     7.39377    84 
Intercept_phys_r2     6.28625     0.11424   55.03           0  ***     6.06618     6.51978   121 
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     0.23597     0.04880      0.15343     0.34459   1118 
var_Intercept_biol_core   0.04311     0.03752      0.00088     0.12955     41 
var_Intercept_biol_r3     0.17171     0.09555      0.00333     0.37375     97 
var_Intercept_biol_r4     0.99973     0.21296      0.62472     1.46906    800 
var_Intercept_phys_core   0.16191     0.05134      0.07141     0.27112    275 
var_Intercept_phys_r2     0.30723     0.11441      0.05260     0.54277    163 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                            Coef.   Std. Err.   [95% Cred.   Interval]   ESS 
var_Intercept_es_core     1.74400     0.05623      1.63869     1.85892   926 
var_Intercept_biol_core   1.61870     0.07219      1.48116     1.75937   641 
var_Intercept_biol_r3     4.59943     0.20000      4.22479     5.01404   761 
var_Intercept_biol_r4     4.73019     0.22882      4.30036     5.19191   970 
var_Intercept_phys_core   1.79642     0.09491      1.61577     1.98337   556 
var_Intercept_phys_r2     2.94175     0.17575      2.60761     3.29369   500 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> 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 
   7.92    1.03  404.81