R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
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Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

To cite R2MLwiN in publications use:

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

A BibTeX entry for LaTeX users is

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

The MLwiN_path option is currently set to C:/Program Files/MLwiN v3.09/
To change this use: options(MLwiN_path="<path to MLwiN>")
> # MLwiN folder
> mlwin <- getOption("MLwiN_path")
> while (!file.access(mlwin, mode = 1) == 0) {
+   cat("Please specify the root MLwiN folder or the full path to the MLwiN executable:\n")
+   mlwin <- scan(what = character(0), sep = "\n")
+   mlwin <- gsub("\\", "/", mlwin, fixed = TRUE)
+ }
> options(MLwiN_path = mlwin)
> 
> # User's input if necessary
> 
> ## 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: 3.09)  multilevel model (Multivariate Normal) 
Estimation algorithm:  IGLS        Elapsed time : 4.17s 
Number of obs:  2439 (from total 2439)        The model converged after 4 iterations.
Log likelihood:      -22211.8 
Deviance statistic:  44423.6 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.        z   Pr(>|z|)         [95% Conf.   Interval] 
Intercept_es_core     8.39414     0.03168   264.94          0   ***      8.33204     8.45624 
Intercept_biol_core   7.06642     0.03699   191.04          0   ***      6.99392     7.13892 
Intercept_biol_r3     6.89700     0.06379   108.12          0   ***      6.77197     7.02203 
Intercept_biol_r4     5.67445     0.07564    75.02          0   ***      5.52619     5.82270 
Intercept_phys_core   7.21197     0.04176   172.71          0   ***      7.13013     7.29382 
Intercept_phys_r2     6.31601     0.06167   102.42          0   ***      6.19514     6.43687 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                                                Coef.   Std. Err. 
var_Intercept_es_core                         2.44834     0.07011 
cov_Intercept_es_core_Intercept_biol_core     0.99227     0.06127 
var_Intercept_biol_core                       3.33712     0.09556 
cov_Intercept_es_core_Intercept_biol_r3       0.57021     0.10048 
cov_Intercept_biol_core_Intercept_biol_r3     0.81959     0.11771 
var_Intercept_biol_r3                         5.15374     0.20824 
cov_Intercept_es_core_Intercept_biol_r4       0.90490     0.11977 
cov_Intercept_biol_core_Intercept_biol_r4     1.85965     0.14322 
cov_Intercept_biol_r3_Intercept_biol_r4       1.51518     0.28626 
var_Intercept_biol_r4                         7.76196     0.31215 
cov_Intercept_es_core_Intercept_phys_core     1.00938     0.06846 
cov_Intercept_biol_core_Intercept_phys_core   1.97690     0.08615 
cov_Intercept_biol_r3_Intercept_phys_core     0.85576     0.13270 
cov_Intercept_biol_r4_Intercept_phys_core     2.11944     0.16179 
var_Intercept_phys_core                       4.25314     0.12179 
cov_Intercept_es_core_Intercept_phys_r2       0.99492     0.09858 
cov_Intercept_biol_core_Intercept_phys_r2     1.80603     0.11845 
cov_Intercept_biol_r3_Intercept_phys_r2       1.11952     0.23076 
cov_Intercept_biol_r4_Intercept_phys_r2       2.91479     0.26492 
cov_Intercept_phys_core_Intercept_phys_r2     2.40201     0.13617 
var_Intercept_phys_r2                         5.53558     0.21790 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> covM1 <- matrix(, 6, 6)
> colnames(covM1) <- rownames(covM1) <- c("cons.es_core", "cons.biol_core", "cons.biol_r3", "cons.biol_r4", "cons.phys_core", 
+   "cons.phys_r2")
> covM1[upper.tri(covM1, diag = TRUE)] <- mymodel@RP
> # covM1[lower.tri(covM1)] <- t(covM1)[lower.tri(covM1)]
> round(cov2cor(t(covM1)), 3)
               cons.es_core cons.biol_core cons.biol_r3 cons.biol_r4
cons.es_core          1.000             NA           NA           NA
cons.biol_core        0.347          1.000           NA           NA
cons.biol_r3          0.161          0.198        1.000           NA
cons.biol_r4          0.208          0.365        0.240        1.000
cons.phys_core        0.313          0.525        0.183        0.369
cons.phys_r2          0.270          0.420        0.210        0.445
               cons.phys_core cons.phys_r2
cons.es_core               NA           NA
cons.biol_core             NA           NA
cons.biol_r3               NA           NA
cons.biol_r4               NA           NA
cons.phys_core          1.000           NA
cons.phys_r2            0.495            1
> 
> # 20.4 A single factor Bayesian model . . . . . . . . . . . . . . . . . . 307
> 
> nfact <- 1
> lev.fact <- 1
> nfactcor <- 0
> factcor <- NULL
> # see FACT in the MCMC manual
> loading <- matrix(c(1, 0, 0, 0, 0, 0, 1), ncol = 7, nrow = nfact, byrow = TRUE)
> constr <- matrix(c(1, 0, 0, 0, 0, 0, 0), ncol = 7, nrow = nfact, byrow = TRUE)
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (1 | student), D = "Multivariate Normal", 
+   estoptions = list(EstM = 1, fact = list(nfact = nfact, lev.fact = lev.fact, nfactcor = nfactcor, factcor = factcor, 
+     loading = loading, constr = constr)), data = hungary1))
MLwiN is running, please wait......
/nogui option ignored
ECHO    0


Echoing is ON
BATC 1

Batch mode is ON
MAXI 2
STAR
iteration 0
iteration 1

Convergence achieved
TOLE 2
MAXI 20
BATC 1

Batch mode is ON
NEXT
iteration 2

Convergence achieved
ECHO 0

Echoing is ON
MCMC   0 500 1 5.8 50 10 G30[1] G30[2]  1 1 1 1 1 4
BURNING IN...
Burning in for 50 iterations out of 500
-2 * Loglike = 63359.391759
Burning in for 100 iterations out of 500
-2 * Loglike = 56692.818665
Burning in for 150 iterations out of 500
-2 * Loglike = 57344.803982
Burning in for 200 iterations out of 500
-2 * Loglike = 56810.614294
Burning in for 250 iterations out of 500
-2 * Loglike = 57175.697941
Burning in for 300 iterations out of 500
-2 * Loglike = 56764.436399
Burning in for 350 iterations out of 500
-2 * Loglike = 56783.691851
Burning in for 400 iterations out of 500
-2 * Loglike = 56902.259944
Burning in for 450 iterations out of 500
-2 * Loglike = 56924.022281
Burning in for 500 iterations out of 500
-2 * Loglike = 56719.502894

ERAS G30
LINK 0 G30
ERAS  c1090 c1091

MCMC 1 5000 1 c1090 c1091 c1003 c1004 1 4
Actual update 50 of 5000, Stored update 50 of 5000
-2 * Loglike = 57062.924495
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 56963.946374
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 56963.060949
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 56735.446241
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 56928.529810
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 57230.767480
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 57081.776284
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 56880.332280
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 57048.754523
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 56976.190897
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 56895.837220
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 56972.550127
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 57083.857692
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 56998.729652
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 56715.158757
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 57087.631160
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 57057.605642
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 56985.964988
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 56653.228335
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 57113.240256
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 57094.161184
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 57237.057358
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 56955.348038
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 56956.790393
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 56838.933990
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 56840.409381
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 56801.176295
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 57149.517139
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 56745.023896
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 57064.631971
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 57138.747473
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 56940.120088
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 57020.550727
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 56934.684627
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 56997.104760
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 56905.845270
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 56824.118364
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 56991.390701
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 56837.371813
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 57094.780015
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 57142.228060
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 57240.918932
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 56915.669400
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 56857.781715
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 56664.050946
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 56905.605855
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 56907.639600
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 56734.013120
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 57084.171232
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 57001.242613
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 56912.046955
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 57307.930235
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 56729.765089
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 56824.239802
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 56840.571344
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 56920.865319
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 57259.989094
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 56908.804286
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 57023.444319
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 57278.180005
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 57098.837215
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 56874.803039
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 57007.463294
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 56650.538730
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 56845.665354
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 57031.963381
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 57065.884385
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 57026.126830
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 56792.859073
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 56711.101195
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 57115.447305
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 57273.347935
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 56906.117388
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 57140.799149
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 56975.245144
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 56781.296864
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 56804.769435
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 56996.405490
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 56815.138143
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 56607.834100
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 56884.215505
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 57121.817374
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 56975.616853
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 57121.969087
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 56591.764534
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 56872.880165
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 56841.666325
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 56976.797050
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 56981.614793
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 56823.546473
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 56842.031439
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 56942.503651
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 57034.973677
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 57117.029086
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 57245.089674
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 56666.818347
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 57109.610542
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 57139.033295
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 56902.641869
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 57170.150971
PUPN c1003 c1004
AVER c1091 b99 b100

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

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.09)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 24.83s 
Number of obs:  2439 (from total 2439)          Number of iter.: 5000  Chains: 1  Burn-in: 500 
Deviance statistic:  46362.2 
--------------------------------------------------------------------------------------------------- 
The model formula:
c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 
    1 + (1 | student)
Level 1: student      
--------------------------------------------------------------------------------------------------- 
The estimates of factor 1 loadings:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
load1_es_core     1.00000     0.00000      1.00000     1.00000 
load1_biol_core   1.87685     0.10539      1.67029     2.08341 
load1_biol_r3     0.92789     0.11488      0.70273     1.15305 
load1_biol_r4     2.11146     0.16136      1.79519     2.42772 
load1_phys_core   2.17924     0.12496      1.93432     2.42416 
load1_phys_r2     2.18845     0.14752      1.89931     2.47759 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
              Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1   0.48250     0.04925      0.38597     0.57902 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39480     0.03137  267.60          0  ***     8.33368     8.45845   1893 
Intercept_biol_core   7.06817     0.03619  195.31          0  ***     6.99661     7.13725   1104 
Intercept_biol_r3     6.89535     0.06339  108.78          0  ***     6.77146     7.01642   1612 
Intercept_biol_r4     5.67607     0.07545   75.23          0  ***     5.52643     5.82459   1273 
Intercept_phys_core   7.21437     0.04059  177.75          0  ***     7.13531     7.29267   1017 
Intercept_phys_r2     6.31474     0.06017  104.94          0  ***     6.19753     6.43559   1123 
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1  
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                            Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_es_core     1.95985     0.06112      1.84247     2.08259   2126 
var_Intercept_biol_core   1.65313     0.07626      1.50357     1.80636    703 
var_Intercept_biol_r3     4.75489     0.20311      4.37593     5.18112   1505 
var_Intercept_biol_r4     5.64647     0.26996      5.12717     6.19806   1028 
var_Intercept_phys_core   1.98247     0.09712      1.79292     2.17602    644 
var_Intercept_phys_r2     3.25402     0.16944      2.93227     3.59242    724 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> ranks <- rank(mymodel@fact.chains$scores)
> plot(x = ranks, mymodel@fact.chains$scores, xlab = "rank", ylab = "factor scores", ylim = c(-2.35, 1.2))
> abline(h = 0, lty = "dotted")
> 
> # 20.5 Adding a second factor to the model . . . . . . . . . . . . . . . .313
> 
> nfact <- 2
> lev.fact <- c(1, 1)
> nfactcor <- 0
> factcor <- NULL
> # see FACT in the MCMC manual
> loading <- matrix(c(1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1), ncol = 7, nrow = nfact, byrow = TRUE)
> constr <- matrix(c(1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0), ncol = 7, nrow = nfact, byrow = TRUE)
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (1 | student), D = "Multivariate Normal", 
+   estoptions = list(EstM = 1, fact = list(nfact = nfact, lev.fact = lev.fact, nfactcor = nfactcor, factcor = factcor, 
+     loading = loading, constr = constr)), data = hungary1))
MLwiN is running, please wait......
/nogui option ignored
ECHO    0


Echoing is ON
BATC 1

Batch mode is ON
MAXI 2
STAR
iteration 0
iteration 1

Convergence achieved
TOLE 2
MAXI 20
BATC 1

Batch mode is ON
NEXT
iteration 2

Convergence achieved
ECHO 0

Echoing is ON
MCMC   0 500 1 5.8 50 10 G30[1] G30[2]  1 1 1 1 1 4
RUNNING ADAPTIVE PROCEDURE AND BURNING IN...
Adapting finished and took 100 iterations
Adapting took 100 iterations
Burning in for 50 iterations out of 500
-2 * Loglike = 56267.470700
Burning in for 100 iterations out of 500
-2 * Loglike = 56301.928468
Burning in for 150 iterations out of 500
-2 * Loglike = 56177.365384
Burning in for 200 iterations out of 500
-2 * Loglike = 56305.747157
Burning in for 250 iterations out of 500
-2 * Loglike = 56740.030202
Burning in for 300 iterations out of 500
-2 * Loglike = 56210.004396
Burning in for 350 iterations out of 500
-2 * Loglike = 56668.415846
Burning in for 400 iterations out of 500
-2 * Loglike = 55733.200402
Burning in for 450 iterations out of 500
-2 * Loglike = 55861.426837
Burning in for 500 iterations out of 500
-2 * Loglike = 55770.808161

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 = 55328.825864
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 55178.243507
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 55591.097699
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 56132.875078
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 55278.883397
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 55794.607981
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 55343.739491
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 54918.412518
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 55519.589653
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 55216.554128
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 55359.770423
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 56156.991031
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 55797.947374
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 55923.608633
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 55176.559729
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 55611.115937
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 55621.426471
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 55537.541142
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 55525.694727
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 55616.904993
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 55342.743494
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 54642.192609
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 54481.594006
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 54466.678754
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 55067.543064
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 54866.001570
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 55533.215010
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 55640.192127
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 55420.199947
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 54520.688979
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 54534.360474
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 54165.060759
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 54391.521401
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 54255.126201
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 54799.734611
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 55738.663310
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 55627.362384
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 55346.004634
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 54559.941487
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 54080.829613
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 53660.110241
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 53190.296213
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 54133.744932
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 54506.861140
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 55105.150165
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 55807.622108
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 55164.469800
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 55439.420026
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 55046.889320
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 53762.024056
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 54669.850543
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 54473.395006
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 53786.448960
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 53637.184519
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 54428.539138
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 54295.199163
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 55025.587083
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 55068.767402
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 55030.605822
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 54738.010681
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 55130.893744
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 56250.185496
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 55961.313562
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 55928.973013
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 55665.625893
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 55444.539070
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 55366.941635
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 55665.905341
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 55225.082480
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 55281.481216
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 55399.541192
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 54753.474759
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 54441.088972
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 54099.347860
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 54002.417442
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 52602.211047
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 53366.876530
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 54127.996461
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 54208.838739
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 54107.953434
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 52810.973045
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 52965.362318
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 53199.055890
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 53629.924850
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 53755.873059
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 53959.703445
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 53419.681001
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 54063.775815
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 54118.434888
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 55149.715361
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 54169.608593
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 53282.792559
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 53193.776833
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 53596.184945
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 53403.152536
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 53630.576848
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 54347.252914
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 53077.728332
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 53846.835785
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 54907.479910
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          54691.
S.D.    =          879.33
S.E.M.  =          12.436

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.09)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 37.36s 
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   1.92562     0.11692      1.69647     2.15477 
load1_biol_r3     0.82847     0.11829      0.59662     1.06032 
load1_biol_r4     1.80644     0.15881      1.49518     2.11771 
load1_phys_core   1.97160     0.10821      1.75950     2.18369 
load1_phys_r2     1.78447     0.13910      1.51184     2.05711 
--------------------------------------------------------------------------------------------------- 
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      5.55868     4.33703     -2.94174    14.05910 
load2_biol_r4     16.88298     9.36370     -1.46955    35.23550 
load2_phys_core    7.40749     3.82635     -0.09202    14.90699 
load2_phys_r2     30.43714    17.25936     -3.39058    64.26486 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.51369     0.04870      0.41823     0.60915 
cov_fact2_fact1   0.00000     0.00000      0.00000     0.00000 
var_fact2         0.00738     0.01208     -0.01630     0.03107 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39511     0.03201  262.24          0  ***     8.33200     8.45646   1442 
Intercept_biol_core   7.06815     0.03875  182.39          0  ***     6.99546     7.14498    659 
Intercept_biol_r3     6.89891     0.06431  107.28          0  ***     6.77393     7.02605   1406 
Intercept_biol_r4     5.68180     0.07662   74.15          0  ***     5.53170     5.83519    964 
Intercept_phys_core   7.21566     0.04276  168.73          0  ***     7.13301     7.30125    686 
Intercept_phys_r2     6.31626     0.06085  103.81          0  ***     6.19656     6.43446    452 
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     1.93131     0.06176      1.81229     2.05232    641 
var_Intercept_biol_core   1.44097     0.10051      1.23608     1.62491    189 
var_Intercept_biol_r3     4.72405     0.19812      4.34143     5.12653   1381 
var_Intercept_biol_r4     5.33893     0.34150      4.61312     5.98313     95 
var_Intercept_phys_core   2.11077     0.09647      1.92414     2.30362    401 
var_Intercept_phys_r2     1.61238     0.59004      0.70458     2.76147     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
RUNNING ADAPTIVE PROCEDURE AND BURNING IN...
Adapting finished and took 100 iterations
Adapting took 100 iterations
Burning in for 50 iterations out of 5000
-2 * Loglike = 56267.470700
Burning in for 100 iterations out of 5000
-2 * Loglike = 56301.928468
Burning in for 150 iterations out of 5000
-2 * Loglike = 56177.365384
Burning in for 200 iterations out of 5000
-2 * Loglike = 56305.747157
Burning in for 250 iterations out of 5000
-2 * Loglike = 56740.030202
Burning in for 300 iterations out of 5000
-2 * Loglike = 56210.004396
Burning in for 350 iterations out of 5000
-2 * Loglike = 56668.415846
Burning in for 400 iterations out of 5000
-2 * Loglike = 55733.200402
Burning in for 450 iterations out of 5000
-2 * Loglike = 55861.426837
Burning in for 500 iterations out of 5000
-2 * Loglike = 55770.808161
Burning in for 550 iterations out of 5000
-2 * Loglike = 54583.222766
Burning in for 600 iterations out of 5000
-2 * Loglike = 55199.487629
Burning in for 650 iterations out of 5000
-2 * Loglike = 55394.343840
Burning in for 700 iterations out of 5000
-2 * Loglike = 55674.663595
Burning in for 750 iterations out of 5000
-2 * Loglike = 55931.098564
Burning in for 800 iterations out of 5000
-2 * Loglike = 55467.506777
Burning in for 850 iterations out of 5000
-2 * Loglike = 55599.339978
Burning in for 900 iterations out of 5000
-2 * Loglike = 55341.420167
Burning in for 950 iterations out of 5000
-2 * Loglike = 55134.324168
Burning in for 1000 iterations out of 5000
-2 * Loglike = 55544.608488
Burning in for 1050 iterations out of 5000
-2 * Loglike = 55152.256182
Burning in for 1100 iterations out of 5000
-2 * Loglike = 55404.583916
Burning in for 1150 iterations out of 5000
-2 * Loglike = 56231.174632
Burning in for 1200 iterations out of 5000
-2 * Loglike = 55792.833203
Burning in for 1250 iterations out of 5000
-2 * Loglike = 55923.522114
Burning in for 1300 iterations out of 5000
-2 * Loglike = 55278.579952
Burning in for 1350 iterations out of 5000
-2 * Loglike = 55805.429125
Burning in for 1400 iterations out of 5000
-2 * Loglike = 55737.714773
Burning in for 1450 iterations out of 5000
-2 * Loglike = 55598.773227
Burning in for 1500 iterations out of 5000
-2 * Loglike = 55509.930218
Burning in for 1550 iterations out of 5000
-2 * Loglike = 55510.512922
Burning in for 1600 iterations out of 5000
-2 * Loglike = 55181.761619
Burning in for 1650 iterations out of 5000
-2 * Loglike = 54560.182466
Burning in for 1700 iterations out of 5000
-2 * Loglike = 54360.615468
Burning in for 1750 iterations out of 5000
-2 * Loglike = 54052.791045
Burning in for 1800 iterations out of 5000
-2 * Loglike = 54906.925151
Burning in for 1850 iterations out of 5000
-2 * Loglike = 54643.584427
Burning in for 1900 iterations out of 5000
-2 * Loglike = 55590.095126
Burning in for 1950 iterations out of 5000
-2 * Loglike = 55489.387467
Burning in for 2000 iterations out of 5000
-2 * Loglike = 55414.402700
Burning in for 2050 iterations out of 5000
-2 * Loglike = 54477.677697
Burning in for 2100 iterations out of 5000
-2 * Loglike = 54642.345765
Burning in for 2150 iterations out of 5000
-2 * Loglike = 54104.384612
Burning in for 2200 iterations out of 5000
-2 * Loglike = 54085.013516
Burning in for 2250 iterations out of 5000
-2 * Loglike = 54499.626738
Burning in for 2300 iterations out of 5000
-2 * Loglike = 54754.213387
Burning in for 2350 iterations out of 5000
-2 * Loglike = 55705.354821
Burning in for 2400 iterations out of 5000
-2 * Loglike = 55602.410569
Burning in for 2450 iterations out of 5000
-2 * Loglike = 55262.717823
Burning in for 2500 iterations out of 5000
-2 * Loglike = 54663.706666
Burning in for 2550 iterations out of 5000
-2 * Loglike = 54087.313698
Burning in for 2600 iterations out of 5000
-2 * Loglike = 53655.571922
Burning in for 2650 iterations out of 5000
-2 * Loglike = 53567.414627
Burning in for 2700 iterations out of 5000
-2 * Loglike = 54204.382952
Burning in for 2750 iterations out of 5000
-2 * Loglike = 54638.874304
Burning in for 2800 iterations out of 5000
-2 * Loglike = 55318.196441
Burning in for 2850 iterations out of 5000
-2 * Loglike = 55983.580559
Burning in for 2900 iterations out of 5000
-2 * Loglike = 55175.057795
Burning in for 2950 iterations out of 5000
-2 * Loglike = 55486.414871
Burning in for 3000 iterations out of 5000
-2 * Loglike = 55017.028157
Burning in for 3050 iterations out of 5000
-2 * Loglike = 53820.287291
Burning in for 3100 iterations out of 5000
-2 * Loglike = 54642.436998
Burning in for 3150 iterations out of 5000
-2 * Loglike = 54598.902544
Burning in for 3200 iterations out of 5000
-2 * Loglike = 53731.724470
Burning in for 3250 iterations out of 5000
-2 * Loglike = 53803.428338
Burning in for 3300 iterations out of 5000
-2 * Loglike = 54223.798112
Burning in for 3350 iterations out of 5000
-2 * Loglike = 54425.694333
Burning in for 3400 iterations out of 5000
-2 * Loglike = 55048.968408
Burning in for 3450 iterations out of 5000
-2 * Loglike = 54795.183127
Burning in for 3500 iterations out of 5000
-2 * Loglike = 55037.512710
Burning in for 3550 iterations out of 5000
-2 * Loglike = 54684.398157
Burning in for 3600 iterations out of 5000
-2 * Loglike = 55113.172549
Burning in for 3650 iterations out of 5000
-2 * Loglike = 56326.788369
Burning in for 3700 iterations out of 5000
-2 * Loglike = 55810.685387
Burning in for 3750 iterations out of 5000
-2 * Loglike = 55969.660163
Burning in for 3800 iterations out of 5000
-2 * Loglike = 55792.740345
Burning in for 3850 iterations out of 5000
-2 * Loglike = 55289.829024
Burning in for 3900 iterations out of 5000
-2 * Loglike = 55129.935058
Burning in for 3950 iterations out of 5000
-2 * Loglike = 55399.636742
Burning in for 4000 iterations out of 5000
-2 * Loglike = 55493.639181
Burning in for 4050 iterations out of 5000
-2 * Loglike = 55274.219600
Burning in for 4100 iterations out of 5000
-2 * Loglike = 55268.672335
Burning in for 4150 iterations out of 5000
-2 * Loglike = 54703.871986
Burning in for 4200 iterations out of 5000
-2 * Loglike = 54379.691231
Burning in for 4250 iterations out of 5000
-2 * Loglike = 54203.166778
Burning in for 4300 iterations out of 5000
-2 * Loglike = 53667.357113
Burning in for 4350 iterations out of 5000
-2 * Loglike = 52646.665795
Burning in for 4400 iterations out of 5000
-2 * Loglike = 53482.042063
Burning in for 4450 iterations out of 5000
-2 * Loglike = 54340.795681
Burning in for 4500 iterations out of 5000
-2 * Loglike = 54182.826775
Burning in for 4550 iterations out of 5000
-2 * Loglike = 54235.527490
Burning in for 4600 iterations out of 5000
-2 * Loglike = 52986.195439
Burning in for 4650 iterations out of 5000
-2 * Loglike = 53116.956034
Burning in for 4700 iterations out of 5000
-2 * Loglike = 53357.000574
Burning in for 4750 iterations out of 5000
-2 * Loglike = 53839.253769
Burning in for 4800 iterations out of 5000
-2 * Loglike = 53749.260244
Burning in for 4850 iterations out of 5000
-2 * Loglike = 53751.075590
Burning in for 4900 iterations out of 5000
-2 * Loglike = 53645.462475
Burning in for 4950 iterations out of 5000
-2 * Loglike = 53875.720474
Burning in for 5000 iterations out of 5000
-2 * Loglike = 54111.888130

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 = 54169.608593
Actual update 100 of 10000, Stored update 100 of 10000
-2 * Loglike = 53282.792559
Actual update 150 of 10000, Stored update 150 of 10000
-2 * Loglike = 53193.776833
Actual update 200 of 10000, Stored update 200 of 10000
-2 * Loglike = 53596.184945
Actual update 250 of 10000, Stored update 250 of 10000
-2 * Loglike = 53403.152536
Actual update 300 of 10000, Stored update 300 of 10000
-2 * Loglike = 53630.576848
Actual update 350 of 10000, Stored update 350 of 10000
-2 * Loglike = 54347.252914
Actual update 400 of 10000, Stored update 400 of 10000
-2 * Loglike = 53077.728332
Actual update 450 of 10000, Stored update 450 of 10000
-2 * Loglike = 53846.835785
Actual update 500 of 10000, Stored update 500 of 10000
-2 * Loglike = 54907.479910
Actual update 550 of 10000, Stored update 550 of 10000
-2 * Loglike = 54568.614892
Actual update 600 of 10000, Stored update 600 of 10000
-2 * Loglike = 55073.831821
Actual update 650 of 10000, Stored update 650 of 10000
-2 * Loglike = 55191.820442
Actual update 700 of 10000, Stored update 700 of 10000
-2 * Loglike = 55472.051812
Actual update 750 of 10000, Stored update 750 of 10000
-2 * Loglike = 55780.676522
Actual update 800 of 10000, Stored update 800 of 10000
-2 * Loglike = 55738.559601
Actual update 850 of 10000, Stored update 850 of 10000
-2 * Loglike = 55587.635016
Actual update 900 of 10000, Stored update 900 of 10000
-2 * Loglike = 55563.106974
Actual update 950 of 10000, Stored update 950 of 10000
-2 * Loglike = 55226.881894
Actual update 1000 of 10000, Stored update 1000 of 10000
-2 * Loglike = 55438.166848
Actual update 1050 of 10000, Stored update 1050 of 10000
-2 * Loglike = 55420.483209
Actual update 1100 of 10000, Stored update 1100 of 10000
-2 * Loglike = 54961.271959
Actual update 1150 of 10000, Stored update 1150 of 10000
-2 * Loglike = 53789.733220
Actual update 1200 of 10000, Stored update 1200 of 10000
-2 * Loglike = 53685.677267
Actual update 1250 of 10000, Stored update 1250 of 10000
-2 * Loglike = 54450.536934
Actual update 1300 of 10000, Stored update 1300 of 10000
-2 * Loglike = 54425.911233
Actual update 1350 of 10000, Stored update 1350 of 10000
-2 * Loglike = 54953.532266
Actual update 1400 of 10000, Stored update 1400 of 10000
-2 * Loglike = 54509.206906
Actual update 1450 of 10000, Stored update 1450 of 10000
-2 * Loglike = 55110.697278
Actual update 1500 of 10000, Stored update 1500 of 10000
-2 * Loglike = 55763.999183
Actual update 1550 of 10000, Stored update 1550 of 10000
-2 * Loglike = 54638.877211
Actual update 1600 of 10000, Stored update 1600 of 10000
-2 * Loglike = 55087.418779
Actual update 1650 of 10000, Stored update 1650 of 10000
-2 * Loglike = 54818.922346
Actual update 1700 of 10000, Stored update 1700 of 10000
-2 * Loglike = 54594.989326
Actual update 1750 of 10000, Stored update 1750 of 10000
-2 * Loglike = 54510.518554
Actual update 1800 of 10000, Stored update 1800 of 10000
-2 * Loglike = 53469.888102
Actual update 1850 of 10000, Stored update 1850 of 10000
-2 * Loglike = 53061.004177
Actual update 1900 of 10000, Stored update 1900 of 10000
-2 * Loglike = 51825.479463
Actual update 1950 of 10000, Stored update 1950 of 10000
-2 * Loglike = 50082.556860
Actual update 2000 of 10000, Stored update 2000 of 10000
-2 * Loglike = 50335.499308
Actual update 2050 of 10000, Stored update 2050 of 10000
-2 * Loglike = 50956.553783
Actual update 2100 of 10000, Stored update 2100 of 10000
-2 * Loglike = 51217.140869
Actual update 2150 of 10000, Stored update 2150 of 10000
-2 * Loglike = 50914.895849
Actual update 2200 of 10000, Stored update 2200 of 10000
-2 * Loglike = 51975.644543
Actual update 2250 of 10000, Stored update 2250 of 10000
-2 * Loglike = 54304.856615
Actual update 2300 of 10000, Stored update 2300 of 10000
-2 * Loglike = 53771.322031
Actual update 2350 of 10000, Stored update 2350 of 10000
-2 * Loglike = 55000.821318
Actual update 2400 of 10000, Stored update 2400 of 10000
-2 * Loglike = 55520.038116
Actual update 2450 of 10000, Stored update 2450 of 10000
-2 * Loglike = 56112.488965
Actual update 2500 of 10000, Stored update 2500 of 10000
-2 * Loglike = 55611.158181
Actual update 2550 of 10000, Stored update 2550 of 10000
-2 * Loglike = 55254.506032
Actual update 2600 of 10000, Stored update 2600 of 10000
-2 * Loglike = 55721.041565
Actual update 2650 of 10000, Stored update 2650 of 10000
-2 * Loglike = 55953.034350
Actual update 2700 of 10000, Stored update 2700 of 10000
-2 * Loglike = 56232.167924
Actual update 2750 of 10000, Stored update 2750 of 10000
-2 * Loglike = 56050.557214
Actual update 2800 of 10000, Stored update 2800 of 10000
-2 * Loglike = 55520.359951
Actual update 2850 of 10000, Stored update 2850 of 10000
-2 * Loglike = 55762.338746
Actual update 2900 of 10000, Stored update 2900 of 10000
-2 * Loglike = 56088.856691
Actual update 2950 of 10000, Stored update 2950 of 10000
-2 * Loglike = 55599.285284
Actual update 3000 of 10000, Stored update 3000 of 10000
-2 * Loglike = 55595.548426
Actual update 3050 of 10000, Stored update 3050 of 10000
-2 * Loglike = 54458.794917
Actual update 3100 of 10000, Stored update 3100 of 10000
-2 * Loglike = 54549.283140
Actual update 3150 of 10000, Stored update 3150 of 10000
-2 * Loglike = 54422.826824
Actual update 3200 of 10000, Stored update 3200 of 10000
-2 * Loglike = 54655.812065
Actual update 3250 of 10000, Stored update 3250 of 10000
-2 * Loglike = 54405.709506
Actual update 3300 of 10000, Stored update 3300 of 10000
-2 * Loglike = 54677.593238
Actual update 3350 of 10000, Stored update 3350 of 10000
-2 * Loglike = 53794.068702
Actual update 3400 of 10000, Stored update 3400 of 10000
-2 * Loglike = 53272.233897
Actual update 3450 of 10000, Stored update 3450 of 10000
-2 * Loglike = 52299.418258
Actual update 3500 of 10000, Stored update 3500 of 10000
-2 * Loglike = 52286.922369
Actual update 3550 of 10000, Stored update 3550 of 10000
-2 * Loglike = 52498.839241
Actual update 3600 of 10000, Stored update 3600 of 10000
-2 * Loglike = 52179.565852
Actual update 3650 of 10000, Stored update 3650 of 10000
-2 * Loglike = 51408.065812
Actual update 3700 of 10000, Stored update 3700 of 10000
-2 * Loglike = 52063.165683
Actual update 3750 of 10000, Stored update 3750 of 10000
-2 * Loglike = 52180.615669
Actual update 3800 of 10000, Stored update 3800 of 10000
-2 * Loglike = 52744.274404
Actual update 3850 of 10000, Stored update 3850 of 10000
-2 * Loglike = 53844.264391
Actual update 3900 of 10000, Stored update 3900 of 10000
-2 * Loglike = 53860.013635
Actual update 3950 of 10000, Stored update 3950 of 10000
-2 * Loglike = 54279.873464
Actual update 4000 of 10000, Stored update 4000 of 10000
-2 * Loglike = 54416.071483
Actual update 4050 of 10000, Stored update 4050 of 10000
-2 * Loglike = 54246.853588
Actual update 4100 of 10000, Stored update 4100 of 10000
-2 * Loglike = 54770.465967
Actual update 4150 of 10000, Stored update 4150 of 10000
-2 * Loglike = 54415.758234
Actual update 4200 of 10000, Stored update 4200 of 10000
-2 * Loglike = 54542.219798
Actual update 4250 of 10000, Stored update 4250 of 10000
-2 * Loglike = 55170.255036
Actual update 4300 of 10000, Stored update 4300 of 10000
-2 * Loglike = 54825.811734
Actual update 4350 of 10000, Stored update 4350 of 10000
-2 * Loglike = 55801.124001
Actual update 4400 of 10000, Stored update 4400 of 10000
-2 * Loglike = 55174.497745
Actual update 4450 of 10000, Stored update 4450 of 10000
-2 * Loglike = 55386.452788
Actual update 4500 of 10000, Stored update 4500 of 10000
-2 * Loglike = 55428.936205
Actual update 4550 of 10000, Stored update 4550 of 10000
-2 * Loglike = 56272.684704
Actual update 4600 of 10000, Stored update 4600 of 10000
-2 * Loglike = 56296.995031
Actual update 4650 of 10000, Stored update 4650 of 10000
-2 * Loglike = 55430.806299
Actual update 4700 of 10000, Stored update 4700 of 10000
-2 * Loglike = 55864.841381
Actual update 4750 of 10000, Stored update 4750 of 10000
-2 * Loglike = 55672.645947
Actual update 4800 of 10000, Stored update 4800 of 10000
-2 * Loglike = 55528.303405
Actual update 4850 of 10000, Stored update 4850 of 10000
-2 * Loglike = 55433.339802
Actual update 4900 of 10000, Stored update 4900 of 10000
-2 * Loglike = 54949.488399
Actual update 4950 of 10000, Stored update 4950 of 10000
-2 * Loglike = 54687.952796
Actual update 5000 of 10000, Stored update 5000 of 10000
-2 * Loglike = 54386.206418
Actual update 5050 of 10000, Stored update 5050 of 10000
-2 * Loglike = 54800.190975
Actual update 5100 of 10000, Stored update 5100 of 10000
-2 * Loglike = 53988.882115
Actual update 5150 of 10000, Stored update 5150 of 10000
-2 * Loglike = 53101.538027
Actual update 5200 of 10000, Stored update 5200 of 10000
-2 * Loglike = 53531.754490
Actual update 5250 of 10000, Stored update 5250 of 10000
-2 * Loglike = 54188.409901
Actual update 5300 of 10000, Stored update 5300 of 10000
-2 * Loglike = 54444.864223
Actual update 5350 of 10000, Stored update 5350 of 10000
-2 * Loglike = 54245.650461
Actual update 5400 of 10000, Stored update 5400 of 10000
-2 * Loglike = 54998.015844
Actual update 5450 of 10000, Stored update 5450 of 10000
-2 * Loglike = 55274.049309
Actual update 5500 of 10000, Stored update 5500 of 10000
-2 * Loglike = 55394.207036
Actual update 5550 of 10000, Stored update 5550 of 10000
-2 * Loglike = 54885.382840
Actual update 5600 of 10000, Stored update 5600 of 10000
-2 * Loglike = 54847.689108
Actual update 5650 of 10000, Stored update 5650 of 10000
-2 * Loglike = 54517.625359
Actual update 5700 of 10000, Stored update 5700 of 10000
-2 * Loglike = 55172.390525
Actual update 5750 of 10000, Stored update 5750 of 10000
-2 * Loglike = 55462.108828
Actual update 5800 of 10000, Stored update 5800 of 10000
-2 * Loglike = 54462.680799
Actual update 5850 of 10000, Stored update 5850 of 10000
-2 * Loglike = 55500.870703
Actual update 5900 of 10000, Stored update 5900 of 10000
-2 * Loglike = 54847.238093
Actual update 5950 of 10000, Stored update 5950 of 10000
-2 * Loglike = 54273.495700
Actual update 6000 of 10000, Stored update 6000 of 10000
-2 * Loglike = 52949.100898
Actual update 6050 of 10000, Stored update 6050 of 10000
-2 * Loglike = 54792.838301
Actual update 6100 of 10000, Stored update 6100 of 10000
-2 * Loglike = 54690.028663
Actual update 6150 of 10000, Stored update 6150 of 10000
-2 * Loglike = 54100.658148
Actual update 6200 of 10000, Stored update 6200 of 10000
-2 * Loglike = 53498.657295
Actual update 6250 of 10000, Stored update 6250 of 10000
-2 * Loglike = 52750.982957
Actual update 6300 of 10000, Stored update 6300 of 10000
-2 * Loglike = 53550.718137
Actual update 6350 of 10000, Stored update 6350 of 10000
-2 * Loglike = 53636.931389
Actual update 6400 of 10000, Stored update 6400 of 10000
-2 * Loglike = 53661.360454
Actual update 6450 of 10000, Stored update 6450 of 10000
-2 * Loglike = 53310.840654
Actual update 6500 of 10000, Stored update 6500 of 10000
-2 * Loglike = 52967.461447
Actual update 6550 of 10000, Stored update 6550 of 10000
-2 * Loglike = 52862.192052
Actual update 6600 of 10000, Stored update 6600 of 10000
-2 * Loglike = 52457.738364
Actual update 6650 of 10000, Stored update 6650 of 10000
-2 * Loglike = 52977.888648
Actual update 6700 of 10000, Stored update 6700 of 10000
-2 * Loglike = 52340.960198
Actual update 6750 of 10000, Stored update 6750 of 10000
-2 * Loglike = 52478.583992
Actual update 6800 of 10000, Stored update 6800 of 10000
-2 * Loglike = 52940.680930
Actual update 6850 of 10000, Stored update 6850 of 10000
-2 * Loglike = 53586.607301
Actual update 6900 of 10000, Stored update 6900 of 10000
-2 * Loglike = 54807.051371
Actual update 6950 of 10000, Stored update 6950 of 10000
-2 * Loglike = 55036.038722
Actual update 7000 of 10000, Stored update 7000 of 10000
-2 * Loglike = 55490.069664
Actual update 7050 of 10000, Stored update 7050 of 10000
-2 * Loglike = 55328.681830
Actual update 7100 of 10000, Stored update 7100 of 10000
-2 * Loglike = 54669.560385
Actual update 7150 of 10000, Stored update 7150 of 10000
-2 * Loglike = 54960.787923
Actual update 7200 of 10000, Stored update 7200 of 10000
-2 * Loglike = 54635.008042
Actual update 7250 of 10000, Stored update 7250 of 10000
-2 * Loglike = 55829.059241
Actual update 7300 of 10000, Stored update 7300 of 10000
-2 * Loglike = 55450.578134
Actual update 7350 of 10000, Stored update 7350 of 10000
-2 * Loglike = 55686.516299
Actual update 7400 of 10000, Stored update 7400 of 10000
-2 * Loglike = 55772.357252
Actual update 7450 of 10000, Stored update 7450 of 10000
-2 * Loglike = 56051.871537
Actual update 7500 of 10000, Stored update 7500 of 10000
-2 * Loglike = 56404.483422
Actual update 7550 of 10000, Stored update 7550 of 10000
-2 * Loglike = 56669.813516
Actual update 7600 of 10000, Stored update 7600 of 10000
-2 * Loglike = 55693.349359
Actual update 7650 of 10000, Stored update 7650 of 10000
-2 * Loglike = 55968.557554
Actual update 7700 of 10000, Stored update 7700 of 10000
-2 * Loglike = 55467.977013
Actual update 7750 of 10000, Stored update 7750 of 10000
-2 * Loglike = 55023.129899
Actual update 7800 of 10000, Stored update 7800 of 10000
-2 * Loglike = 55786.304706
Actual update 7850 of 10000, Stored update 7850 of 10000
-2 * Loglike = 55879.746569
Actual update 7900 of 10000, Stored update 7900 of 10000
-2 * Loglike = 56093.590188
Actual update 7950 of 10000, Stored update 7950 of 10000
-2 * Loglike = 55638.405231
Actual update 8000 of 10000, Stored update 8000 of 10000
-2 * Loglike = 55280.285036
Actual update 8050 of 10000, Stored update 8050 of 10000
-2 * Loglike = 55496.604294
Actual update 8100 of 10000, Stored update 8100 of 10000
-2 * Loglike = 55478.387374
Actual update 8150 of 10000, Stored update 8150 of 10000
-2 * Loglike = 55063.237330
Actual update 8200 of 10000, Stored update 8200 of 10000
-2 * Loglike = 54181.036186
Actual update 8250 of 10000, Stored update 8250 of 10000
-2 * Loglike = 53688.842651
Actual update 8300 of 10000, Stored update 8300 of 10000
-2 * Loglike = 55053.638590
Actual update 8350 of 10000, Stored update 8350 of 10000
-2 * Loglike = 55134.684109
Actual update 8400 of 10000, Stored update 8400 of 10000
-2 * Loglike = 54419.244078
Actual update 8450 of 10000, Stored update 8450 of 10000
-2 * Loglike = 55665.924605
Actual update 8500 of 10000, Stored update 8500 of 10000
-2 * Loglike = 55371.836464
Actual update 8550 of 10000, Stored update 8550 of 10000
-2 * Loglike = 55168.531273
Actual update 8600 of 10000, Stored update 8600 of 10000
-2 * Loglike = 54946.903013
Actual update 8650 of 10000, Stored update 8650 of 10000
-2 * Loglike = 54837.981975
Actual update 8700 of 10000, Stored update 8700 of 10000
-2 * Loglike = 55396.441708
Actual update 8750 of 10000, Stored update 8750 of 10000
-2 * Loglike = 55794.982388
Actual update 8800 of 10000, Stored update 8800 of 10000
-2 * Loglike = 55869.036725
Actual update 8850 of 10000, Stored update 8850 of 10000
-2 * Loglike = 54939.513266
Actual update 8900 of 10000, Stored update 8900 of 10000
-2 * Loglike = 54665.891054
Actual update 8950 of 10000, Stored update 8950 of 10000
-2 * Loglike = 55568.316334
Actual update 9000 of 10000, Stored update 9000 of 10000
-2 * Loglike = 55915.883037
Actual update 9050 of 10000, Stored update 9050 of 10000
-2 * Loglike = 55550.257864
Actual update 9100 of 10000, Stored update 9100 of 10000
-2 * Loglike = 54721.112223
Actual update 9150 of 10000, Stored update 9150 of 10000
-2 * Loglike = 55607.606581
Actual update 9200 of 10000, Stored update 9200 of 10000
-2 * Loglike = 55571.831874
Actual update 9250 of 10000, Stored update 9250 of 10000
-2 * Loglike = 56110.757409
Actual update 9300 of 10000, Stored update 9300 of 10000
-2 * Loglike = 55988.658868
Actual update 9350 of 10000, Stored update 9350 of 10000
-2 * Loglike = 55365.510696
Actual update 9400 of 10000, Stored update 9400 of 10000
-2 * Loglike = 55368.254817
Actual update 9450 of 10000, Stored update 9450 of 10000
-2 * Loglike = 55642.829113
Actual update 9500 of 10000, Stored update 9500 of 10000
-2 * Loglike = 55574.262927
Actual update 9550 of 10000, Stored update 9550 of 10000
-2 * Loglike = 53874.480477
Actual update 9600 of 10000, Stored update 9600 of 10000
-2 * Loglike = 53413.247275
Actual update 9650 of 10000, Stored update 9650 of 10000
-2 * Loglike = 54269.948724
Actual update 9700 of 10000, Stored update 9700 of 10000
-2 * Loglike = 53767.650438
Actual update 9750 of 10000, Stored update 9750 of 10000
-2 * Loglike = 53849.919272
Actual update 9800 of 10000, Stored update 9800 of 10000
-2 * Loglike = 53175.518883
Actual update 9850 of 10000, Stored update 9850 of 10000
-2 * Loglike = 53887.670090
Actual update 9900 of 10000, Stored update 9900 of 10000
-2 * Loglike = 52985.733185
Actual update 9950 of 10000, Stored update 9950 of 10000
-2 * Loglike = 51976.256832
Actual update 10000 of 10000, Stored update 10000 of 10000
-2 * Loglike = 52367.350150
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =          10000
Average =          54511.
S.D.    =          1251.8
S.E.M.  =          12.518

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.09)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 98.09s 
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   1.94661     0.11789      1.71556     2.17766 
load1_biol_r3     0.84783     0.11285      0.62664     1.06902 
load1_biol_r4     1.85662     0.15815      1.54665     2.16659 
load1_phys_core   2.00490     0.12350      1.76284     2.24695 
load1_phys_r2     1.85801     0.15803      1.54828     2.16775 
--------------------------------------------------------------------------------------------------- 
The estimates of factor 2 loadings:
                     Coef.   Std. Err.   [95% Conf.   Interval] 
load2_es_core      0.00000     0.00000      0.00000     0.00000 
load2_biol_core    1.00000     0.00000      1.00000     1.00000 
load2_biol_r3     10.74801     6.50724     -2.00596    23.50197 
load2_biol_r4     33.81855    11.51442     11.25071    56.38639 
load2_phys_core   13.61835     4.77691      4.25578    22.98092 
load2_phys_r2     58.87974    20.16710     19.35295    98.40653 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.50659     0.05187      0.40492     0.60825 
cov_fact2_fact1   0.00000     0.00000      0.00000     0.00000 
var_fact2         0.00076     0.00044     -0.00010     0.00162 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39365     0.03176  264.29          0  ***     8.33162     8.45567   3002 
Intercept_biol_core   7.06567     0.03755  188.15          0  ***     6.99162     7.13885   1465 
Intercept_biol_r3     6.89392     0.06460  106.71          0  ***     6.76609     7.02043   2924 
Intercept_biol_r4     5.67566     0.07628   74.40          0  ***     5.52709     5.82745   1860 
Intercept_phys_core   7.21142     0.04246  169.85          0  ***     7.12938     7.29462   1487 
Intercept_phys_r2     6.31351     0.06184  102.09          0  ***     6.19272     6.43344    752 
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     1.93819     0.06264      1.81948     2.06437   1415 
var_Intercept_biol_core   1.43538     0.10882      1.22143     1.64743    271 
var_Intercept_biol_r3     4.71676     0.20490      4.32101     5.12232   1672 
var_Intercept_biol_r4     5.29785     0.42448      4.17574     5.96178     62 
var_Intercept_phys_core   2.11018     0.10445      1.90135     2.31178    430 
var_Intercept_phys_r2     1.60486     0.72664      0.38473     3.00327     15 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> loads <- mymodel@fact.chains$loadings
> 
> sixway(loads[, "load2_biol_r3", drop = FALSE], acf.maxlag = 500, name = "load2.3")
> 
> # 20.7 Correlated factor . . . . . . . . . . . . . . . . . . . . . . . .319
> 
> nfact <- 2
> lev.fact <- c(1, 1)
> nfactcor <- 1
> factcor <- c(1, 2, 0, 0)
> # see FACT in the MCMC manual
> loading <- matrix(c(1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1), ncol = 7, nrow = nfact, byrow = TRUE)
> constr <- matrix(c(1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0), ncol = 7, nrow = nfact, byrow = TRUE)
> 
> (mymodel <- runMLwiN(c(es_core, biol_core, biol_r3, biol_r4, phys_core, phys_r2) ~ 1 + (1 | student), D = "Multivariate Normal", 
+   estoptions = list(EstM = 1, fact = list(nfact = nfact, lev.fact = lev.fact, nfactcor = nfactcor, factcor = factcor, 
+     loading = loading, constr = constr), mcmcMeth = list(burnin = 5000, iterations = 10000)), data = hungary1))
MLwiN is running, please wait......
/nogui option ignored
ECHO    0


Echoing is ON
BATC 1

Batch mode is ON
MAXI 2
STAR
iteration 0
iteration 1

Convergence achieved
TOLE 2
MAXI 20
BATC 1

Batch mode is ON
NEXT
iteration 2

Convergence achieved
ECHO 0

Echoing is ON
MCMC   0 5000 1 5.8 50 10 G30[1] G30[2]  1 1 1 1 1 4
RUNNING ADAPTIVE PROCEDURE AND BURNING IN...
Adapting finished and took 100 iterations
Adapting took 100 iterations
Burning in for 50 iterations out of 5000
-2 * Loglike = 56046.655489
Burning in for 100 iterations out of 5000
-2 * Loglike = 56370.226602
Burning in for 150 iterations out of 5000
-2 * Loglike = 56107.720191
Burning in for 200 iterations out of 5000
-2 * Loglike = 56352.476724
Burning in for 250 iterations out of 5000
-2 * Loglike = 55950.225148
Burning in for 300 iterations out of 5000
-2 * Loglike = 56202.839601
Burning in for 350 iterations out of 5000
-2 * Loglike = 56419.376436
Burning in for 400 iterations out of 5000
-2 * Loglike = 56135.463189
Burning in for 450 iterations out of 5000
-2 * Loglike = 56138.968813
Burning in for 500 iterations out of 5000
-2 * Loglike = 56327.818375
Burning in for 550 iterations out of 5000
-2 * Loglike = 55614.457989
Burning in for 600 iterations out of 5000
-2 * Loglike = 55670.766595
Burning in for 650 iterations out of 5000
-2 * Loglike = 55994.235559
Burning in for 700 iterations out of 5000
-2 * Loglike = 56414.060911
Burning in for 750 iterations out of 5000
-2 * Loglike = 56301.817206
Burning in for 800 iterations out of 5000
-2 * Loglike = 56148.841359
Burning in for 850 iterations out of 5000
-2 * Loglike = 56201.710534
Burning in for 900 iterations out of 5000
-2 * Loglike = 55975.391927
Burning in for 950 iterations out of 5000
-2 * Loglike = 56012.414969
Burning in for 1000 iterations out of 5000
-2 * Loglike = 56019.125985
Burning in for 1050 iterations out of 5000
-2 * Loglike = 55427.967658
Burning in for 1100 iterations out of 5000
-2 * Loglike = 56044.845875
Burning in for 1150 iterations out of 5000
-2 * Loglike = 55993.904041
Burning in for 1200 iterations out of 5000
-2 * Loglike = 56134.082138
Burning in for 1250 iterations out of 5000
-2 * Loglike = 55955.489297
Burning in for 1300 iterations out of 5000
-2 * Loglike = 56187.869450
Burning in for 1350 iterations out of 5000
-2 * Loglike = 55957.644734
Burning in for 1400 iterations out of 5000
-2 * Loglike = 56385.212361
Burning in for 1450 iterations out of 5000
-2 * Loglike = 56350.980259
Burning in for 1500 iterations out of 5000
-2 * Loglike = 56140.516472
Burning in for 1550 iterations out of 5000
-2 * Loglike = 56026.419659
Burning in for 1600 iterations out of 5000
-2 * Loglike = 56603.350116
Burning in for 1650 iterations out of 5000
-2 * Loglike = 55841.634327
Burning in for 1700 iterations out of 5000
-2 * Loglike = 55086.849945
Burning in for 1750 iterations out of 5000
-2 * Loglike = 55081.682175
Burning in for 1800 iterations out of 5000
-2 * Loglike = 55707.393540
Burning in for 1850 iterations out of 5000
-2 * Loglike = 55268.287144
Burning in for 1900 iterations out of 5000
-2 * Loglike = 56169.975765
Burning in for 1950 iterations out of 5000
-2 * Loglike = 56314.628671
Burning in for 2000 iterations out of 5000
-2 * Loglike = 55942.258265
Burning in for 2050 iterations out of 5000
-2 * Loglike = 55935.894116
Burning in for 2100 iterations out of 5000
-2 * Loglike = 56254.658980
Burning in for 2150 iterations out of 5000
-2 * Loglike = 55762.490026
Burning in for 2200 iterations out of 5000
-2 * Loglike = 55252.513096
Burning in for 2250 iterations out of 5000
-2 * Loglike = 55234.068170
Burning in for 2300 iterations out of 5000
-2 * Loglike = 55264.979000
Burning in for 2350 iterations out of 5000
-2 * Loglike = 55741.178969
Burning in for 2400 iterations out of 5000
-2 * Loglike = 55943.635295
Burning in for 2450 iterations out of 5000
-2 * Loglike = 55847.220705
Burning in for 2500 iterations out of 5000
-2 * Loglike = 55477.798697
Burning in for 2550 iterations out of 5000
-2 * Loglike = 56014.749033
Burning in for 2600 iterations out of 5000
-2 * Loglike = 55312.714332
Burning in for 2650 iterations out of 5000
-2 * Loglike = 55884.391065
Burning in for 2700 iterations out of 5000
-2 * Loglike = 55990.589214
Burning in for 2750 iterations out of 5000
-2 * Loglike = 56331.979882
Burning in for 2800 iterations out of 5000
-2 * Loglike = 55540.017666
Burning in for 2850 iterations out of 5000
-2 * Loglike = 55227.295843
Burning in for 2900 iterations out of 5000
-2 * Loglike = 55478.108096
Burning in for 2950 iterations out of 5000
-2 * Loglike = 55474.073303
Burning in for 3000 iterations out of 5000
-2 * Loglike = 55516.436675
Burning in for 3050 iterations out of 5000
-2 * Loglike = 56117.058996
Burning in for 3100 iterations out of 5000
-2 * Loglike = 55724.207237
Burning in for 3150 iterations out of 5000
-2 * Loglike = 55539.770789
Burning in for 3200 iterations out of 5000
-2 * Loglike = 55870.638130
Burning in for 3250 iterations out of 5000
-2 * Loglike = 56091.231094
Burning in for 3300 iterations out of 5000
-2 * Loglike = 55905.410512
Burning in for 3350 iterations out of 5000
-2 * Loglike = 55884.368192
Burning in for 3400 iterations out of 5000
-2 * Loglike = 55375.623393
Burning in for 3450 iterations out of 5000
-2 * Loglike = 55703.924397
Burning in for 3500 iterations out of 5000
-2 * Loglike = 55781.389645
Burning in for 3550 iterations out of 5000
-2 * Loglike = 55689.172841
Burning in for 3600 iterations out of 5000
-2 * Loglike = 55896.440308
Burning in for 3650 iterations out of 5000
-2 * Loglike = 56392.100054
Burning in for 3700 iterations out of 5000
-2 * Loglike = 55864.906415
Burning in for 3750 iterations out of 5000
-2 * Loglike = 55962.735815
Burning in for 3800 iterations out of 5000
-2 * Loglike = 56030.674812
Burning in for 3850 iterations out of 5000
-2 * Loglike = 55647.299478
Burning in for 3900 iterations out of 5000
-2 * Loglike = 55091.644698
Burning in for 3950 iterations out of 5000
-2 * Loglike = 56118.150687
Burning in for 4000 iterations out of 5000
-2 * Loglike = 55969.795746
Burning in for 4050 iterations out of 5000
-2 * Loglike = 56029.118796
Burning in for 4100 iterations out of 5000
-2 * Loglike = 55826.679666
Burning in for 4150 iterations out of 5000
-2 * Loglike = 55654.247844
Burning in for 4200 iterations out of 5000
-2 * Loglike = 55965.528034
Burning in for 4250 iterations out of 5000
-2 * Loglike = 56289.773445
Burning in for 4300 iterations out of 5000
-2 * Loglike = 56016.539480
Burning in for 4350 iterations out of 5000
-2 * Loglike = 56256.622041
Burning in for 4400 iterations out of 5000
-2 * Loglike = 55845.279877
Burning in for 4450 iterations out of 5000
-2 * Loglike = 55736.112311
Burning in for 4500 iterations out of 5000
-2 * Loglike = 56050.013366
Burning in for 4550 iterations out of 5000
-2 * Loglike = 55955.492400
Burning in for 4600 iterations out of 5000
-2 * Loglike = 56144.125785
Burning in for 4650 iterations out of 5000
-2 * Loglike = 56367.136053
Burning in for 4700 iterations out of 5000
-2 * Loglike = 56080.809143
Burning in for 4750 iterations out of 5000
-2 * Loglike = 56263.731507
Burning in for 4800 iterations out of 5000
-2 * Loglike = 55970.400956
Burning in for 4850 iterations out of 5000
-2 * Loglike = 55620.822361
Burning in for 4900 iterations out of 5000
-2 * Loglike = 56448.514633
Burning in for 4950 iterations out of 5000
-2 * Loglike = 55936.068870
Burning in for 5000 iterations out of 5000
-2 * Loglike = 56377.106035

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 = 55454.141850
Actual update 100 of 10000, Stored update 100 of 10000
-2 * Loglike = 56017.784818
Actual update 150 of 10000, Stored update 150 of 10000
-2 * Loglike = 56491.265373
Actual update 200 of 10000, Stored update 200 of 10000
-2 * Loglike = 56151.470456
Actual update 250 of 10000, Stored update 250 of 10000
-2 * Loglike = 55428.374515
Actual update 300 of 10000, Stored update 300 of 10000
-2 * Loglike = 55913.253923
Actual update 350 of 10000, Stored update 350 of 10000
-2 * Loglike = 56388.212609
Actual update 400 of 10000, Stored update 400 of 10000
-2 * Loglike = 55885.556360
Actual update 450 of 10000, Stored update 450 of 10000
-2 * Loglike = 55883.201773
Actual update 500 of 10000, Stored update 500 of 10000
-2 * Loglike = 56068.650984
Actual update 550 of 10000, Stored update 550 of 10000
-2 * Loglike = 56226.785403
Actual update 600 of 10000, Stored update 600 of 10000
-2 * Loglike = 56103.006784
Actual update 650 of 10000, Stored update 650 of 10000
-2 * Loglike = 55650.702520
Actual update 700 of 10000, Stored update 700 of 10000
-2 * Loglike = 56285.416760
Actual update 750 of 10000, Stored update 750 of 10000
-2 * Loglike = 56384.153063
Actual update 800 of 10000, Stored update 800 of 10000
-2 * Loglike = 55669.965869
Actual update 850 of 10000, Stored update 850 of 10000
-2 * Loglike = 55670.249814
Actual update 900 of 10000, Stored update 900 of 10000
-2 * Loglike = 55973.490221
Actual update 950 of 10000, Stored update 950 of 10000
-2 * Loglike = 56012.425063
Actual update 1000 of 10000, Stored update 1000 of 10000
-2 * Loglike = 55960.231175
Actual update 1050 of 10000, Stored update 1050 of 10000
-2 * Loglike = 55925.799243
Actual update 1100 of 10000, Stored update 1100 of 10000
-2 * Loglike = 56087.867753
Actual update 1150 of 10000, Stored update 1150 of 10000
-2 * Loglike = 56226.138502
Actual update 1200 of 10000, Stored update 1200 of 10000
-2 * Loglike = 55509.659568
Actual update 1250 of 10000, Stored update 1250 of 10000
-2 * Loglike = 55517.350566
Actual update 1300 of 10000, Stored update 1300 of 10000
-2 * Loglike = 55468.984246
Actual update 1350 of 10000, Stored update 1350 of 10000
-2 * Loglike = 55536.115565
Actual update 1400 of 10000, Stored update 1400 of 10000
-2 * Loglike = 55984.069260
Actual update 1450 of 10000, Stored update 1450 of 10000
-2 * Loglike = 55489.885422
Actual update 1500 of 10000, Stored update 1500 of 10000
-2 * Loglike = 55208.794102
Actual update 1550 of 10000, Stored update 1550 of 10000
-2 * Loglike = 55273.045750
Actual update 1600 of 10000, Stored update 1600 of 10000
-2 * Loglike = 55426.854471
Actual update 1650 of 10000, Stored update 1650 of 10000
-2 * Loglike = 55234.677590
Actual update 1700 of 10000, Stored update 1700 of 10000
-2 * Loglike = 55983.445288
Actual update 1750 of 10000, Stored update 1750 of 10000
-2 * Loglike = 55598.433424
Actual update 1800 of 10000, Stored update 1800 of 10000
-2 * Loglike = 55863.052635
Actual update 1850 of 10000, Stored update 1850 of 10000
-2 * Loglike = 56378.427980
Actual update 1900 of 10000, Stored update 1900 of 10000
-2 * Loglike = 55957.868209
Actual update 1950 of 10000, Stored update 1950 of 10000
-2 * Loglike = 56222.835593
Actual update 2000 of 10000, Stored update 2000 of 10000
-2 * Loglike = 55587.844341
Actual update 2050 of 10000, Stored update 2050 of 10000
-2 * Loglike = 55599.544863
Actual update 2100 of 10000, Stored update 2100 of 10000
-2 * Loglike = 55332.468097
Actual update 2150 of 10000, Stored update 2150 of 10000
-2 * Loglike = 55300.023918
Actual update 2200 of 10000, Stored update 2200 of 10000
-2 * Loglike = 56341.502941
Actual update 2250 of 10000, Stored update 2250 of 10000
-2 * Loglike = 56133.166622
Actual update 2300 of 10000, Stored update 2300 of 10000
-2 * Loglike = 56129.614270
Actual update 2350 of 10000, Stored update 2350 of 10000
-2 * Loglike = 56175.891683
Actual update 2400 of 10000, Stored update 2400 of 10000
-2 * Loglike = 56301.573921
Actual update 2450 of 10000, Stored update 2450 of 10000
-2 * Loglike = 56324.576638
Actual update 2500 of 10000, Stored update 2500 of 10000
-2 * Loglike = 56239.660826
Actual update 2550 of 10000, Stored update 2550 of 10000
-2 * Loglike = 56130.514706
Actual update 2600 of 10000, Stored update 2600 of 10000
-2 * Loglike = 56262.267256
Actual update 2650 of 10000, Stored update 2650 of 10000
-2 * Loglike = 56127.956057
Actual update 2700 of 10000, Stored update 2700 of 10000
-2 * Loglike = 55947.325887
Actual update 2750 of 10000, Stored update 2750 of 10000
-2 * Loglike = 56524.798157
Actual update 2800 of 10000, Stored update 2800 of 10000
-2 * Loglike = 56337.735182
Actual update 2850 of 10000, Stored update 2850 of 10000
-2 * Loglike = 55624.694693
Actual update 2900 of 10000, Stored update 2900 of 10000
-2 * Loglike = 55998.693188
Actual update 2950 of 10000, Stored update 2950 of 10000
-2 * Loglike = 56284.230313
Actual update 3000 of 10000, Stored update 3000 of 10000
-2 * Loglike = 55503.466500
Actual update 3050 of 10000, Stored update 3050 of 10000
-2 * Loglike = 56452.336126
Actual update 3100 of 10000, Stored update 3100 of 10000
-2 * Loglike = 55876.221675
Actual update 3150 of 10000, Stored update 3150 of 10000
-2 * Loglike = 56163.695486
Actual update 3200 of 10000, Stored update 3200 of 10000
-2 * Loglike = 56427.295155
Actual update 3250 of 10000, Stored update 3250 of 10000
-2 * Loglike = 56478.368633
Actual update 3300 of 10000, Stored update 3300 of 10000
-2 * Loglike = 56190.307217
Actual update 3350 of 10000, Stored update 3350 of 10000
-2 * Loglike = 56218.053892
Actual update 3400 of 10000, Stored update 3400 of 10000
-2 * Loglike = 56148.503590
Actual update 3450 of 10000, Stored update 3450 of 10000
-2 * Loglike = 56416.314938
Actual update 3500 of 10000, Stored update 3500 of 10000
-2 * Loglike = 56535.514372
Actual update 3550 of 10000, Stored update 3550 of 10000
-2 * Loglike = 56061.994322
Actual update 3600 of 10000, Stored update 3600 of 10000
-2 * Loglike = 55161.477668
Actual update 3650 of 10000, Stored update 3650 of 10000
-2 * Loglike = 55455.447110
Actual update 3700 of 10000, Stored update 3700 of 10000
-2 * Loglike = 55523.691409
Actual update 3750 of 10000, Stored update 3750 of 10000
-2 * Loglike = 55529.949364
Actual update 3800 of 10000, Stored update 3800 of 10000
-2 * Loglike = 55861.511702
Actual update 3850 of 10000, Stored update 3850 of 10000
-2 * Loglike = 55415.632619
Actual update 3900 of 10000, Stored update 3900 of 10000
-2 * Loglike = 55375.197068
Actual update 3950 of 10000, Stored update 3950 of 10000
-2 * Loglike = 56287.238135
Actual update 4000 of 10000, Stored update 4000 of 10000
-2 * Loglike = 55504.288766
Actual update 4050 of 10000, Stored update 4050 of 10000
-2 * Loglike = 56078.613118
Actual update 4100 of 10000, Stored update 4100 of 10000
-2 * Loglike = 56661.610153
Actual update 4150 of 10000, Stored update 4150 of 10000
-2 * Loglike = 56224.556457
Actual update 4200 of 10000, Stored update 4200 of 10000
-2 * Loglike = 55472.359512
Actual update 4250 of 10000, Stored update 4250 of 10000
-2 * Loglike = 56387.312433
Actual update 4300 of 10000, Stored update 4300 of 10000
-2 * Loglike = 56103.173694
Actual update 4350 of 10000, Stored update 4350 of 10000
-2 * Loglike = 55807.919249
Actual update 4400 of 10000, Stored update 4400 of 10000
-2 * Loglike = 55737.940899
Actual update 4450 of 10000, Stored update 4450 of 10000
-2 * Loglike = 55721.880379
Actual update 4500 of 10000, Stored update 4500 of 10000
-2 * Loglike = 55472.046332
Actual update 4550 of 10000, Stored update 4550 of 10000
-2 * Loglike = 55773.751557
Actual update 4600 of 10000, Stored update 4600 of 10000
-2 * Loglike = 55307.834113
Actual update 4650 of 10000, Stored update 4650 of 10000
-2 * Loglike = 55487.705374
Actual update 4700 of 10000, Stored update 4700 of 10000
-2 * Loglike = 56118.565277
Actual update 4750 of 10000, Stored update 4750 of 10000
-2 * Loglike = 56205.582210
Actual update 4800 of 10000, Stored update 4800 of 10000
-2 * Loglike = 56440.882966
Actual update 4850 of 10000, Stored update 4850 of 10000
-2 * Loglike = 55947.346203
Actual update 4900 of 10000, Stored update 4900 of 10000
-2 * Loglike = 55662.130674
Actual update 4950 of 10000, Stored update 4950 of 10000
-2 * Loglike = 56218.011475
Actual update 5000 of 10000, Stored update 5000 of 10000
-2 * Loglike = 55613.859062
Actual update 5050 of 10000, Stored update 5050 of 10000
-2 * Loglike = 55510.434984
Actual update 5100 of 10000, Stored update 5100 of 10000
-2 * Loglike = 55762.480428
Actual update 5150 of 10000, Stored update 5150 of 10000
-2 * Loglike = 55634.931310
Actual update 5200 of 10000, Stored update 5200 of 10000
-2 * Loglike = 56115.413176
Actual update 5250 of 10000, Stored update 5250 of 10000
-2 * Loglike = 56115.327237
Actual update 5300 of 10000, Stored update 5300 of 10000
-2 * Loglike = 55778.926968
Actual update 5350 of 10000, Stored update 5350 of 10000
-2 * Loglike = 55347.130909
Actual update 5400 of 10000, Stored update 5400 of 10000
-2 * Loglike = 55259.819746
Actual update 5450 of 10000, Stored update 5450 of 10000
-2 * Loglike = 55893.898291
Actual update 5500 of 10000, Stored update 5500 of 10000
-2 * Loglike = 56002.522640
Actual update 5550 of 10000, Stored update 5550 of 10000
-2 * Loglike = 55379.898223
Actual update 5600 of 10000, Stored update 5600 of 10000
-2 * Loglike = 55301.895653
Actual update 5650 of 10000, Stored update 5650 of 10000
-2 * Loglike = 55039.648604
Actual update 5700 of 10000, Stored update 5700 of 10000
-2 * Loglike = 55466.740005
Actual update 5750 of 10000, Stored update 5750 of 10000
-2 * Loglike = 55684.125513
Actual update 5800 of 10000, Stored update 5800 of 10000
-2 * Loglike = 55394.964482
Actual update 5850 of 10000, Stored update 5850 of 10000
-2 * Loglike = 55845.610484
Actual update 5900 of 10000, Stored update 5900 of 10000
-2 * Loglike = 55376.171561
Actual update 5950 of 10000, Stored update 5950 of 10000
-2 * Loglike = 54534.060405
Actual update 6000 of 10000, Stored update 6000 of 10000
-2 * Loglike = 54826.438200
Actual update 6050 of 10000, Stored update 6050 of 10000
-2 * Loglike = 55190.905469
Actual update 6100 of 10000, Stored update 6100 of 10000
-2 * Loglike = 56118.746153
Actual update 6150 of 10000, Stored update 6150 of 10000
-2 * Loglike = 55808.975946
Actual update 6200 of 10000, Stored update 6200 of 10000
-2 * Loglike = 56389.128289
Actual update 6250 of 10000, Stored update 6250 of 10000
-2 * Loglike = 55827.456736
Actual update 6300 of 10000, Stored update 6300 of 10000
-2 * Loglike = 55483.111468
Actual update 6350 of 10000, Stored update 6350 of 10000
-2 * Loglike = 55516.291302
Actual update 6400 of 10000, Stored update 6400 of 10000
-2 * Loglike = 55864.638940
Actual update 6450 of 10000, Stored update 6450 of 10000
-2 * Loglike = 55558.892570
Actual update 6500 of 10000, Stored update 6500 of 10000
-2 * Loglike = 56026.497520
Actual update 6550 of 10000, Stored update 6550 of 10000
-2 * Loglike = 56063.801983
Actual update 6600 of 10000, Stored update 6600 of 10000
-2 * Loglike = 55398.547475
Actual update 6650 of 10000, Stored update 6650 of 10000
-2 * Loglike = 55943.759067
Actual update 6700 of 10000, Stored update 6700 of 10000
-2 * Loglike = 56059.439752
Actual update 6750 of 10000, Stored update 6750 of 10000
-2 * Loglike = 55509.814345
Actual update 6800 of 10000, Stored update 6800 of 10000
-2 * Loglike = 56133.466669
Actual update 6850 of 10000, Stored update 6850 of 10000
-2 * Loglike = 55654.375992
Actual update 6900 of 10000, Stored update 6900 of 10000
-2 * Loglike = 56275.610007
Actual update 6950 of 10000, Stored update 6950 of 10000
-2 * Loglike = 55795.027732
Actual update 7000 of 10000, Stored update 7000 of 10000
-2 * Loglike = 55759.356934
Actual update 7050 of 10000, Stored update 7050 of 10000
-2 * Loglike = 55712.738757
Actual update 7100 of 10000, Stored update 7100 of 10000
-2 * Loglike = 55902.559490
Actual update 7150 of 10000, Stored update 7150 of 10000
-2 * Loglike = 56199.163515
Actual update 7200 of 10000, Stored update 7200 of 10000
-2 * Loglike = 56018.965019
Actual update 7250 of 10000, Stored update 7250 of 10000
-2 * Loglike = 56378.316032
Actual update 7300 of 10000, Stored update 7300 of 10000
-2 * Loglike = 55954.202830
Actual update 7350 of 10000, Stored update 7350 of 10000
-2 * Loglike = 56004.095175
Actual update 7400 of 10000, Stored update 7400 of 10000
-2 * Loglike = 55455.447277
Actual update 7450 of 10000, Stored update 7450 of 10000
-2 * Loglike = 55503.517193
Actual update 7500 of 10000, Stored update 7500 of 10000
-2 * Loglike = 56197.920748
Actual update 7550 of 10000, Stored update 7550 of 10000
-2 * Loglike = 55906.733918
Actual update 7600 of 10000, Stored update 7600 of 10000
-2 * Loglike = 56145.199280
Actual update 7650 of 10000, Stored update 7650 of 10000
-2 * Loglike = 56204.402845
Actual update 7700 of 10000, Stored update 7700 of 10000
-2 * Loglike = 55662.962908
Actual update 7750 of 10000, Stored update 7750 of 10000
-2 * Loglike = 55918.721141
Actual update 7800 of 10000, Stored update 7800 of 10000
-2 * Loglike = 55614.319117
Actual update 7850 of 10000, Stored update 7850 of 10000
-2 * Loglike = 56060.125718
Actual update 7900 of 10000, Stored update 7900 of 10000
-2 * Loglike = 56321.590604
Actual update 7950 of 10000, Stored update 7950 of 10000
-2 * Loglike = 55854.856205
Actual update 8000 of 10000, Stored update 8000 of 10000
-2 * Loglike = 55507.063908
Actual update 8050 of 10000, Stored update 8050 of 10000
-2 * Loglike = 55516.446203
Actual update 8100 of 10000, Stored update 8100 of 10000
-2 * Loglike = 55543.335649
Actual update 8150 of 10000, Stored update 8150 of 10000
-2 * Loglike = 55862.654688
Actual update 8200 of 10000, Stored update 8200 of 10000
-2 * Loglike = 55625.750952
Actual update 8250 of 10000, Stored update 8250 of 10000
-2 * Loglike = 55213.364230
Actual update 8300 of 10000, Stored update 8300 of 10000
-2 * Loglike = 55587.002791
Actual update 8350 of 10000, Stored update 8350 of 10000
-2 * Loglike = 55762.402672
Actual update 8400 of 10000, Stored update 8400 of 10000
-2 * Loglike = 55763.900518
Actual update 8450 of 10000, Stored update 8450 of 10000
-2 * Loglike = 56107.541458
Actual update 8500 of 10000, Stored update 8500 of 10000
-2 * Loglike = 55588.073311
Actual update 8550 of 10000, Stored update 8550 of 10000
-2 * Loglike = 55816.193946
Actual update 8600 of 10000, Stored update 8600 of 10000
-2 * Loglike = 55751.546094
Actual update 8650 of 10000, Stored update 8650 of 10000
-2 * Loglike = 56035.280251
Actual update 8700 of 10000, Stored update 8700 of 10000
-2 * Loglike = 55547.184918
Actual update 8750 of 10000, Stored update 8750 of 10000
-2 * Loglike = 56164.297204
Actual update 8800 of 10000, Stored update 8800 of 10000
-2 * Loglike = 55520.251686
Actual update 8850 of 10000, Stored update 8850 of 10000
-2 * Loglike = 55838.286866
Actual update 8900 of 10000, Stored update 8900 of 10000
-2 * Loglike = 55806.185395
Actual update 8950 of 10000, Stored update 8950 of 10000
-2 * Loglike = 56211.580115
Actual update 9000 of 10000, Stored update 9000 of 10000
-2 * Loglike = 55861.302598
Actual update 9050 of 10000, Stored update 9050 of 10000
-2 * Loglike = 55956.426840
Actual update 9100 of 10000, Stored update 9100 of 10000
-2 * Loglike = 56143.382060
Actual update 9150 of 10000, Stored update 9150 of 10000
-2 * Loglike = 55918.959917
Actual update 9200 of 10000, Stored update 9200 of 10000
-2 * Loglike = 55985.020726
Actual update 9250 of 10000, Stored update 9250 of 10000
-2 * Loglike = 56093.928544
Actual update 9300 of 10000, Stored update 9300 of 10000
-2 * Loglike = 55612.206055
Actual update 9350 of 10000, Stored update 9350 of 10000
-2 * Loglike = 56281.192943
Actual update 9400 of 10000, Stored update 9400 of 10000
-2 * Loglike = 56030.218409
Actual update 9450 of 10000, Stored update 9450 of 10000
-2 * Loglike = 56070.738812
Actual update 9500 of 10000, Stored update 9500 of 10000
-2 * Loglike = 56408.295127
Actual update 9550 of 10000, Stored update 9550 of 10000
-2 * Loglike = 55791.877444
Actual update 9600 of 10000, Stored update 9600 of 10000
-2 * Loglike = 55629.766179
Actual update 9650 of 10000, Stored update 9650 of 10000
-2 * Loglike = 55902.494673
Actual update 9700 of 10000, Stored update 9700 of 10000
-2 * Loglike = 56357.056072
Actual update 9750 of 10000, Stored update 9750 of 10000
-2 * Loglike = 56434.003235
Actual update 9800 of 10000, Stored update 9800 of 10000
-2 * Loglike = 56237.151463
Actual update 9850 of 10000, Stored update 9850 of 10000
-2 * Loglike = 55973.303653
Actual update 9900 of 10000, Stored update 9900 of 10000
-2 * Loglike = 55711.621353
Actual update 9950 of 10000, Stored update 9950 of 10000
-2 * Loglike = 55544.997159
Actual update 10000 of 10000, Stored update 10000 of 10000
-2 * Loglike = 55918.824674
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =          10000
Average =          55877.
S.D.    =          375.15
S.E.M.  =          3.7515

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.09)  multilevel model (Multivariate Normal) 
Estimation algorithm:  MCMC      Elapsed time : 185.11s 
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   1.67112     0.21010      1.25933     2.08291 
load1_biol_r3     0.74662     0.20892      0.33714     1.15609 
load1_biol_r4     1.45298     0.57631      0.32343     2.58252 
load1_phys_core   1.79318     0.31976      1.16647     2.41989 
load1_phys_r2     1.59478     0.57319      0.47135     2.71821 
--------------------------------------------------------------------------------------------------- 
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     0.92350     0.51851     -0.09276     1.93976 
load2_biol_r4     3.33378     0.99830      1.37715     5.29042 
load2_phys_core   1.64770     0.30723      1.04554     2.24985 
load2_phys_r2     3.24271     0.76863      1.73622     4.74919 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                     Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1          0.59532     0.07284      0.45257     0.73808 
cov_fact2_fact1   -0.01226     0.09124     -0.19110     0.16657 
var_fact2          0.17374     0.05427      0.06738     0.28010 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z   Pr(>|z|)       [95% Cred.   Interval]    ESS 
Intercept_es_core     8.39367     0.03200  262.28          0  ***     8.33133     8.45629   3629 
Intercept_biol_core   7.06614     0.03691  191.43          0  ***     6.99424     7.13844   1708 
Intercept_biol_r3     6.89291     0.06389  107.88          0  ***     6.76842     7.01900   3061 
Intercept_biol_r4     5.68098     0.07546   75.28          0  ***     5.53388     5.82754   1930 
Intercept_phys_core   7.21154     0.04237  170.20          0  ***     7.12920     7.29490   1670 
Intercept_phys_r2     6.30850     0.06298  100.17          0  ***     6.18351     6.43249   1440 
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     1.85268     0.07497      1.70778     2.00088    170 
var_Intercept_biol_core   1.59019     0.08904      1.40989     1.75903    496 
var_Intercept_biol_r3     4.71076     0.20368      4.32432     5.11719   1388 
var_Intercept_biol_r4     4.93978     0.62628      3.32788     5.86399     58 
var_Intercept_phys_core   2.02421     0.10450      1.81391     2.22555    417 
var_Intercept_phys_r2     2.65184     0.38373      1.75470     3.28875     72 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> # 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: 3.09)  multilevel model (Multivariate Normal) 
        N min     mean max N_complete min_complete mean_complete max_complete
school 99  12 24.63636  34         99           12      24.63636           34
Estimation algorithm:  IGLS        Elapsed time : 12.87s 
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
RUNNING ADAPTIVE PROCEDURE AND BURNING IN...
Adapting finished and took 100 iterations
Adapting took 100 iterations
Burning in for 50 iterations out of 500
-2 * Loglike = 55728.149764
Burning in for 100 iterations out of 500
-2 * Loglike = 55208.460853
Burning in for 150 iterations out of 500
-2 * Loglike = 55404.926144
Burning in for 200 iterations out of 500
-2 * Loglike = 55408.040501
Burning in for 250 iterations out of 500
-2 * Loglike = 55468.934640
Burning in for 300 iterations out of 500
-2 * Loglike = 55632.361011
Burning in for 350 iterations out of 500
-2 * Loglike = 55781.261056
Burning in for 400 iterations out of 500
-2 * Loglike = 55764.251871
Burning in for 450 iterations out of 500
-2 * Loglike = 55636.991242
Burning in for 500 iterations out of 500
-2 * Loglike = 55750.109844

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 = 55468.049585
Actual update 100 of 5000, Stored update 100 of 5000
-2 * Loglike = 55456.716374
Actual update 150 of 5000, Stored update 150 of 5000
-2 * Loglike = 55630.682697
Actual update 200 of 5000, Stored update 200 of 5000
-2 * Loglike = 55658.843586
Actual update 250 of 5000, Stored update 250 of 5000
-2 * Loglike = 55845.000195
Actual update 300 of 5000, Stored update 300 of 5000
-2 * Loglike = 55575.922544
Actual update 350 of 5000, Stored update 350 of 5000
-2 * Loglike = 55289.483264
Actual update 400 of 5000, Stored update 400 of 5000
-2 * Loglike = 55428.982908
Actual update 450 of 5000, Stored update 450 of 5000
-2 * Loglike = 55703.709607
Actual update 500 of 5000, Stored update 500 of 5000
-2 * Loglike = 55151.497936
Actual update 550 of 5000, Stored update 550 of 5000
-2 * Loglike = 55409.201471
Actual update 600 of 5000, Stored update 600 of 5000
-2 * Loglike = 55483.908792
Actual update 650 of 5000, Stored update 650 of 5000
-2 * Loglike = 55693.819439
Actual update 700 of 5000, Stored update 700 of 5000
-2 * Loglike = 55673.518637
Actual update 750 of 5000, Stored update 750 of 5000
-2 * Loglike = 55430.435860
Actual update 800 of 5000, Stored update 800 of 5000
-2 * Loglike = 55535.485117
Actual update 850 of 5000, Stored update 850 of 5000
-2 * Loglike = 55481.113060
Actual update 900 of 5000, Stored update 900 of 5000
-2 * Loglike = 55714.903813
Actual update 950 of 5000, Stored update 950 of 5000
-2 * Loglike = 55949.929106
Actual update 1000 of 5000, Stored update 1000 of 5000
-2 * Loglike = 55590.479867
Actual update 1050 of 5000, Stored update 1050 of 5000
-2 * Loglike = 55757.923168
Actual update 1100 of 5000, Stored update 1100 of 5000
-2 * Loglike = 55712.377740
Actual update 1150 of 5000, Stored update 1150 of 5000
-2 * Loglike = 55761.560602
Actual update 1200 of 5000, Stored update 1200 of 5000
-2 * Loglike = 55755.960615
Actual update 1250 of 5000, Stored update 1250 of 5000
-2 * Loglike = 55619.430159
Actual update 1300 of 5000, Stored update 1300 of 5000
-2 * Loglike = 55667.711277
Actual update 1350 of 5000, Stored update 1350 of 5000
-2 * Loglike = 55756.108429
Actual update 1400 of 5000, Stored update 1400 of 5000
-2 * Loglike = 55890.196654
Actual update 1450 of 5000, Stored update 1450 of 5000
-2 * Loglike = 55396.889800
Actual update 1500 of 5000, Stored update 1500 of 5000
-2 * Loglike = 55438.328786
Actual update 1550 of 5000, Stored update 1550 of 5000
-2 * Loglike = 55723.538589
Actual update 1600 of 5000, Stored update 1600 of 5000
-2 * Loglike = 55569.529575
Actual update 1650 of 5000, Stored update 1650 of 5000
-2 * Loglike = 55564.878908
Actual update 1700 of 5000, Stored update 1700 of 5000
-2 * Loglike = 55665.890967
Actual update 1750 of 5000, Stored update 1750 of 5000
-2 * Loglike = 55491.231733
Actual update 1800 of 5000, Stored update 1800 of 5000
-2 * Loglike = 55642.100117
Actual update 1850 of 5000, Stored update 1850 of 5000
-2 * Loglike = 55551.794136
Actual update 1900 of 5000, Stored update 1900 of 5000
-2 * Loglike = 55741.033378
Actual update 1950 of 5000, Stored update 1950 of 5000
-2 * Loglike = 55577.234233
Actual update 2000 of 5000, Stored update 2000 of 5000
-2 * Loglike = 55454.006354
Actual update 2050 of 5000, Stored update 2050 of 5000
-2 * Loglike = 55902.356121
Actual update 2100 of 5000, Stored update 2100 of 5000
-2 * Loglike = 55560.559549
Actual update 2150 of 5000, Stored update 2150 of 5000
-2 * Loglike = 55527.087942
Actual update 2200 of 5000, Stored update 2200 of 5000
-2 * Loglike = 55775.848563
Actual update 2250 of 5000, Stored update 2250 of 5000
-2 * Loglike = 55394.130935
Actual update 2300 of 5000, Stored update 2300 of 5000
-2 * Loglike = 55317.021073
Actual update 2350 of 5000, Stored update 2350 of 5000
-2 * Loglike = 55790.948040
Actual update 2400 of 5000, Stored update 2400 of 5000
-2 * Loglike = 55707.155644
Actual update 2450 of 5000, Stored update 2450 of 5000
-2 * Loglike = 55818.878275
Actual update 2500 of 5000, Stored update 2500 of 5000
-2 * Loglike = 55695.697418
Actual update 2550 of 5000, Stored update 2550 of 5000
-2 * Loglike = 55884.126557
Actual update 2600 of 5000, Stored update 2600 of 5000
-2 * Loglike = 55633.333884
Actual update 2650 of 5000, Stored update 2650 of 5000
-2 * Loglike = 55388.567026
Actual update 2700 of 5000, Stored update 2700 of 5000
-2 * Loglike = 55886.183831
Actual update 2750 of 5000, Stored update 2750 of 5000
-2 * Loglike = 55600.542929
Actual update 2800 of 5000, Stored update 2800 of 5000
-2 * Loglike = 55870.821942
Actual update 2850 of 5000, Stored update 2850 of 5000
-2 * Loglike = 55693.292273
Actual update 2900 of 5000, Stored update 2900 of 5000
-2 * Loglike = 55638.339200
Actual update 2950 of 5000, Stored update 2950 of 5000
-2 * Loglike = 55728.993445
Actual update 3000 of 5000, Stored update 3000 of 5000
-2 * Loglike = 55554.442512
Actual update 3050 of 5000, Stored update 3050 of 5000
-2 * Loglike = 55917.887778
Actual update 3100 of 5000, Stored update 3100 of 5000
-2 * Loglike = 56101.117459
Actual update 3150 of 5000, Stored update 3150 of 5000
-2 * Loglike = 55600.225833
Actual update 3200 of 5000, Stored update 3200 of 5000
-2 * Loglike = 55417.930339
Actual update 3250 of 5000, Stored update 3250 of 5000
-2 * Loglike = 55865.178523
Actual update 3300 of 5000, Stored update 3300 of 5000
-2 * Loglike = 55896.069245
Actual update 3350 of 5000, Stored update 3350 of 5000
-2 * Loglike = 55609.001354
Actual update 3400 of 5000, Stored update 3400 of 5000
-2 * Loglike = 55729.934372
Actual update 3450 of 5000, Stored update 3450 of 5000
-2 * Loglike = 55374.476767
Actual update 3500 of 5000, Stored update 3500 of 5000
-2 * Loglike = 55745.005207
Actual update 3550 of 5000, Stored update 3550 of 5000
-2 * Loglike = 55531.190092
Actual update 3600 of 5000, Stored update 3600 of 5000
-2 * Loglike = 55396.954296
Actual update 3650 of 5000, Stored update 3650 of 5000
-2 * Loglike = 55853.200133
Actual update 3700 of 5000, Stored update 3700 of 5000
-2 * Loglike = 55690.325164
Actual update 3750 of 5000, Stored update 3750 of 5000
-2 * Loglike = 55260.489714
Actual update 3800 of 5000, Stored update 3800 of 5000
-2 * Loglike = 55390.943281
Actual update 3850 of 5000, Stored update 3850 of 5000
-2 * Loglike = 55704.796417
Actual update 3900 of 5000, Stored update 3900 of 5000
-2 * Loglike = 55392.961252
Actual update 3950 of 5000, Stored update 3950 of 5000
-2 * Loglike = 55536.922057
Actual update 4000 of 5000, Stored update 4000 of 5000
-2 * Loglike = 55348.139582
Actual update 4050 of 5000, Stored update 4050 of 5000
-2 * Loglike = 55568.576570
Actual update 4100 of 5000, Stored update 4100 of 5000
-2 * Loglike = 55720.199737
Actual update 4150 of 5000, Stored update 4150 of 5000
-2 * Loglike = 55176.568959
Actual update 4200 of 5000, Stored update 4200 of 5000
-2 * Loglike = 55336.749737
Actual update 4250 of 5000, Stored update 4250 of 5000
-2 * Loglike = 55786.928841
Actual update 4300 of 5000, Stored update 4300 of 5000
-2 * Loglike = 55717.370889
Actual update 4350 of 5000, Stored update 4350 of 5000
-2 * Loglike = 55769.106974
Actual update 4400 of 5000, Stored update 4400 of 5000
-2 * Loglike = 55767.816767
Actual update 4450 of 5000, Stored update 4450 of 5000
-2 * Loglike = 55705.827357
Actual update 4500 of 5000, Stored update 4500 of 5000
-2 * Loglike = 55693.498608
Actual update 4550 of 5000, Stored update 4550 of 5000
-2 * Loglike = 55969.577205
Actual update 4600 of 5000, Stored update 4600 of 5000
-2 * Loglike = 55629.699133
Actual update 4650 of 5000, Stored update 4650 of 5000
-2 * Loglike = 55411.294917
Actual update 4700 of 5000, Stored update 4700 of 5000
-2 * Loglike = 55666.604467
Actual update 4750 of 5000, Stored update 4750 of 5000
-2 * Loglike = 55894.917906
Actual update 4800 of 5000, Stored update 4800 of 5000
-2 * Loglike = 55733.539500
Actual update 4850 of 5000, Stored update 4850 of 5000
-2 * Loglike = 55612.290283
Actual update 4900 of 5000, Stored update 4900 of 5000
-2 * Loglike = 55489.072595
Actual update 4950 of 5000, Stored update 4950 of 5000
-2 * Loglike = 55570.990404
Actual update 5000 of 5000, Stored update 5000 of 5000
-2 * Loglike = 55306.479305
PUPN c1003 c1004
AVER c1091 b99 b100

Count   =           5000
Average =          55619.
S.D.    =          179.90
S.E.M.  =          2.5442

ECHO 0
Execution completed


-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
MLwiN (version: 3.09)  multilevel model (Multivariate Normal) 
        N min     mean max N_complete min_complete mean_complete max_complete
school 99  12 24.63636  34         99           12      24.63636           34
Estimation algorithm:  MCMC      Elapsed time : 45.06s 
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   1.79031     0.14676      1.50266     2.07795 
load1_biol_r3     0.84478     0.15524      0.54053     1.14904 
load1_biol_r4     1.95866     0.21851      1.53039     2.38694 
load1_phys_core   2.17239     0.19130      1.79746     2.54733 
load1_phys_r2     2.32702     0.22660      1.88290     2.77114 
--------------------------------------------------------------------------------------------------- 
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   2.52064     0.69005      1.16817     3.87311 
load2_biol_r3     1.33060     0.46024      0.42855     2.23266 
load2_biol_r4     2.73722     0.86217      1.04740     4.42705 
load2_phys_core   2.83557     0.85436      1.16106     4.51008 
load2_phys_r2     2.34777     0.69685      0.98198     3.71356 
--------------------------------------------------------------------------------------------------- 
The estimates of factor covariances:
                    Coef.   Std. Err.   [95% Conf.   Interval] 
var_fact1         0.31687     0.04632      0.22607     0.40766 
cov_fact2_fact1   0.00000     0.00000      0.00000     0.00000 
var_fact2         0.13668     0.06985     -0.00023     0.27359 
--------------------------------------------------------------------------------------------------- 
The fixed part estimates:  
                        Coef.   Std. Err.       z     Pr(>|z|)       [95% Cred.   Interval]   ESS 
Intercept_es_core     8.36510     0.07003  119.46            0  ***     8.22012     8.49881   182 
Intercept_biol_core   7.02566     0.09464   74.24            0  ***     6.85122     7.20504    75 
Intercept_biol_r3     6.86445     0.08885   77.26            0  ***     6.69350     7.04024   312 
Intercept_biol_r4     5.65591     0.15406   36.71   4.709e-295  ***     5.37408     5.97580   201 
Intercept_phys_core   7.16027     0.11256   63.61            0  ***     6.93721     7.38259    91 
Intercept_phys_r2     6.28157     0.11495   54.64            0  ***     6.06057     6.51176   120 
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     0.24258     0.05067      0.15688     0.35385   282 
var_Intercept_biol_core   0.05287     0.04123      0.00160     0.14774    44 
var_Intercept_biol_r3     0.17793     0.08257      0.04440     0.36331   199 
var_Intercept_biol_r4     0.98538     0.22342      0.60420     1.49041   716 
var_Intercept_phys_core   0.14661     0.06520      0.00717     0.26993    67 
var_Intercept_phys_r2     0.31857     0.10121      0.14176     0.53877   306 
--------------------------------------------------------------------------------------------------- 
The random part estimates at the student level: 
                            Coef.   Std. Err.   [95% Cred.   Interval]    ESS 
var_Intercept_es_core     1.73954     0.05775      1.62998     1.85582    807 
var_Intercept_biol_core   1.61743     0.07375      1.47518     1.76110    656 
var_Intercept_biol_r3     4.59389     0.19949      4.22328     5.01109   1393 
var_Intercept_biol_r4     4.74193     0.23641      4.30141     5.20667    903 
var_Intercept_phys_core   1.80202     0.09602      1.60788     1.98539    316 
var_Intercept_phys_r2     2.94459     0.17255      2.61527     3.29393    596 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
> 
> 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 
   7.68    1.21  418.54