R version 2.4.0 beta (2006-09-25 r39510)
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ISBN 3-900051-07-0
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> library(mlmRev)
Loading required package: lme4
Loading required package: Matrix
Loading required package: lattice
> options(show.signif.stars = FALSE)
> cntr <- list()
> (fm01 <- lmer(langPOST ~ IQ.ver.cen+avg.IQ.ver.cen+(1|schoolNR), bdf))
Linear mixed-effects model fit by REML
Formula: langPOST ~ IQ.ver.cen + avg.IQ.ver.cen + (1 | schoolNR)
Data: bdf
AIC BIC logLik MLdeviance REMLdeviance
15240 15263 -7616 15228 15232
Random effects:
Groups Name Variance Std.Dev.
schoolNR (Intercept) 7.8859 2.8082
Residual 42.1723 6.4940
number of obs: 2287, groups: schoolNR, 131
Fixed effects:
Estimate Std. Error t value
(Intercept) 40.74101 0.28660 142.16
IQ.ver.cen 2.41477 0.07168 33.69
avg.IQ.ver.cen 1.58916 0.31477 5.05
Correlation of Fixed Effects:
(Intr) IQ.vr.
IQ.ver.cen 0.000
avg.IQ.vr.c 0.077 -0.228
> (fm02 <- lmer(langPOST ~ IQ.ver.cen+avg.IQ.ver.cen+(IQ.ver.cen|schoolNR), bdf))
Linear mixed-effects model fit by REML
Formula: langPOST ~ IQ.ver.cen + avg.IQ.ver.cen + (IQ.ver.cen | schoolNR)
Data: bdf
AIC BIC logLik MLdeviance REMLdeviance
15230 15264 -7609 15214 15218
Random effects:
Groups Name Variance Std.Dev. Corr
schoolNR (Intercept) 8.07566 2.84177
IQ.ver.cen 0.20801 0.45608 -0.642
Residual 41.34967 6.43037
number of obs: 2287, groups: schoolNR, 131
Fixed effects:
Estimate Std. Error t value
(Intercept) 40.74958 0.28808 141.45
IQ.ver.cen 2.45983 0.08364 29.41
avg.IQ.ver.cen 1.40893 0.32374 4.35
Correlation of Fixed Effects:
(Intr) IQ.vr.
IQ.ver.cen -0.274
avg.IQ.vr.c 0.029 -0.213
> (fm03 <- lmer(math ~ year+(1|childid)+(1|schoolid), egsingle))
Linear mixed-effects model fit by REML
Formula: math ~ year + (1 | childid) + (1 | schoolid)
Data: egsingle
AIC BIC logLik MLdeviance REMLdeviance
16767 16795 -8380 16747 16759
Random effects:
Groups Name Variance Std.Dev.
childid (Intercept) 0.66992 0.81849
schoolid (Intercept) 0.18693 0.43235
Residual 0.34700 0.58907
number of obs: 7230, groups: childid, 1721; schoolid, 60
Fixed effects:
Estimate Std. Error t value
(Intercept) -0.780482 0.061088 -12.78
year 0.746123 0.005396 138.26
Correlation of Fixed Effects:
(Intr)
year -0.031
> (fm04 <- lmer(math ~ year+(1|childid)+(year|schoolid), egsingle))
Linear mixed-effects model fit by REML
Formula: math ~ year + (1 | childid) + (year | schoolid)
Data: egsingle
AIC BIC logLik MLdeviance REMLdeviance
16494 16536 -8241 16472 16482
Random effects:
Groups Name Variance Std.Dev. Corr
childid (Intercept) 0.672304 0.81994
schoolid (Intercept) 0.166812 0.40843
year 0.011584 0.10763 0.443
Residual 0.324516 0.56966
number of obs: 7230, groups: childid, 1721; schoolid, 60
Fixed effects:
Estimate Std. Error t value
(Intercept) -0.77709 0.05823 -13.34
year 0.76296 0.01533 49.76
Correlation of Fixed Effects:
(Intr)
year 0.358
> (fm05 <- lmer(normexam ~ standLRT + sex + schgend + (1|school), Exam))
Linear mixed-effects model fit by REML
Formula: normexam ~ standLRT + sex + schgend + (1 | school)
Data: Exam
AIC BIC logLik MLdeviance REMLdeviance
9360 9398 -4674 9326 9348
Random effects:
Groups Name Variance Std.Dev.
school (Intercept) 0.085829 0.29297
Residual 0.562534 0.75002
number of obs: 4059, groups: school, 65
Fixed effects:
Estimate Std. Error t value
(Intercept) -0.001049 0.055569 -0.02
standLRT 0.559754 0.012450 44.96
sexM -0.167392 0.034100 -4.91
schgendboys 0.177691 0.113475 1.57
schgendgirls 0.158997 0.089403 1.78
Correlation of Fixed Effects:
(Intr) stnLRT sexM schgndb
standLRT -0.014
sexM -0.316 0.061
schgendboys -0.395 -0.003 -0.145
schgendgrls -0.622 0.009 0.197 0.245
> (fm06 <- lmer(score ~ gcsecnt + (1|school) + (1|lea), Chem97))
Linear mixed-effects model fit by REML
Formula: score ~ gcsecnt + (1 | school) + (1 | lea)
Data: Chem97
AIC BIC logLik MLdeviance REMLdeviance
141705 141738 -70848 141686 141697
Random effects:
Groups Name Variance Std.Dev.
school (Intercept) 1.166197 1.07991
lea (Intercept) 0.014766 0.12151
Residual 5.154203 2.27029
number of obs: 31022, groups: school, 2410; lea, 131
Fixed effects:
Estimate Std. Error t value
(Intercept) 5.63545 0.03123 180.4
gcsecnt 2.47256 0.01690 146.3
Correlation of Fixed Effects:
(Intr)
gcsecnt 0.058
> (fm07 <- lmer(height ~ age + I(age^2) + I(age^3) + I(age^4) + (age + I(age^2)|Subject),
+ Oxboys))
Linear mixed-effects model fit by REML
Formula: height ~ age + I(age^2) + I(age^3) + I(age^4) + (age + I(age^2) | Subject)
Data: Oxboys
AIC BIC logLik MLdeviance REMLdeviance
669.5 707.5 -323.7 644.7 647.5
Random effects:
Groups Name Variance Std.Dev. Corr
Subject (Intercept) 62.74004 7.9209
age 2.81669 1.6783 0.607
I(age^2) 0.38576 0.6211 0.607 1.000
Residual 0.28112 0.5302
number of obs: 234, groups: Subject, 26
Fixed effects:
Estimate Std. Error t value
(Intercept) 149.0185 1.5547 95.85
age 6.1754 0.3609 17.11
I(age^2) 1.1310 0.3755 3.01
I(age^3) 0.4523 0.1847 2.45
I(age^4) -0.3796 0.3414 -1.11
Correlation of Fixed Effects:
(Intr) age I(g^2) I(g^3)
age 0.554
I(age^2) 0.169 0.276
I(age^3) -0.001 -0.382 0.027
I(age^4) 0.024 0.018 -0.912 -0.021
Warning message:
nlminb returned message false convergence (8)
in: `LMEoptimize<-`(`*tmp*`, value = list(maxIter = 200, tolerance = 1.49011611938477e-08,
> (fm08 <- lmer(height ~ poly(age,4) + (age + I(age^2)|Subject), Oxboys))
Linear mixed-effects model fit by REML
Formula: height ~ poly(age, 4) + (age + I(age^2) | Subject)
Data: Oxboys
AIC BIC logLik MLdeviance REMLdeviance
658.3 696.3 -318.2 644.5 636.3
Random effects:
Groups Name Variance Std.Dev. Corr
Subject (Intercept) 62.17477 7.88510
age 2.72854 1.65183 0.609
I(age^2) 0.35817 0.59847 0.609 1.000
Residual 0.28269 0.53169
number of obs: 234, groups: Subject, 26
Fixed effects:
Estimate Std. Error t value
(Intercept) 149.5197 1.5818 94.52
poly(age, 4)1 64.5424 3.2613 19.79
poly(age, 4)2 4.2034 0.8508 4.94
poly(age, 4)3 1.2862 0.5317 2.42
poly(age, 4)4 -0.5897 0.5317 -1.11
Correlation of Fixed Effects:
(Intr) p(,4)1 p(,4)2 p(,4)3
poly(ag,4)1 0.623
poly(ag,4)2 0.493 0.770
poly(ag,4)3 0.000 0.000 0.000
poly(ag,4)4 0.000 0.000 0.000 0.000
Warning message:
nlminb returned message function evaluation limit reached without convergence (9)
in: `LMEoptimize<-`(`*tmp*`, value = list(maxIter = 200, tolerance = 1.49011611938477e-08,
> (fm09 <- lmer(attain ~ verbal * sex+(1|primary)+(1|second), ScotsSec))
Linear mixed-effects model fit by REML
Formula: attain ~ verbal * sex + (1 | primary) + (1 | second)
Data: ScotsSec
AIC BIC logLik MLdeviance REMLdeviance
14880 14917 -7434 14843 14868
Random effects:
Groups Name Variance Std.Dev.
primary (Intercept) 0.275457 0.52484
second (Intercept) 0.014747 0.12144
Residual 4.253113 2.06231
number of obs: 3435, groups: primary, 148; second, 19
Fixed effects:
Estimate Std. Error t value
(Intercept) 5.914713 0.076795 77.02
verbal 0.158356 0.003787 41.81
sexF 0.121553 0.072413 1.68
verbal:sexF 0.002593 0.005388 0.48
Correlation of Fixed Effects:
(Intr) verbal sexF
verbal 0.177
sexF -0.482 -0.178
verbal:sexF -0.122 -0.680 0.161
> (fm10 <- lmer(attain ~ verbal + sex+(1|primary)+(sex|second), ScotsSec))
Linear mixed-effects model fit by REML
Formula: attain ~ verbal + sex + (1 | primary) + (sex | second)
Data: ScotsSec
AIC BIC logLik MLdeviance REMLdeviance
14862 14905 -7424 14832 14848
Random effects:
Groups Name Variance Std.Dev. Corr
primary (Intercept) 0.268596 0.51826
second (Intercept) 0.046389 0.21538
sexF 0.145830 0.38188 -0.798
Residual 4.218513 2.05390
number of obs: 3435, groups: primary, 148; second, 19
Fixed effects:
Estimate Std. Error t value
(Intercept) 5.927407 0.086603 68.44
verbal 0.159591 0.002771 57.59
sexF 0.098448 0.114517 0.86
Correlation of Fixed Effects:
(Intr) verbal
verbal 0.115
sexF -0.624 -0.060
>