[R-sig-ME] Error in documentation of lmer?
Lyman, Mark
Mark.Lyman at atk.com
Fri Sep 18 18:02:37 CEST 2009
According to the documentation of lmer, the way to get the fitting
algorithm steps is by setting the control = list(msVerbose=TRUE). For
me, this seems to be ignored.
> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy,
control=list(msVerbose=TRUE)))
Linear mixed model fit by REML
Formula: Reaction ~ Days + (Days | Subject)
Data: sleepstudy
AIC BIC logLik deviance REMLdev
1756 1775 -871.8 1752 1744
Random effects:
Groups Name Variance Std.Dev. Corr
Subject (Intercept) 612.092 24.7405
Days 35.072 5.9221 0.066
Residual 654.941 25.5918
Number of obs: 180, groups: Subject, 18
Fixed effects:
Estimate Std. Error t value
(Intercept) 251.405 6.825 36.84
Days 10.467 1.546 6.77
Correlation of Fixed Effects:
(Intr)
Days -0.138
However, after looking at the lmer function, it appears that by setting
verbose=TRUE, I can get the steps.
> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy,
verbose=TRUE))
0: 1768.4124: 0.516398 0.0967302 0.00000
1: 1761.9813: 0.571375 0.550876 0.167097
2: 1755.4534: 0.790274 0.455893 0.215675
3: 1745.0053: 0.812187 0.239613 0.105945
4: 1744.2582: 0.817183 0.213879 0.0692586
5: 1743.9764: 0.834405 0.230507 0.0310488
6: 1743.8121: 0.877690 0.218240 0.0280506
7: 1743.7121: 0.964311 0.243094 0.0246631
8: 1743.6293: 0.970155 0.232066 0.0135558
9: 1743.6284: 0.966654 0.230511 0.0163398
10: 1743.6283: 0.966755 0.230912 0.0156969
11: 1743.6283: 0.966734 0.230909 0.0156904
Linear mixed model fit by REML
Formula: Reaction ~ Days + (Days | Subject)
Data: sleepstudy
AIC BIC logLik deviance REMLdev
1756 1775 -871.8 1752 1744
Random effects:
Groups Name Variance Std.Dev. Corr
Subject (Intercept) 612.092 24.7405
Days 35.072 5.9221 0.066
Residual 654.941 25.5918
Number of obs: 180, groups: Subject, 18
Fixed effects:
Estimate Std. Error t value
(Intercept) 251.405 6.825 36.84
Days 10.467 1.546 6.77
Correlation of Fixed Effects:
(Intr)
Days -0.138
Is this a mistake in the documentation? Or have I missed something. I
have seen this on R 2.9.1 on Windows XP and on R 2.9.0 on Linux with
lme4 0.999375-31
Mark Lyman
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