[R-sig-ME] lmer verbose output and random effects tables confusion
Adam D. I. Kramer
adik at ilovebacon.org
Sun Jul 4 22:11:00 CEST 2010
Hello,
For my own edification, could someone explain the relationship
between the output of "verbose-mode" model fitting in lmer and the lmer
object output? I had been led to believe that the last line of the verbose
output would be the random effects table (and then for nonlinear models, the
fixed effects would follow), but when I fit this (rather complicated) model:
lmer(formula = rating ~ rvalue + m:option.1000 + m:option2 + m + (1 +
rvalue + m:option.1000 + m:option2 + m | studyID),
data=cc2[as.logical(cc2$chosen),], verbose=TRUE, control=list(maxIter=10000,
maxFN=10000))
...I get this output:
(...8895 rows of output...)
8896: 1231.8223: 3.75608 0.0485706 0.381782 0.00000 0.141926 0.00000
0.0226706 -0.0359946 -0.192479 6.02644 5.82712 -10.4730 -6.48680 -30.9794
47.8011 -2.39961 9.36467 108.544 10.9610 -94.6165 -51.5401 124.184
-41.8534 -48.6679 42.8230 2.19496 -1.26584 16.5468
...and this random effects table:
Random effects:
Groups Name Variance Std.Dev. Corr
studyID (Intercept) 6.5123e+00 2.551915
rvalue 9.5263e-03 0.097603 -0.941
ml 1.3536e+00 1.163462 -0.422 0.100
mh:option.1000 2.4708e+02 15.718900 0.978 -0.887 -0.461
ml:option.1000 8.2346e+02 28.696035 0.518 -0.489 -0.407 0.352
mh:option2 8.9316e+02 29.885807 -0.894 0.845 0.269 -0.955
ml:option2 1.3245e+03 36.393087 -0.455 0.461 0.303 -0.275
Residual 4.6160e-01 0.679410
...they do not correspond. Or do they? What might I be missing here? (I note
that the deviance is reported correctly). Some of the numbers are close, but
others are way off (for example, the zeroes in the verbose output show no
corresponding zeroes here). What's up? How should I read this verbose
output? Fixed effects follow, but also do not correspond:
Fixed effects:
Estimate Std. Error t value
(Intercept) 18.4601702 0.6169761 29.920
rating 0.4912713 0.0956698 5.135
ml -8.6768828 0.3568779 -24.313
mh:option 0.1097410 0.0371654 2.953
ml:option 0.0899163 0.0245243 3.666
mh:option2 -0.0012794 0.0004101 -3.120
ml:option2 -0.0010715 0.0002906 -3.688
Correlation of Fixed Effects:
(Intr) rating ml mh:ptn ml:ptn mh:pt2
rating -0.934
ml -0.521 0.340
mh:option -0.207 0.022 0.337
ml:option -0.003 0.023 -0.530 -0.007
mh:option2 0.096 0.075 -0.258 -0.924 0.017
ml:option2 -0.098 0.090 0.459 0.092 -0.882 -0.024
...I note also that this is important for the user level because testing shows
that when the user provides start values (via start=...), the verbose output
starts out with the start values verbatim.
Thanks,
Adam
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