Error in documentation of lmer?
Hmm, both control = list(msVerbose = TRUE) and verbose = TRUE should result in verbose output from the optimization, although verbose = TRUE is the preferred form now. It looks as if at some point I got carried away with cleaning up the code and removed the part of lmer that handles the control argument. I have restored that and will issue a new version of the lme4 package. Thanks for the report.
On Fri, Sep 18, 2009 at 11:02 AM, Lyman, Mark <Mark.Lyman at atk.com> wrote:
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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