[R] summary of linear fixed effects model is different than the HSAUR book
Christopher W. Ryan
cryan at binghamton.edu
Mon Jul 23 00:33:53 CEST 2007
Running R 2.5.1 and a newly downloaded lme4 package on WinXP
I'm trying to work my way through Everitt and Hothorn's "Handbook of
Statistical Analyses Using R," c 2006. (No, it's not homework.)
Chapter 10 discusses linear mixed effects models for longitudinal data.
I've called my long data frame BtheB.long
Here's the model from the book, which I run.
lmer1 <- lmer(bdi ~ bdi.pre + months + treatment + drug + length + (1 |
subject), data = BtheB.long, method = "ML", na.action = na.omit)
Here is the summary of the model that I see:
> summary(lmer1)
Linear mixed-effects model fit by maximum likelihood
Formula: bdi ~ bdi.pre + months + treatment + drug + length + (1 | subject)
Data: BtheB.long
AIC BIC logLik MLdeviance REMLdeviance
1885 1910 -935.3 1871 1866
Random effects:
Groups Name Variance Std.Dev.
subject (Intercept) 48.299 6.9498
Residual 25.129 5.0128
number of obs: 280, groups: subject, 97
Fixed effects:
Estimate Std. Error t value
(Intercept) 5.94372 2.24915 2.643
bdi.pre 0.63819 0.07759 8.225
months -0.71703 0.14606 -4.909
treatmentBtheB -2.37311 1.66368 -1.426
drugYes -2.79786 1.71993 -1.627
length>6m 0.25639 1.63213 0.157
Correlation of Fixed Effects:
(Intr) bdi.pr months trtmBB drugYs
bdi.pre -0.678
months -0.264 0.023
tretmntBthB -0.389 0.121 0.022
drugYes -0.071 -0.237 -0.025 -0.323
length>6m -0.238 -0.242 -0.043 0.002 0.158
But on page 169, summary() is shown to produce additional columns in the
"fixed effects" section, namely degrees of freedom and the P-value (with
significance stars).
How can I produce that output? Am I doing something wrong? Has lme4
changed?
Thanks.
--
Christopher W. Ryan, MD
SUNY Upstate Medical University Clinical Campus at Binghamton
40 Arch Street, Johnson City, NY 13790
cryanatbinghamtondotedu
PGP public keys available at http://home.stny.rr.com/ryancw/
"If you want to build a ship, don't drum up the men to gather wood,
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