> library(lattice) # Functions: xyplot
> library(lme4)  
Loading required package: Matrix

Attaching package: ‘lme4’

The following object is masked from ‘package:stats’:

    AIC, BIC

> epilepsy = read.table("http://www.hsph.harvard.edu/fitzmaur/ala2e/epilepsy.dat", header=FALSE)
> names(epilepsy) = c("ID","trt","age","Week0","Week2","Week4","Week6","Week8")
> epilepsy$trt = factor(epilepsy$trt, levels=c(0,1), labels=c("Placebo","Progabide"))
> 
> # Convert to long form:
> epi.long = reshape(epilepsy, idvar="ID", varying=list(4:8), v.names="Count", timevar="Time", direction="long")
> epi.long$Time = (epi.long$Time-1)*2
> 
> # Attach long form to R session:
> attach(epi.long)
> head(epi.long)
    ID     trt age Time Count
1.1  1 Placebo  31    0    11
2.1  2 Placebo  30    0    11
3.1  3 Placebo  25    0     6
4.1  4 Placebo  36    0     8
5.1  5 Placebo  22    0    66
6.1  6 Placebo  29    0    27
> PostBase = (Time!=0)  # Indicator for post-baseline
> head(PostBase)
[1] FALSE FALSE FALSE FALSE FALSE FALSE
> PostBase
  [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
 [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
 [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
 [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
 [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE
 [61]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
 [73]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
 [85]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
 [97]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[109]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[121]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[133]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[145]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[157]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[169]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[181]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[193]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[205]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[217]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[229]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[241]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[253]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[265]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[277]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
[289]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
> Weeks = 8*(PostBase==F) + 2*(PostBase==T)
> Weeks
  [1] 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8
 [37] 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 2 2 2 2 2 2 2 2 2 2 2 2 2
 [73] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[109] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[145] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[181] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[217] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[253] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[289] 2 2 2 2 2 2 2
> mod1 = lmer(Count ~ trt*PostBase + (PostBase | ID), offset=log(Weeks), family=poisson, data=epi.long)
> # Very close to Table 14.6 on p. 424:
> summary(mod1)
Generalized linear mixed model fit by the Laplace approximation 
Formula: Count ~ trt * PostBase + (PostBase | ID) 
   Data: epi.long 
   AIC   BIC logLik deviance
 802.8 828.6 -394.4    788.8
Random effects:
 Groups Name         Variance Std.Dev. Corr  
 ID     (Intercept)  0.49989  0.70703        
        PostBaseTRUE 0.23197  0.48163  0.160 
Number of obs: 295, groups: ID, 59

Fixed effects:
                            Estimate Std. Error z value Pr(>|z|)    
(Intercept)                1.0708655  0.1398540   7.657  1.9e-14 ***
trtProgabide               0.0512061  0.1927000   0.266   0.7904    
PostBaseTRUE              -0.0004666  0.1078765  -0.004   0.9965    
trtProgabide:PostBaseTRUE -0.3062694  0.1501357  -2.040   0.0414 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Correlation of Fixed Effects:
            (Intr) trtPrg PBTRUE
trtProgabid -0.726              
PostBasTRUE  0.022 -0.016       
trtP:PBTRUE -0.016  0.026 -0.719
>