All,
I'm using lmer for some repeated measures data and have specified
the contrasts for a time factor such that say time 3 is the base. This
works fine. However, when
I next use the subset argument to remove the last two time values, the
output indicates that
the specified contrast is not maintained (see below). I can solve this
by creating a new dataframe
for the subset of interest and redefining the constrasts, but I was
wondering if there is a direct method that
allows me to continue w/ the subset argument? (perhaps via supplying a
contrast argument to lmer
directly, but this doesn't seem possible based on the defintion of this
argument in model.matrix.default).
Thanks,
Dave
z <- rnorm(24, mean=0, sd=1)
time <- factor(paste("Time-", rep(1:6, 4), sep=""))
Patient <- rep(1:4, each = 6)
drug <- factor(rep(c("D", "P"), each = 6, times = 2)) ## P = placebo, D
= Drug
dat.new <- data.frame(time, drug, z, Patient)
### specify the contrast as time 3:
contrasts(dat.new$time) <- contr.treatment(6, base=3)
dimnames(contrasts(dat.new$time))[[1]] <-
as.character(levels(dat.new$time))
dimnames(contrasts(dat.new$time))[[2]] <-
as.character(levels(dat.new$time)[-3])
fm1 <- lmer(z ~ drug + time + (1 | Patient), data = dat.new )
Fixed effects:
Estimate Std. Error t value
(Intercept) -0.182774 0.464014 -0.39390
drugP -0.281103 0.352309 -0.79789
timeTime-1 0.150505 0.606462 0.24817
timeTime-2 0.612016 0.606462 1.00916
timeTime-4 0.775342 0.606462 1.27847
timeTime-5 0.093741 0.606462 0.15457
timeTime-6 0.452442 0.606462 0.74604
## time 3 is the base as specified
fm2 <- lmer(z ~ drug + time + (1 | Patient), data = dat.new,
subset = dat.new$time !="Time-6" & dat.new$time != "Time-5")
Fixed effects:
Estimate Std. Error t value
(Intercept) 0.052975 0.500675 0.10581
drugP -0.451593 0.447818 -1.00843
timeTime-2 0.461511 0.633310 0.72873
timeTime-3 -0.150505 0.633310 -0.23765
timeTime-4 0.624837 0.633310 0.98662
### time 3 no longer the base; was expecting to see the fixed effects
for time-1, time-2, and time-4, w/ Intercept
### representing time-3
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