[R] lme4 and lmeSplines

From: Kevin Wright <kwright68_at_gmail.com>
Date: Thu 03 Aug 2006 - 05:25:20 EST


I'm trying to use the lmeSplines package together with lme4.

Below is (1) an example of lmeSplines together with nlme (2) an attempt to use lmeSplines with lme4 (3) then a comparison of the random effects from the two different methods.

(1)

require(lmeSplines)
data(smSplineEx1)
dat <- smSplineEx1
dat.lo <- loess(y~time, data=dat)
plot(dat.lo)
dat$all <- rep(1,nrow(dat))
times20 <- seq(1,100,length=20)
Zt20 <- smspline(times20)
dat$Zt20 <- approx.Z(Zt20, times20, dat$time) fit1.20 <- lme(y~time, data=dat, random=list(all=pdIdent(~Zt20-1)))
# Loess model

dat.lo <- loess(y~time, data=dat)
plot(dat.lo)
# Spline model

with(dat, lines(fitted(fit1.20)~time, col="red"))
# Save random effects for later

ranef.nlme <- unlist(ranef(fit1.20))

(2) Now an attempt to use lme4:

library(lmeSplines)
detach(package:nlme)
library(lme4)
data(smSplineEx1)
# Use 20 spline in lme4

dat <- smSplineEx1
times20 <- seq(1,100,length=20)
Zt20 <- smspline(times20)
dat <- cbind(dat, approx.Z(Zt20, times20, dat$time)) names(dat)[4:21] <- paste("Zt",names(dat)[4:21],sep="") dat$all <- rep(1, nrow(dat))
fit1.20 <- lmer(y~time

             +(-1+Zt1|all)+(-1+Zt2|all)+(-1+Zt3|all)+(-1+Zt4|all)+(-1+Zt5|all)+(-1+Zt6|all)
             +(-1+Zt7|all)+(-1+Zt8|all)+(-1+Zt9|all)+(-1+Zt10|all)+(-1+Zt11|all)+(-1+Zt12|all)
             +(-1+Zt13|all)+(-1+Zt14|all)+(-1+Zt15|all)+(-1+Zt16|all)+(-1+Zt17|all)+(-1+Zt18|all),
             data=dat)

#summary(fit1)
# Plot the data and loess fit

dat.lo <- loess(y~time, data=dat)
plot(dat.lo)
# Fitting with splines

with(dat, lines(fitted(fit1.20)~time, col="red")) ranef.lme4 <- unlist(ranef(fit1.20))

(3) Compare nlme lme4 random effects

plot(ranef.nlme~ranef.lme4)

The plot of fitted values from lme4 is visually appealing, but the random effects from lme4 are peculiar--three are non-zero and the rest are essentially zero.

Any help in getting lme4 + lmeSplines working would be appreciated. It is not unlikely that I have the lmer syntax wrong.

Kevin Wright



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