[R] lme4 and lmeSplines

[Spencer Graves]

	   At least at one time, to use lmer after lme, you had to quit R 
before loading 'lme4' because of substantive conflicts between 'nlme' 
and 'lme4' / 'Matrix'.  That may be the source of your problem.  I can 
think of two possible ways to get around this:

	  1.  I might try quitting R and restarting after your use of 
'lmeSplines' but before 'lmer'.

	  2.  If that failed, I might try making local copies of everything I 
needed from 'lmeSplines' and using them with 'lmer'.  If that failed, 
I'd use 'debug' to walk through the code (or local copies of whatever I 
needed, possibly with name changes) until I figured it out.

	  I know this is not what you wanted to hear, but I hope it helps.
	  Spencer Graves

Kevin Wright wrote:
> 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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