[R] How to mimic pdMat of lme under lmer?
Joris De Wolf
joris.dewolf at cropdesign.com
Mon Sep 19 18:24:07 CEST 2005
Dear members,
I would like to switch from nlme to lme4 and try to translate some of my
models that worked fine with lme.
I have problems with the pdMat classes.
Below a toy dataset with a fixed effect F and a random effect R. I gave
also 2 similar lme models.
The one containing pdLogChol (lme1) is easy to translate (as it is an
explicit notation of the default model)
The more parsimonious model with pdDiag replacing pdLogChol I cannot
reproduce with lmer. The obvious choice for me would be my model lmer2,
but this is yielding different result.
Somebody any idea?
Thanks,
Joris
I am using R version 2.1.0 for Linux
and the most recent downloads of Matrix and nlme
#dataset from McLean, Sanders and Stroup
F <- factor(c(1,1,1,1,1,1,2,2,2,2,2,2))
R <- factor(c(1,1,2,2,3,3,1,1,2,2,3,3))
s <-
c(51.43,51.28,50.93,50.75,50.47,50.83,51.91,52.43,52.26,52.33,51.58,51.23)
DS <- data.frame(F,R,s)
DS$F <- as.factor(DS$F)
DS$R <- as.factor(DS$R)
library(nlme)
lme1 <- lme(data = DS,s ~ F,random = list(R = pdLogChol(~F)))
lme2 <- lme(data = DS,s ~ F,random = list(R = pdDiag(~F)))
summary(lme1)
summary(lme2)
library(lme4)
lmer1 <- lmer(data = DS,s ~ F + (F|R))
lmer2 <- lmer(data = DS,s ~ F + (1|R) + (1|F))
summary(lmer1)
summary(lmer2)
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