Hi, Doug:
I just confirmed a discrepancy (reported by Paul Cossens) between the
output of lme and lmer using the Oxide example in Pinheiro and Bates,
pp. 167-170. It appears that coef(lmer(...)) adds only the ranef for
Wafer and omits the one for Lot.
Consider the following:
library(nlme)
Oxide - Oxide
#data(Oxide,package=nlme)
fit.lme - lme(Thickness~1,Oxide)
coef.lme - coef(fit.lme)
exit R, restart
library(lme4)
fm3Oxide-lmer(Thickness~ (1|Lot)+(1|Lot:Wafer),data=Oxide)
coef.lme4 - coef(fm3Oxide)
The following matches the first 3 numbers in coef.lme but not in
coef.lme4:
fixef(fm3Oxide)+ranef(fm3Oxide)[[2]][1]+ranef(fm3Oxide)[[1]][1:3]
Best Wishes,
spencer graves
Paul Cossens wrote:
My question relates to problems that I'm having matching lme and lmer
examples in PB.
using Matix 0.995
In the Oxide example in p167-170 I can't get the level 2 coefficient
estimates to match
the fm1Oxide model in lme is
data(Oxide,package=nlme)
lme(Thickness~1,Oxide)
which I translate in Lmer syntax to
fm3Oxide-lmer(Thickness~ (1|Lot)+(1|Lot:Wafer),data=Oxide)
#or alternatively which gives the same result
Oxide$LW-with(Oxide,Lot:Wafer)[drop=TRUE]
fm4Oxide-lmer(Thickness~ (1|Lot)+(1|LW),data=Oxide)
however if you look at say Lot 8, lme gives
81993.767
8/11993.677
8/21995.170
8/31990.693
while lmer gives
coef(fm3Oxide)
81993.767
8:1 2000.062
8:2 2001.555
8:3 1997.078
To me this looks like lmer in not including the lot random effect (8=
-6.385129, Intercept 2000.153 ). Is this because I'm not specifying the
model correctly?
Thanks Paul
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