Message-ID: <SNT131-w364FB531093A14FDDFC3BAF7D0@phx.gbl>
Date: 2011-06-01T05:58:13Z
From: Taro Miyagawa
Subject: different results from lme() and lmer()
Hello R-help,
I'm studying an example in the R book.?
The data file is available from the link below.http://www.bio.ic.ac.uk/research/mjcraw/therbook/data/fertilizer.txt
Could you explain Why the results from lme() and lmer() are different in the following case? In other examples, I can get the same results using the two functions, but not here...?
Thank you.Miya
library(lme4)library(nlme)# object dat contains the data
> summary(lme(root~fertilizer,random=~week|plant,data=dat))Linear mixed-effects model fit by REML?Data: dat?? ? ? ?AIC ? ? ?BIC ? ?logLik? 171.0236 183.3863 -79.51181
Random effects:?Formula: ~week | plant?Structure: General positive-definite, Log-Cholesky parametrization? ? ? ? ? ? StdDev ? ?Corr ?(Intercept) 2.8639832 (Intr)week ? ? ? ?0.9369412 -0.999Residual ? ?0.4966308 ? ? ??
Fixed effects: root ~ fertilizer?? ? ? ? ? ? ? ? ? ? ? Value Std.Error DF ? t-value p-value(Intercept) ? ? ? ?2.799710 0.1438367 48 19.464499 ? 0e+00fertilizercontrol -1.039383 0.2034158 10 -5.109645 ? 5e-04?Correlation:?? ? ? ? ? ? ? ? ? (Intr)fertilizercontrol -0.707
Standardized Within-Group Residuals:? ? ? ?Min ? ? ? ? Q1 ? ? ? ?Med ? ? ? ? Q3 ? ? ? ?Max?-1.9928118 -0.6586834 -0.1004301 ?0.6949714 ?2.0225381?
Number of Observations: 60Number of Groups: 12?
> lmer(root~fertilizer+(week|plant),data=dat)Linear mixed model fit by REML?Formula: root ~ fertilizer + (week | plant)?? ?Data: dat?? ?AIC BIC logLik deviance REMLdev?174.4 187 -81.21 ? ?159.7 ? 162.4Random effects:?Groups ? Name ? ? ? ?Variance ? Std.Dev. ? Corr ??plant ? ?(Intercept) 4.1416e-18 2.0351e-09 ? ? ??? ? ? ? ? week ? ? ? ?8.7452e-01 9.3516e-01 0.000??Residual ? ? ? ? ? ? 2.2457e-01 4.7389e-01 ? ? ??Number of obs: 60, groups: plant, 12
Fixed effects:? ? ? ? ? ? ? ? ? Estimate Std. Error t value(Intercept) ? ? ? ?-0.1847 ? ? 0.2024 ?-0.913fertilizercontrol ?-0.7612 ? ? 0.2862 ?-2.660
Correlation of Fixed Effects:? ? ? ? ? ? (Intr)frtlzrcntrl -0.707