[R-sig-ME] [R] lmer() vs. lme() gave different variance component estimates
array chip
arrayprofile at yahoo.com
Fri Sep 17 22:50:30 CEST 2010
Thank you Peter. Actually 3 people from mixed model mailing list tried my code
using lmer(). They got the same results as what I got from lme4(). So they
couldn't replicate my lmer() results:
Random effects:
Groups Name Variance Std.Dev.
eye:id (Intercept) 3.59531 1.89613
id (Intercept) 3.51025 1.87357
Residual 0.01875 0.13693
Number of obs: 640, groups: eye:id, 160; id, 80
The only difference they can think of is they are using Mac and FreeBSD while
mine is PC. I can't imagine this can be the reason. I re-install lme4 package,
but still got weird results with lmer().
Per your suggestion, here is the results for aov()
summary(aov(score~trt+Error(id/eye), data=dat))
Error: id
Df Sum Sq Mean Sq F value Pr(>F)
trt 7 1353.6 193.378 4.552 0.0002991 ***
Residuals 72 3058.7 42.482
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Error: id:eye
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 80 1152 14.4
Error: Within
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 480 9 0.01875
As can be seen, thr within subject variance estimate (0.01875) is the same
between aov, lmer and lme. But I am not sure how to relate results between aov
and lmer/lme for the other 2 variance components (id and eye%in%id).
Thanks
John
----- Original Message ----
From: Peter Dalgaard <pdalgd at gmail.com>
To: array chip <arrayprofile at yahoo.com>
Cc: r-help at r-project.org
Sent: Fri, September 17, 2010 1:05:27 PM
Subject: Re: [R] lmer() vs. lme() gave different variance component estimates
On 09/17/2010 09:14 PM, array chip wrote:
> Hi, I asked this on mixed model mailing list, but that list is not very active,
>
> so I'd like to try the general R mailing list. Sorry if anyone receives the
> double post.
>
>
> Hi, I have a dataset of animals receiving some eye treatments. There are 8
>
> treatments, each animal's right and left eye was measured with some scores
> (ranging from 0 to 7) 4 times after treatment. So there are nesting groups eyes
>
> within animal. Dataset attached
>
>> dat<-read.table("dat.txt",sep='\t',header=T,row.names=1)
>> dat$id<-factor(dat$id)
>> str(dat)
> 'data.frame': 640 obs. of 5 variables:
> $ score: int 0 2 0 7 4 7 0 2 0 7 ...
> $ id : Factor w/ 80 levels "1","3","6","10",..: 7 48 66 54 18 26 38 52 39 63
> ...
> $ rep : int 1 1 1 1 1 1 1 1 1 1 ...
> $ eye : Factor w/ 2 levels "L","R": 2 2 2 2 2 2 2 2 2 2 ...
> $ trt : Factor w/ 8 levels "A","B","C","Control",..: 1 1 1 1 1 1 1 1 1 1 ...
>
> I fit a mixed model using both lmer() from lme4 package and lme() from nlme
> package:
>
>> lmer(score~trt+(1|id/eye),dat)
>
> Linear mixed model fit by REML
> Formula: score ~ trt + (1 | id/eye)
> Data: dat
> AIC BIC logLik deviance REMLdev
> 446.7 495.8 -212.4 430.9 424.7
> Random effects:
> Groups Name Variance Std.Dev.
> eye:id (Intercept) 6.9208e+00 2.630742315798
> id (Intercept) 1.4471e-16 0.000000012030
> Residual 1.8750e-02 0.136930641909
> Number of obs: 640, groups: eye:id, 160; id, 80
>
>> summary(lme(score~trt, random=(~1|id/eye), dat))
>
> Linear mixed-effects model fit by REML
> Data: dat
> AIC BIC logLik
> 425.1569 474.0947 -201.5785
>
> Random effects:
> Formula: ~1 | id
> (Intercept)
> StdDev: 1.873576
>
> Formula: ~1 | eye %in% id
> (Intercept) Residual
> StdDev: 1.896126 0.1369306
>
> As you can see, the variance components estimates of random effects are quite
> different between the 2 model fits. From the data, I know that the variance
> component for "id" can't be near 0, which is what lmer() fit produced, so I
> think the lme() fit is correct while lmer() fit is off. This can also be seen
> from AIC, BIC etc. lme() fit has better values than lmer() fit.
>
>
> I guess this might be due to lmer() didn't converge very well, is there anyway
> to adjust to make lmer() converge better to get similar results as lme()?
That's your guess... I'd be more careful about jumping to conclusions.
If this is a balanced data set, perhaps you could supply the result of
summary(aov(score~trt+Error(id/eye), data=dat))
The correct estimates should be computable from the ANOVA table.
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
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