[R] random effects with lmer() and lme(), three random factors

From: Xianqun (Wilson) Wang <xwang_at_aviaradx.com>
Date: Sat 29 Jul 2006 - 09:43:38 EST

Hi, all,  

I have a question about random effects model. I am dealing with a three-factor experiment dataset. The response variable y is modeled against three factors: Samples, Operators, and Runs. The experimental design is as follow:  

4 samples were randomly chosen from a large pool of test samples. Each of the 4 samples was analyzed by 4 operators, randomly selected from a group of operators. Each operator independently analyzed same samples over 5 runs (runs nested in operator). I would like to know the following things:  

(1) the standard deviation within each run;

(2) the standard deviation between runs;

(3) the standard deviation within operator

(4) the standard deviation between operator.

With this data, I assumed the three factors are all random effects. So the model I am looking for is  

Model: y = Samples(random) + Operator(random) + Operator:Run(random) + Error(Operator) + Error(Operator:Run) + Residuals  

I am using lme function in nlme package. Here is the R code I have  

  1. using lme:

First I created a grouped data using

gx <- groupedData(y ~ 1 | Sample, data=x)

gx$dummy <- factor(rep(1,nrow(gx)))  

then I run the lme  

fm<- lme(y ~ 1, data=gx,



    finally, I use VarCorr to extract the variance components  

           vc <- VarCorr(fm)  

                     Variance           StdDev  

Operator:Run 1.595713e-10:20 1.263215e-05:20

Sample 5.035235e+00: 4 2.243933e+00: 4

Operator 5.483145e-04: 4 2.341612e-02: 4

Residuals 8.543601e-02: 1 2.922944e-01: 1    

2. Using lmer in Matrix package:  

fm <- lmer(y ~ (1 | Sample) + (1 | Operator) +

           (1|Operator:Run), data=x)


Linear mixed-effects model fit by REML

Formula: H.I.Index ~ (1 | Sample.Name) + (1 | Operator) + (1 | Operator:Run)

          Data: x

      AIC BIC logLik MLdeviance REMLdeviance

 96.73522 109.0108 -44.36761 90.80064 88.73522

Random effects:

 Groups Name Variance Std.Dev.

 Operator:Run (Intercept) 4.2718e-11 6.5359e-06

 Operator (Intercept) 5.4821e-04 2.3414e-02

 Sample (Intercept) 5.0352e+00 2.2439e+00

 Residual                 8.5436e-02 2.9229e-01

number of obs: 159, groups: Operator:Run, 20; Operator, 4; Sample.Name, 4  

Fixed effects:

             Estimate Std. Error t value

(Intercept) 0.0020818 1.1222683 0.001855

There is a difference between lmer and lme is for the factor Operator:Run. I cannot find where the problem is. Could anyone point me out if my model specification is correct for the problem I am dealing with. I am pretty new user to lme and lmer. Thanks for your help!    

Wilson Wang    

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