[R] Lme does not work without a random effect (UNCLASSIFIED)

From: Park, Kyong H Mr ECBC <kyong.ho.park_at_us.army.mil>
Date: Fri, 14 Mar 2008 15:25:52 -0400


Classification: UNCLASSIFIED
Caveats: NONE

Dear R users,

I'm interested in finding a random effect of the Block in the data shown below, but 'lme' does not work without the random effect. I'm not sure how to group the data without continuous value which is shown in the error message at the bottom line. If I use 'aov' with Error(Block), is there a test method comparing between with and without the Block random effect. I'm using R 2.4.1.

Appreciate your help.

Kyong

     LCU ST1 SURF Block
1  6.71   A    N     1
2  6.97   A    Y     1
3  6.77   B    N     1
4  6.90   B    Y     1
5  6.63   C    N     1
6  6.94   C    Y     1
7  6.79   D    N     1
8  6.93   D    Y     1
9  6.23   A    N     2
10 6.83   A    Y     2
11 6.61   B    N     2
12 6.86   B    Y     2
13 6.51   C    N     2
14 6.90   C    Y     2
15 5.90   D    N     2
16 6.97   D    Y     2

A result with the random effect:

Anal1<-lme(LCU~ST1*SURF,random=~1|Block,data=data1)
> summary(Anal1)

Linear mixed-effects model fit by REML
 Data: data1

       AIC BIC logLik
  25.38958 26.18399 -2.694789

Random effects:
 Formula: ~1 | Block

        (Intercept) Residual
StdDev: 0.1421141 0.218483

Fixed effects: LCU ~ ST1 * SURF

             Value Std.Error DF t-value p-value

(Intercept)  6.470 0.1842977  7 35.10625  0.0000
ST1B         0.220 0.2184830  7  1.00694  0.3475
ST1C         0.100 0.2184830  7  0.45770  0.6610
ST1D        -0.125 0.2184830  7 -0.57213  0.5851
SURFY        0.430 0.2184830  7  1.96812  0.0897
ST1B:SURFY  -0.240 0.3089816  7 -0.77675  0.4627
ST1C:SURFY  -0.080 0.3089816  7 -0.25892  0.8031
ST1D:SURFY   0.175 0.3089816  7  0.56638  0.5888

Without the random effect:

Anal2<-lme(LCU~ST1*SURF,data=data1)
Error in getGroups.data.frame(dataMix, groups) :

        Invalid formula for groups
Classification: UNCLASSIFIED
Caveats: NONE

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