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

From: Sundar Dorai-Raj <sundar.dorai-raj_at_pdf.com>
Date: Fri, 14 Mar 2008 12:40:57 -0700

Park, Kyong H Mr ECBC said the following on 3/14/2008 12:25 PM:
> 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
>
>

Use "lm" to fit the model without random effect and use anova to compare:

z <- read.table(con <- textConnection("     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"), header = TRUE)
close(con)

library(nlme)
fit <- lme(LCU~ST1*SURF,random=~1|Block,data=z) fit0 <- lm(LCU~ST1*SURF,data=z)
anova(fit, fit0)

HTH, --sundar



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