[R] how to test the random factor effect in lme
Xiang Gao
xianggao2006 at gmail.com
Tue Feb 14 23:36:25 CET 2012
Hi
I am working on a Nested one-way ANOVA. I don't know how to implement
R code to test the significance of the random factor
My R code so far can only test the fixed factor :
anova(lme(PCB~Area,random=~1|Sites, data = PCBdata))
numDF denDF F-value p-value
(Intercept) 1 12 1841.7845 <.0001
Area 1 4 4.9846 0.0894
Here is my data and my hand calculation.
> PCBdata
Area Sites PCB
1 A 1 18
2 A 1 16
3 A 1 16
4 A 2 19
5 A 2 20
6 A 2 19
7 A 3 18
8 A 3 18
9 A 3 20
10 B 4 21
11 B 4 20
12 B 4 18
13 B 5 19
14 B 5 20
15 B 5 21
16 B 6 19
17 B 6 23
18 B 6 21
By hand calculation, the result should be:
Source SS DF MS
Areas 18.00 1 18.00
Sites 14.44 4 3.61
Error 20.67 12 1.72
Total 53.11 17 ---
MSareas/MSsites = 4.99 --- matching the R output
MSsites/MSE = 2.10
Conclusion is that Neither of Areas nor Sites make differences.
My R code so far can only test the fixed effect :
anova(lme(PCB~Area,random=~1|Sites, data = PCBdata))
numDF denDF F-value p-value
(Intercept) 1 12 1841.7845 <.0001
Area 1 4 4.9846 0.0894
--
Xiang Gao, Ph.D.
Department of Biology
University of North Texas
More information about the R-help
mailing list