[R] Incomplete block design with random effects

[R DF]

Dear R Users,

I am facing a problem analyzing an incomplete block design with two
replicates. As you can see in the attached .xls file, the factor2 (6
levels) nested within factor1(two levels) nested within replicates all were
chosen as random effects in the statistical model (see below). Note that
the replicates are incomplete. The effect of year crossed with these
factors as random.  To handle incomplete design and random effects, I used
lme package instead of aov as follows:

*library(nlme)*

*data<- read.table("C:\\Users\\user\\Desktop\\sb.txt",header=T)*

*attach(data)*

*model<-lme(var~1+ year+ year*replicates+ year*factor1+ year*factor2,
random=~1|replicates/factor1/factor2)*

*summary(model)*



 The above-code is runnable. However, could you please make me sure of the
following points?


1- Have I defined the interactions correctly (particularly year by other
factors) ?



2- Which one should I include into the statistical model, replicates or
block.incomplete?



3- How can I compare different levels of each factor (i.e. factor1,
factor2, year)? In other words, is there any way to use LSD or SED methods
in the package lme?



Your help would be highly appreciated.



Best regards,

Reza
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Plot	year	replicates	block.incomplete	factor1	factor2	var
1	1990	1	1	t2	G2	10
2	1990	1	1	t2	G3	12
3	1990	1	1	t2	G4	16
4	1990	1	1	t2	C1	12
5	1990	1	1	t2	C2	11
6	1990	1	1	t2	G1	13
7	1990	1	2	t1	G1	19
8	1990	1	2	t1	G2	29
9	1990	1	2	t1	G3	30
10	1990	1	2	t1	C1	23
11	1990	1	2	t1	R	32
12	1990	1	2	t1	C2	33
13	1990	2	1	t2	G4	12
14	1990	2	1	t2	C1	14
15	1990	2	1	t2	C2	18
16	1990	2	1	t2	G1	14
17	1990	2	1	t2	G2	13
18	1990	2	1	t2	G3	15
19	1990	2	2	t1	C1	21
20	1990	2	2	t1	R	31
21	1990	2	2	t1	C2	32
22	1990	2	2	t1	G1	25
23	1990	2	2	t1	G2	34
24	1990	2	2	t1	G3	35
1	1996	1	1	t2	G1	28
2	1996	1	1	t2	G2	30
3	1996	1	1	t2	G3	34
4	1996	1	1	t2	G4	30
5	1996	1	1	t2	C1	29
6	1996	1	1	t2	C2	31
7	1996	1	2	t1	C2	37
8	1996	1	2	t1	G1	47
9	1996	1	2	t1	G2	48
10	1996	1	2	t1	G3	41
11	1996	1	2	t1	C1	50
12	1996	1	2	t1	R	51
13	1996	2	1	t2	G3	30
14	1996	2	1	t2	G4	32
15	1996	2	1	t2	C1	36
16	1996	2	1	t2	C2	32
17	1996	2	1	t2	G1	31
18	1996	2	1	t2	G2	33
19	1996	2	2	t1	G3	39
20	1996	2	2	t1	C1	49
21	1996	2	2	t1	R	50
22	1996	2	2	t1	C2	43
23	1996	2	2	t1	G1	52
24	1996	2	2	t1	G2	53
1	2002	1	1	t2	C1	16
2	2002	1	1	t2	C2	18
3	2002	1	1	t2	G1	22
4	2002	1	1	t2	G2	18
5	2002	1	1	t2	G3	17
6	2002	1	1	t2	G4	19
7	2002	1	2	t1	C1	25
8	2002	1	2	t1	R	35
9	2002	1	2	t1	C2	36
10	2002	1	2	t1	G1	29
11	2002	1	2	t1	G2	38
12	2002	1	2	t1	G3	39
13	2002	2	1	t2	G1	18
14	2002	2	1	t2	G2	20
15	2002	2	1	t2	G3	24
16	2002	2	1	t2	G4	20
17	2002	2	1	t2	C1	19
18	2002	2	1	t2	C2	21
19	2002	2	2	t1	G1	27
20	2002	2	2	t1	G2	37
21	2002	2	2	t1	G3	38
22	2002	2	2	t1	C1	31
23	2002	2	2	t1	R	40
24	2002	2	2	t1	C2	41