[R-sig-ME] Data sheet notation and model structure for GLMM with 3 non-factorial factors

[Raldo Kruger]

Hi R users,

I have 3 factors in a non-factorial design (G, K and N), as well as
two time periods (Year) and a random factor (Site), with Plant numbers
as the response variable.

My 1st question relates to the the notation of the treatments in the
data frame. Is it appropriate to use an expanded treatment notation,
such as this, when using glmer{lme4}:

Site	Year	Plant	G	K	N
A	1	5	0	0	0
A	1	4	1	0	0
A	1	7	0	1	0
A	1	10	0	0	1
A	2	3	0	0	0
A	2	4	1	0	0
A	2	8	0	1	0
A	2	12	0	0	1
B	1	7	0	0	0
B	1	3	1	0	0
B	1	7	0	1	0
B	1	12	0	0	1
B	2	4	0	0	0
B	2	5	1	0	0
B	2	6	0	1	0
B	2	11	0	0	1

With the model

m1<-glmer(Plant~G+K+N+Year+(1|Site), ...)

Or is it better to use a single column for the treatments, like this:

Site	Year	Plant	Treatment
A	1	5	C
A	1	4	G
A	1	7	K
A	1	10	N
A	2	3	C
A	2	4	G
A	2	8	K
A	2	12	N
B	1	7	C
B	1	3	G
B	1	7	K
B	1	12	N
B	2	4	C
B	2	5	G
B	2	6	K
B	2	11	N

With the following model:
m1<-glmer(Plants~Treatment+Year+(1|Site), ...)

Many thanks,
-- 
Raldo Kruger
MSc student
University of Cape Town