My design has a total of 20 sites. 5 sites belong to each of four land covers: A, B, C and D. In each site, I have 5 sampling locations, 2 metres from each other. From each sampling location, I collected soil, and measured phosphatase activity in the soil from the sampling location.
I want to test for the effect of Land Cover type on soil phosphatase activity. Note that the land covers are NOT nested within a site. Rather, 5 sampling locations (pseudoreplicates) are nested within each site. Total 5 sites per land cover type. Total 4 land cover types.
I am confused regarding what exactly should be the random effects structure. Preliminary data exploration shows that the inter-Site variation is different in the different land cover types. What I understand from this is that the random effects should be different for the 4 land cover types.
In this case, what model specification do I need to use in nlme?
Activity ~ LandCoverType, random = 1|Site?
Activity ~ LandCoverType, random = LandCoverType|Site?
or some other way?
I am confused because I have read that the second kind of model specification means that the effect of LandCoverType on Activity depends on the Site.... However, this doesn't seem to make sense in my case, since I do not have all four land cover types in each Site!