Doubts about models in glmmADMB
On 14-05-14 08:56 AM, Carlos Barboza wrote:
Dear Dr. Bolker,
(note this is sent to the mixed models list, not just to me ...)
I'm working with spatial factors: sectors are spaced by kilometers, sites (randomly sampled within sectors) are spaced by hundred of meters, and points (randomly sampled within sites) are spaced by dozen of meters. I have, 3 sectors, 3 sites within each sector and 3 points within each site, replicated 5 times (n=135). Sectors specify a pollution gradient. So I want to investigate the sector's effect (fixed) and the spatial variability within each sector by two spatial scales, sites and points. Labels were coded like your example in http://glmm.wikidot.com/faq: (e.g. A1, A2, ???, B1, B2, ???), the only difference is to include points (A11,A12,A13.....A33). So this was my doubt:
model.1<- glmmadmb(total ~ sector + (1 | sector/site/point),...
or
model.2<-glmmadmb(total ~ sector + (1 | site/point),...
when I want to include all spatial variability????
Given what you have said, the second specification is correct. The first includes sector, redundantly, both as a fixed effect and as a grouping variable for variation in intercepts.
# since I want to test if a model including only sector or sector and within spatial variability of each sectors, are better then a null model, I specified this null model with the intercept only:
null.model<-glmmadmb(total ~ 1 ,..
Sounds reasonable, although keep in mind the issues with using likelihood ratio tests to test null hypotheses of zero variance ... Ben Bolker