Dear Dr. Bolker,

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????

# 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 ,..

Again, I want to thank you very much by all your attention and help me to
understand this fascinating world of glm !!!

very best wishes
Carlos


2014-05-13 15:11 GMT-03:00 Carlos Barboza <carlosambarboza@gmail.com>:

> > I'm a phd student from The Federal University of Rio de Janeiro
> > Brazil in Marine Biology. First it's a pleasure to to send you a
> message. The reason
> > for it is that I'm using glmmADMB package for run my analyses and I
> > have some doubts. In a simple way I have the following model:
> > sectors a fixed factor; sites (nested in sectors, random), points
> > (nested in sites, random). So:
> >
> > teste1<- glmmadmb(total ~ sector + (1 | sector/site/point),...
> >
> > # why  did the result gave me the effect of the factor sector alone,
> > also in the random effects...? since the random effect included
> > only the nested factors and must include only the effects of
> > sector/site and sector/site/point
> >
> > # but if I try:
> >
> > teste1<- glmmadmb(total ~ set + (1 | site/point),...
> >
> > # I get that result, but I think that with this path, site/point
> > were not nested within sector
> >
> > # in another ocasion it is correct to code only random effects like:
> > model<- glmmadmb(log(total+1) ~ 1, random= ~ 1 | set/loc/pon,
> family=......
>
> > # whatever the case, I thank for all your attention
> >
> >  # Best regards Carlos Barboza
>

	[[alternative HTML version deleted]]

