[R-sig-ME] model specification for continuous environmental vars

[Hans Ekbrand]

On Thu, Dec 12, 2013 at 01:39:04PM -0500, Tim Howard wrote:
> List members - 
> I am learning a lot, quickly, but still have a way to go. I would 
> greatly appreciate some help with model specification in glmer.
> I can't find a good example that parallels what I've got.
> 
> My dataset consists of spatially-balanced random samples of rare 
> plants within alpine summits. There were two sampling bouts (yr1 and yr2)
> with yr2 collected 6 years after yr1. A new set of random plots were 
> collected at each bout (e.g. new estimate of the population, not repeated 
> measures). I would like to test the difference in plant density from yr1 to yr2, overall. 

If you only want to test if there is a difference in plant density
between yr1 and yr2, then I don't think you should include the
environmental variables, since difference in the outcome that relates
to changes in the environmental variables between yr1 and yr2 would be
attributed to the enviromental variables and "hide" the actual
differences in outcome between yr1 and yr2.

mod <- glmer(count ~ samp + (1|summit), data = dat, family="poisson")

would be more appropriate, I think.

Inclusions of the envirmental variables should only be done if you
want to explain differences between yr1 and yr2, not for estimating
their size.