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

[Hans Ekbrand]

On Fri, Dec 13, 2013 at 08:40:55AM -0500, Tim Howard wrote:
> >From: Hans Ekbrand <hans.ekbrand at gmail.com>
> >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.
> These are good points. My reasoning was that I need to control for these
> variables somehow. What if I have higher densities in yr2 but it is completely 
> due to sampling -- that my plots happened to be at elevations where there are
> higher densities? I want to remove the effect of differences in elevation when 
> testing for the differences between yr1 and yr2. 

OK, I thought about real changes between yr1 and yr2, not artifacts
due to sampling. elevation and slope does not vary over time, but
solar radiation could vary over time, I guess.

If your research question is about changes over time, then why did you
change the sampled areas between the measure points?