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

[Tim Howard]

>>>> Hans Ekbrand <hans.ekbrand at gmail.com> 12/13/2013 12:42 PM >>>
>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?
 
I am following the idea of Probabilistic Survey designs championed by USEPA (authors
are primarily Kincaid and Olsen, randomization method is GRTS using R package spsurvey). The main
idea is that you get an estimate of the target population through a random sample at T1 and then 
another estimate of the population through a separate random sample at T2. 
 
http://www.epa.gov/nheerl/arm/designpages/monitdesign/survey_overview.htm 
 
Perhaps that was a bad idea! :)  But, it actually would have been VERY 
hard to visit the exact same locations again and again so this approach does 
make sense in this context. 
 
Best, 
Tim