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List:       r-sig-mixed-models
Subject:    Re: [R-sig-ME] year and site
From:       Will Morris <wkmor1 () gmail ! com>
Date:       2009-09-26 22:17:23
Message-ID: a5dabfa60909261517h7bbec593j946f3babcdb78a8b () mail ! gmail ! com
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I'll save you the trouble---below is the paper the book chapter is taken
from.
http://www.stat.columbia.edu/~gelman/research/published/taumain.pdf

On Sun, Sep 27, 2009 at 6:07 AM, Andrew J Tyre <atyre2@unlnotes.unl.edu>wrote:

> When I'm doing mcmc I'm usually using a gamma prior:
>
> plot(dgamma(x,1,1)~x)
>
> but you're suggesting
> lines(dcauchy(x,0,1)~x)
>
> or rather
> lines(dcauchy(x,0,1)*2~x)
>
> thanks, I'll look up that reference!
>
> Drew Tyre
>
> School of Natural Resources
> University of Nebraska-Lincoln
> 416 Hardin Hall, East Campus
> 3310 Holdrege Street
> Lincoln, NE 68583-0974
>
> phone: +1 402 472 4054
> fax: +1 402 472 2946
> email: atyre2@unl.edu
> http://snr.unl.edu/tyre
> http://aminpractice.blogspot.com
>
> r-sig-mixed-models-bounces@r-project.org wrote on 09/26/2009 08:41:20 AM:
>
> > Will Morris <wkmor1@gmail.com>
> > Sent by: r-sig-mixed-models-bounces@r-project.org
> >
> > 09/26/2009 08:43 AM
> >
> > To
> >
> > Andrew J Tyre <atyre2@unlnotes.unl.edu>
> >
> > cc
> >
> > "r-sig-mixed-models@r-project.org" <r-sig-mixed-models@r-project.org>
> >
> > Subject
> >
> > Re: [R-sig-ME] year and site
> >
> > Gelman suggests that specifying a weakly informative half-Cauchy
> > distribution for the group level standard deviation can overcome the
> > difficulty in estimation experienced when there are few groups and
> > your using a uniform prior (and I presume using Maximum likelihood
> > too). See Gelman & Hill, 2007.
> >
> > Will Morris
> > Masters of Philosophy candidate
> > Vesk Plant Ecology Lab
> > The School of Botany
> > The University of Melbourne
> > Australia
> > Phone: +61 3 8344 0120
> > http://www.botany.unimelb.edu.au/vesk/
> >
> > On 26/09/2009, at 23:29, Andrew J Tyre <atyre2@unlnotes.unl.edu> wrote:
> >
> > > Hi all,
> > >
> > > in ecology year a study is done in, and the site it is done at, are
> > > obvious random effects. However, for most student projects, and
> > > indeed,
> > > even larger projects, having more than 2-3 years of data is unusual.
> > > Having more than 2-3 sites is more common, but even then the number is
> > > very limited. This means that estimating a random effect of year
> > > crossed
> > > with site is difficult. The solution that I've tried a couple times
> > > is to
> > > create a "siteyear" random effect, where each year at each site is a
> > > different level. This gives many more levels with which to estimate
> > > variances, and seems to work well. The only downside that I've been
> > > able
> > > to come up with is that if there are "site" effects that are
> > > consistent
> > > through time, or year effects consistent across space, then this
> > > approach
> > > misses separating them, at a minimum. What I'm concerned about is
> > > that it
> > > might lead to bias as well - I don't think it will, but I'd rather be
> > > certain!
> > >
> > > I have used the "fallback" of fitting year and/or site as a fixed
> > > effect,
> > > but I'm hearing some concern from reviewers who've been sold on the
> > > random
> > > effects idea convincingly enough to reject a paper that doesn't
> > > treat year
> > > or site as random without recognizing that it doesn't help when the
> > > number
> > > of levels is low. Also, if there is a continuous covariate whose
> > > effect
> > > varies by siteyear, the fixed effect interaction term gets ugly, fast.
> > >
> > > Any discussion or insights appreciated!
> > >
> > > thanks,
> > >
> > >
> > >
> > > Drew Tyre
> > >
> > > School of Natural Resources
> > > University of Nebraska-Lincoln
> > > 416 Hardin Hall, East Campus
> > > 3310 Holdrege Street
> > > Lincoln, NE 68583-0974
> > >
> > > phone: +1 402 472 4054
> > > fax: +1 402 472 2946
> > > email: atyre2@unl.edu
> > > http://snr.unl.edu/tyre
> > > http://aminpractice.blogspot.com
> > >    [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > R-sig-mixed-models@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >
> > _______________________________________________
> > R-sig-mixed-models@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>



-- 
Will Morris
Masters of Philosophy candidate
Vesk Plant Ecology Lab
The School of Botany
The University of Melbourne
Australia
Phone: +61 3 8344 0120
http://www.botany.unimelb.edu.au/vesk/

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