[R-sig-ME] / vs : operators in model specifications
Douglas Bates
bates at stat.wisc.edu
Tue Mar 4 00:12:35 CET 2008
On Mon, Mar 3, 2008 at 4:21 PM, Martin Eklund
<martin.eklund at farmbio.uu.se> wrote:
> Hi all,
> I'm new to mixed models and lme4 and would appreciate any help on
> specifying models in lme4. Specifically I'm wondering about
> specifying nested variables. As I understand it lmer is capable of
> determining the nesting structure by itself (as long as the nesting
> is not implicit in the factors), so is there ever a need for
> specifying the nesting structure in the model specification when
> using lmer? Assuming A and B are random factors, B is nested in A,
> and Y is a response. What would be the difference between the
> following model specifications?
>
> (i) lmer(Y ~ (1|A) + (1|B))
> (ii) lmer(Y ~ (1|A) + (1|A:B))
> (iii) lmer(Y ~ (1|A) + (1|A/B))
They should be the same provided that the levels of B are not
implicitly nested in the levels of A, which is what you indicated
would be the case.
The specification (1|A) + (1|A/B) is redundant as (1|A/B) expands to
(1|A) + (1|A:B) so (iii) could be written as
lmer(Y ~ 1|A/B)
> On a different note: using the mcmcsamp method, is it possible to
> change the choice of priors? I understand that this is a longshot and
> that it is most likely not possible, but I'm still asking just to be
> sure. Is there another way this can be done (i.e. sampling from the
> posterior distribution of a mixed model but with a general choice of
> prior)?
Unfortunately, no, there is no convenient way of specifying an
arbitrary prior for the mcmcsamp function. To make it practical to
use that function routinely, the sampling scheme is hard-wired into
compiled code and based upon having an improper, locally uniform prior
on the fixed effects and improper, locally uniform priors on the
logarithms of the variance components.
> Thank you very much!
>
> Best regards,
>
> Martin.
>
> ========================================
> Martin Eklund
> PhD Student
> Department of Pharmaceutical Biosciences
> Uppsala University, Sweden
> Ph: +46-18-4714281
> ========================================
>
>
>
>
>
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>
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