[R-sig-ME] Fwd: R - specify estimated residual variance
Douglas Bates
bates at stat.wisc.edu
Fri Apr 4 16:19:40 CEST 2008
---------- Forwarded message ----------
From: Douglas Bates <bates at stat.wisc.edu>
Date: Fri, Apr 4, 2008 at 7:38 AM
Subject: Re: R - specify estimated residual variance
To: Kelly Wauters <Kelly.wauters at kuleuven-kortrijk.be>
On Fri, Apr 4, 2008 at 7:11 AM, Kelly Wauters
<Kelly.wauters at kuleuven-kortrijk.be> wrote:
> Dear Prof. dr. Bates,
> I want to use lmer to fit a glmm with a dichotomous dependent variable
> (family binomial - link logit). The scores on the lowest level follow a
> binomial distribution. This indicates that the variance of the lowest
> level is defined by the estimated residual variance multiplied by
> pi(1-pi). This means that the estimated residual variance has to be
> equal to 1. In SAS you can do this by means of the code
> proc glimmix data= dichotoom noclprint noitprint asycov ;
> class school id item;
> PARMS 0.34 1/HOLD=2;
> model scores=/ dist=binomial solution;
> random intercept/ subject=id;
> random _residual_;
> run;
> How can I translate the code into R code?
> > dichloso$school<-as.factor(dichloso$school)
> > dichloso$id<-as.factor(dichloso$id)
> > dichloso$item<-as.factor(dichloso$item)
Transforming those variables to factors is a good practice but not
strictly necessary to fit the model shown below.
> > model <- lmer(scores~1+(1|id), dichotoom,
family=binomial(link="logit"),...)
> I don't know how I can translate the code PARMS 0.34 1/HOLD=2; into R
> code. Can you help me on this?
I'm afraid I can't help you on this because I don't know what the SAS
code does. I don't use SAS myself.
It is possible that there is no need to specify this parameter in R as
having a constant value. My guess, but this is just a guess, is that
the distinction between holding that parameter constant at 1 and
allowing it to vary is equivalent to using the binomial family or the
quasibinomial family in lmer.
May I send a copy of this reply to the
R-SIG-Mixed-Models at r-project.org mailing list? ("SIG" == "Special
Interest Group")? (I ask your permission to send the copy because I am
quoting your original question.) Some who subscribe to that mailing
list may have experience with SAS PROC GLIMMIX and be able to describe
the equivalent code for lmer.
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