Re: [R] R package that has (much) the same capabilities as SAS v9 PROC GENMOD

From: Wensui Liu <>
Date: Tue 05 Apr 2005 - 08:53:03 EST

check glm()

On Apr 4, 2005 6:46 PM, William M. Grove <> wrote:
> I need capabilities, for my data analysis, like the Pinheiro & Bates
> S-Plus/R package nlme() but with binomial family and logit link.
> I need multiple crossed, possibly interacting fixed effects (age cohort of
> twin when entered study, sex of twin, sampling method used to acquire twin
> pair, and twin zygosity), a couple of random effects other than the cluster
> variable, and the ability to have a variable of the sort that P&B call
> "outer" to the clustering variable---zygosity. Dependent variables are all
> parental (mom, dad separately of course) psychiatric diagnoses.
> In my data, twin pair ID is the clustering variable; correlations are
> expected to be exchangeable but substantially different between members of
> monozygotic twin pairs and members of dizygotic twin pairs. Hence, in my
> analyses, the variable that's "outer" to twin pair is monozygotic vs.
> dizygotic which of course applies to the whole pair.
> nlme() does all that but requires quasi-continuous responses, according to
> the preface/intro of P&B's mixed models book and what I infer from online
> help (i.e., no family= or link= argument).
> The repeated() library by Lindsey seems to handle just one nested random
> effect, or so I believe I read while scanning backlogs of the R-Help list.
> glmmPQL() is in the ballpark of what I need, but once again seems to lack
> the "outer" variable specification that nlme() has, and which PROC GENMOD
> also has---and which I need.
> I read someplace of yags() that apparently uses GEE to estimate parameters
> of nonlinear models including GLIMs/mixed models, just the way PROC GENMOD
> (and many another program) does. But on trying to install it (either
> or v4.0-2.tar.gz from Carey's site, or Ripley's Windows port)
> from a local, downloaded zip file (or tar.gz file converted to zip file), I
> always get an error saying:
> > Error in file(file, "r") : unable to open connection
> > In addition: Warning message:
> > cannot open file `YAGS/DESCRIPTION'
> with no obvious solution.
> So I can't really try it out to see if it does what I want.
> You may ask: Why not just use GENMOD and skip the R hassles? Because I
> want to embed the GLIM/mixed model analysis in a stratified resampling
> bootstrapping loop. Very easy to implement in R, moderately painful to do
> in SAS.
> Can anybody give me a lead, or some guidance, about getting this job done
> in R? Thanks in advance for your help.
> Regards,
> Will Grove | Iohannes Paulus PP. II, xxx
> Psychology Dept. |
> U. of Minnesota |
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> Will Grove&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; | Iohannes Paulus PP. II,
> xxx <br>
> Psychology Dept. |<br>
> U. of Minnesota&nbsp; |<br>
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WenSui Liu, MS MA
Senior Decision Support Analyst
Division of Health Policy and Clinical Effectiveness
Cincinnati Children Hospital Medical Center

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Received on Tue Apr 05 08:57:35 2005

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