[R-sig-ME] A three-level GLMM with binomial link in R

[Robert Long]

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On Fri, 5 Mar 2021, 21:18 Hedyeh Ahmadi, <hedyehah using usc.edu> wrote:

> Hi - Thank you for the informative replies.
>
> I will try those other packages. If MASS::glmmPQL uses lme() then this
> should work for me.
>
> My data structure is complex so it's hard to give reproducible example but
> for example for two of my models I get the following errors in lmer() while
> lme() runs smoothly.
>
> 1- Error: cannot allocate vector of size 2.3 Gb.
>
> 2- Error: couldn't evaluate grouping factor id:(family:site) within model
> frame: try adding grouping factor to data frame explicitly if possible.
> (note that the id variable works for simpler lmer() models so the variable
> itself is not an issue)
>
> My model looks like the following nested structure:
> lmer(Y ~ 1 + X1 + X2 + X3 + (1|site/family/id), data=dd, REML = FALSE)
>
> Best,
>
> Hedyeh Ahmadi, Ph.D.
> Statistician
> Keck School of Medicine
> Department of Preventive Medicine
> University of Southern California
>
> Postdoctoral Scholar
> Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
> University of California, Irvine
>
> LinkedIn
> www.linkedin.com/in/hedyeh-ahmadi<http://www.linkedin.com/in/hedyeh-ahmadi
> >
> <http://www.linkedin.com/in/hedyeh-ahmadi><
> http://www.linkedin.com/in/hedyeh-ahmadi>
>
>
>
>
> ________________________________
> From: Dexter Locke <dexter.locke using gmail.com>
> Sent: Friday, March 5, 2021 1:01 PM
> To: Hedyeh Ahmadi <hedyehah using usc.edu>
> Cc: r-sig-mixed-models using r-project.org <r-sig-mixed-models using r-project.org>;
> Megan M. Herting <herting using usc.edu>; Elisabeth Burnor <burnor using usc.edu>
> Subject: Re: [R-sig-ME] A three-level GLMM with binomial link in R
>
> Hi Hedyeh,
>
> What is the problem you are having? Specifically, what is the estimation
> issue with lmer and lme?
>
> Can you provide a reproducible example? Can you provide the complete
> errors you are seeing?
>
> The current questions are vague, so it will be challenging for list
> members to provide much guidance.
>
> -Dexter
>
>
> On Fri, Mar 5, 2021 at 3:27 PM Hedyeh Ahmadi <hedyehah using usc.edu<mailto:
> hedyehah using usc.edu>> wrote:
> Hi All,
> I was wondering what would be a powerful package in R to run GLMM with
> logit link that can handle a data set with N=22945 and 3 nested random
> intercepts. So far, I have tried glmer() from lme4 and it's giving me a lot
> of estimation issues. Any other package I should try?
>
> I am asking for another package as I am having the same issue with lmer()
> for similar LMM with continuous outcome, while lme() from nlme package runs
> the models with no problem.
>
> Thank you in advance.
>
> Best,
>
> Hedyeh Ahmadi, Ph.D.
> Statistician
> Keck School of Medicine
> Department of Preventive Medicine
> University of Southern California
>
> Postdoctoral Scholar
> Institute for Interdisciplinary Salivary Bioscience Research (IISBR)
> University of California, Irvine
>
> LinkedIn
> www.linkedin.com/in/hedyeh-ahmadi<
> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> ><http://www.linkedin.com/in/hedyeh-ahmadi<
> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
> >>
> <http://www.linkedin.com/in/hedyeh-ahmadi<
> https://urldefense.com/v3/__http://www.linkedin.com/in/hedyeh-ahmadi__;!!LIr3w8kk_Xxm!8UfGozITdR3cNo929aSVEsbVNgbIul9f91q4hA3PAf0ywits0jIKVDAQdYkAXFg$
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> >>
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