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

[Hedyeh Ahmadi]

Thank you for the reply Robert - If I am running out of memory in lmer(), do you know why lme() runs just fine?

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>
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________________________________
From: Robert Long <longrob604 using gmail.com>
Sent: Friday, March 5, 2021 1:43 PM
To: Hedyeh Ahmadi <hedyehah using usc.edu>
Cc: Dexter Locke <dexter.locke using gmail.com>; R-mixed models mailing list <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

You've run out of memory. Try running it on a machine with much larger RAM.

On Fri, 5 Mar 2021, 21:18 Hedyeh Ahmadi, <hedyehah using usc.edu<mailto: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
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________________________________
From: Dexter Locke <dexter.locke using gmail.com<mailto:dexter.locke using gmail.com>>
Sent: Friday, March 5, 2021 1:01 PM
To: Hedyeh Ahmadi <hedyehah using usc.edu<mailto:hedyehah using usc.edu>>
Cc: r-sig-mixed-models using r-project.org<mailto:r-sig-mixed-models using r-project.org> <r-sig-mixed-models using r-project.org<mailto:r-sig-mixed-models using r-project.org>>; Megan M. Herting <herting using usc.edu<mailto:herting using usc.edu>>; Elisabeth Burnor <burnor using usc.edu<mailto: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><mailto: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

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