[R-sig-ME] ICC for glmer Poisson

dani orchidn at live.com
Mon Feb 5 01:37:14 CET 2018

Thank you so much for these great suggestions!


From: Paul Johnson <paul.johnson at glasgow.ac.uk>
Sent: Friday, February 2, 2018 2:46 PM
To: dani
Cc: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] ICC for glmer Poisson


Have a look at

Nakagawa, Shinichi, and Holger Schielzeth. 2010. “Repeatability for Gaussian and Non-Gaussian Data: A Practical Guide for Biologists.” Biological Reviews of the Cambridge Philosophical Society 85 (4): 935–56. doi:10.1111/j.1469-185X.2010.00141.x.

and the related rptR package:

Stoffel, M., Nakagawa, S. & Schielzeth, H. (2017) rptR: Repeatability estimation and variance decomposition by generalized linear mixed-effects models.. Methods Ecol Evol. Accepted Author Manuscript. doi:10.1111/2041-210X.12797

There are various ways to get CIs for variances, the easiest is applying confint() to a glmer fit (in fact I think this gives CIs for the SDs). For getting confidence (credible) intervals from variance estimates though I think MCMC (e.g. MCMCglmm) works best.
For testing random effects, see:
GLMM FAQ - GitHub Pages<http://bbolker.github.io/mixedmodels-misc/glmmFAQ.html#testing-significance-of-random-effects>
Introduction. This is an informal FAQ list for the r-sig-mixed-models mailing list. The most commonly used functions for mixed modeling in R are. linear mixed models ...

Good luck,

> On 2 Feb 2018, at 17:31, dani <orchidn at live.com> wrote:
> Hello everyone,
> I am looking for information regarding the calculation of the ICC for a Poisson Glmer model.
> I remember seeing somewhere that the within group variance is considered to be 1 in the calculation of the ICC for Poisson, but I do not have a reference for that. I did some research online but I could not find much.
> Any help would be very appreciated.
> Also, is there a way to determine significance and CIs for variances? I was thinking that variance can be tested by comparing a Glm model (without random effects) and the Glmer model (with random effects) using anova(), but I have no idea how to calculate the CIs.
> Thank you all!
> MD
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