[R-sig-ME] predict.glmmTMB when "cloglog" link is used.

Rolf Turner r@turner @end|ng |rom @uck|@nd@@c@nz
Mon Mar 23 22:58:57 CET 2020

On 23/03/20 11:51 pm, Mollie Brooks wrote:

> This sounds like a bug, but I can’t repeat the behavior. I get
> reasonable values in p2 and they look highly correlated to p1. Are
> you using the latest version from CRAN, 1.0.1? It should be
> essentially the same as the master branch on GitHub (only one
> vignette is behind). I can’t remember any recent changes (to either
> the CRAN or GitHub versions) that would make a difference, but
> updating is worth a try.
> cheers,
> Mollie

Turned out I was using version 1.0.0; I upgraded to 1.0.1 and the 
problem went away.

The key to the mystery may be that I was actually using the *patched* 
version that Ben Bolker had put up on github, which I installed via

> remotes::install_github("glmmTMB/glmmTMB/glmmTMB using cloglog_fix") 

Ben was trying to alleviate a problem that I'd encountered in trying to 
use glmmTMB() to fit models that involved the betabinomial family and 
the "cloglog" link.  Perhaps he buggered something up in attempting the 
fix (which turned out not to work anyway!).

Anyhow, predict.glmmTMB() now seems to work, at least.




Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

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