[R-sig-ME] nAGQ = 0

Conor Michael Goold conor.goold at nmbu.no
Thu Sep 7 10:04:59 CEST 2017

Hi Rolf, 

Just a quick point: running the brms model with a logit link works fine for me.

Best regards
Conor Goold
PhD Student
Phone:        +47 67 23 27 24

Norwegian University of Life Sciences
Campus Ås. www.nmbu.no

From: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> on behalf of Rolf Turner <r.turner at auckland.ac.nz>
Sent: Thursday, September 7, 2017 6:12 AM
To: Poe, John
Cc: r-sig-mixed-models
Subject: Re: [R-sig-ME] nAGQ = 0

On 07/09/17 10:57, Poe, John wrote:

> This is where my being a political scientist on a listserv full of
> definitely not political scientists is going to make me look dumb. I've
> never actually seen a model specification like that before for a
> multilevel model. Is the outcome supposed to be the proportion dead out
> of the total population for each row? I'm missing something about this
> that is probably very obvious.
> After fiddling with it I was able to get it to converge for one chain
> but I wouldn't trust it at all right now.

Well, I hadn't seen a model specification quite like that either.  It's
brm() syntax, which is a bit different from glm() or glmer() syntax.

The model being fitted is a binomial model, with success probability p
modelled by

     g(p) = beta_0 + beta_1 * x + Z_0 + Z_1 * x

where the Z_k are the random effects, and where g() is the link
function, e.g. cloglog(). (I *think* I've got that right.)

Of course beta_0 and beta_1 depend on treatment group and Z_0 and Z_1
depend on "Rep", which is nested within treatment group.

Note that we are talking *generalized* linear mixed models here; the
responses are binomial success counts.  "Success" = Dead, since one is
trying to kill the bugs.

For what it's worth the glmer() syntax is

    glmer(cbind(Dead,Alive) ~ (0 + Trt)/x + (x | Rep),

I got the brm() syntax from the vignette; as I said, I'd never seen it



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