inlabru: "You might want to consider to setting ``control.predictor=list(link=...)''"

[Seth Flaxman]

Hi all. Can someone please tell me the syntax that is expected for control.predictor?

My code:

fit <- bru(y ~ age,  family = "binomial", data = df)

Which gives the following warning:

*** Warning *** You might want to consider to setting ``control.predictor=list(link=...)''
*** Warning *** otherwise the identity link will be used to compute the fitted values for NA data

In vanilla INLA, I'd pass

    control.family = list(control.link = list(model = "logit"))

to inla(...)

but I'm not sure what the equivalent is here.

Thanks!

Seth

[Thierry Onkelinx]

Dear Seth,

Simply add control.predictor=list(link= 1). The number refers to the number of the response. So always 1, unless you are using multiple response variables in the same model.

fit <- bru(y ~ age,  family = "binomial", data = df, control.predictor=list(link= 1))

Best regards,

ir. Thierry Onkelinx

Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry....@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

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Op di 3 okt 2023 om 13:18 schreef Seth Flaxman <fla...@gmail.com>:

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[Finn Lindgren]

Hmmm, inlabru is supposed to set the link information automatically, so there might be something else going on here.

But for control.family in bru(), you specify it as an ordinary argument or as an argument to the like() function. (Other control. arguments need to be given in the options list argument.)

Finn

On 3 Oct 2023, at 12:18, Seth Flaxman <fla...@gmail.com> wrote:



--

[Finn Lindgren]

Control.predictor has to be given as options=list(control.predictor=…) in bru() calls.

But the needed link info should be automatically supplied by bru(), so there may be a bug. Seth, are you able to send a reprex (e.g. via GitHub issue)?

Finn

On 3 Oct 2023, at 12:57, 'Thierry Onkelinx' via R-inla discussion group <r-inla-disc...@googlegroups.com> wrote:



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