Log-transformation needed for predictions by negative-binomial model?

[Charlotte Taelman]

Dear INLA community,

I constructed a spatial-temporal model, with a zero-inflated negative binomial distribution. I want to plot the predictions made by INLA ("predicted summary fitted values") for a certain number of scenarios. Do these predicted values need to be backtransformed (exp) due to the link functions, or are these already the transformed ones?

Kind regards and thanks in advance,

Charlotte Taelman

[Thierry Onkelinx]

Dear Charlotte,

summary.fitted.values are on the natural scale, summary.linear.predictor are on the link scale.

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

Postadres: Koning Albert II-laan 15 bus 186, 1210 Brussel
Poststukken die naar dit adres worden gestuurd, worden ingescand en digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar dossiers volledig digitaal behandelen. Poststukken met de vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde bezorgd.
www.inbo.be

///////////////////////////////////////////////////////////////////////////////////////////

To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
///////////////////////////////////////////////////////////////////////////////////////////

Op ma 12 mei 2025 om 12:05 schreef Charlotte Taelman <charlotte...@gmail.com>:

--
You received this message because you are subscribed to the Google Groups "R-inla discussion group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to r-inla-discussion...@googlegroups.com.
To view this discussion, visit https://groups.google.com/d/msgid/r-inla-discussion-group/0c25caed-e4b7-4d62-9f03-44f7c37249b5n%40googlegroups.com.

[Charlotte Taelman]

Thank you very much!

Op ma 12 mei 2025 om 13:20 schreef Thierry Onkelinx <thierry....@inbo.be>:

[Håvard Rue]

Hi

only the linear predictor in the negative binomial part, is there in
'fitted.values'. this depends on you have set the 'link' argument indication
which family a NA observation is attached to.

If you want to predict with the zero-inflated value, this has to be done
manually, like using inla.posterior.sample and inla.posterior.sample.eval

it should be something like the attached one. I *think* its correct but its
written in a hurry, please verify

H

> --
> You received this message because you are subscribed to the Google Groups "R-
> inla discussion group" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to r-inla-discussion...@googlegroups.com.
> To view this discussion, visit
> https://groups.google.com/d/msgid/r-inla-discussion-group/0c25caed-e4b7-4d62-9f03-44f7c37249b5n%40googlegroups.com
> .

--
Håvard Rue
hr...@r-inla.org