easystats / easystats/modelbased
re.form: query about documentation
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Description
The Technical Note in https://easystats.github.io/modelbased/articles/mixed_models.html#generalized-linear-mixed-models says:
For backend = "marginaleffects", the re.form argument is set to NULL for mixed models by default, to calculate marginal predictions. You can use for instance re.form = NA in your estimate_means() call to change the default value (NA will produce conditional predictions).
Documentation of glmmTMB's predict function says:
re.form \code{NULL} to specify individual-level predictions; \code{~0} or \code{NA} to specify population-level predictions (i.e., setting all random effects to zero)
That seems contradictory to me, i.e. I read Tech Note as saying re.form=NA produces conditional predictions whereas glmmTMB is saying re.form=NA gives population-level predictions.
(I'm assuming that estimate_means with backend="marginaleffects" and estimate="average" calls marginaleffects::avg_predictions)
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the Technical Note in articles/mixed_models.html and the estimate_means() reference linked in the issue. Compare their re.form explanation with the linked glmmTMB predict documentation and the assumed marginaleffects::avg_predictions behavior. Done means the prediction terminology is reconciled and the documentation no longer appears contradictory.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100