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Issue #438: Use class as default for family and reexport common families and formula function #449

Merged
merged 11 commits into from
Nov 19, 2024
Merged

Issue #438: Use class as default for family and reexport common families and formula function #449

merged 11 commits into from
Nov 19, 2024

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athowes
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@athowes athowes commented Nov 16, 2024 •
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Description

This PR closes #438.

Reexports brms::lognormal, brms::weibull, stats::Gamma and brms::bf.

Changes default to lognormal() away from "lognormal".

I've also altered the test on the recovery of simulated fit_sex parameters to use the right link functions so that they pass. Also on sampling from prior.

I am wondering if lognormal() has different link functions by default than "lognormal". In particular it uses exp() on the SD whereas maybe the string one just uses identity (which would be bad to do, so good we've moved away from it).

Checklist

  • My PR is based on a package issue and I have explicitly linked it.
  • I have included the target issue or issues in the PR title in the for Issue(s) issue-numbers: PR title
  • I have read the contribution guidelines.
  • I have tested my changes locally.
  • I have added or updated unit tests where necessary.
  • I have updated the documentation if required.
  • My code follows the established coding standards.
  • I have added a news item linked to this PR.
  • I have reviewed CI checks for this PR and addressed them as far as I am able.

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@athowes athowes requested a review from seabbs November 18, 2024 12:33
@athowes athowes marked this pull request as ready for review November 18, 2024 12:33
@seabbs seabbs force-pushed the revert-family-string-default branch from cad21af to 9c96cb5 Compare November 19, 2024 10:26
@seabbs seabbs enabled auto-merge (squash) November 19, 2024 10:28
@seabbs seabbs merged commit 3991f2f into main Nov 19, 2024
8 checks passed
@seabbs seabbs deleted the revert-family-string-default branch November 19, 2024 10:57
@athowes athowes mentioned this pull request Nov 19, 2024
Closed
seabbs pushed a commit that referenced this pull request Jan 10, 2025
@athowes
Issue #438: Use class as default for family and reexport common famil…
41dfb5e 
…ies and formula function (#449)

* Add 3 families and bf as reexports

* Use lognormal() as default and document it

* Use lognormal() not "lognormal"

* Stop with brms::bf and use bf

* Remove more calls to brms::lognormal that can be lognormal

* We are also exporting stats::Gamma

* Another one

* Document

* Use predictions in test of sex effect

* Can do this without predict_delay_pars

* Change to link function here

Former-commit-id: 8b6f99d3c05117cc2e5c8be1afc3627fb3619870 [formerly 7e594460374bbeef99ff031663befa07fe579e80]
Former-commit-id: 0f4a99d8a8b5e1e3be0d6a8e806e68597c05d7ca
seabbs pushed a commit that referenced this pull request Jan 21, 2025
@athowes
Issue #438: Use class as default for family and reexport common famil…
5d86fe0 
…ies and formula function (#449)

* Add 3 families and bf as reexports

* Use lognormal() as default and document it

* Use lognormal() not "lognormal"

* Stop with brms::bf and use bf

* Remove more calls to brms::lognormal that can be lognormal

* We are also exporting stats::Gamma

* Another one

* Document

* Use predictions in test of sex effect

* Can do this without predict_delay_pars

* Change to link function here

Former-commit-id: 3991f2f
Former-commit-id: ff40773bd7e215f5bea27216f841f2212a34b971
seabbs pushed a commit that referenced this pull request Jan 21, 2025
@athowes
Issue #438: Use class as default for family and reexport common famil…
cf08449 
…ies and formula function (#449)

* Add 3 families and bf as reexports

* Use lognormal() as default and document it

* Use lognormal() not "lognormal"

* Stop with brms::bf and use bf

* Remove more calls to brms::lognormal that can be lognormal

* We are also exporting stats::Gamma

* Another one

* Document

* Use predictions in test of sex effect

* Can do this without predict_delay_pars

* Change to link function here

Former-commit-id: 3991f2f
Former-commit-id: ff40773bd7e215f5bea27216f841f2212a34b971
seabbs pushed a commit that referenced this pull request Jan 21, 2025
@athowes
Issue #438: Use class as default for family and reexport common famil…
15b81cd 
…ies and formula function (#449)

* Add 3 families and bf as reexports

* Use lognormal() as default and document it

* Use lognormal() not "lognormal"

* Stop with brms::bf and use bf

* Remove more calls to brms::lognormal that can be lognormal

* We are also exporting stats::Gamma

* Another one

* Document

* Use predictions in test of sex effect

* Can do this without predict_delay_pars

* Change to link function here

Former-commit-id: 3991f2f
Former-commit-id: ff40773bd7e215f5bea27216f841f2212a34b971
seabbs pushed a commit that referenced this pull request Jan 21, 2025
@athowes
Issue #438: Use class as default for family and reexport common famil…
09f93b1 
…ies and formula function (#449)

* Add 3 families and bf as reexports

* Use lognormal() as default and document it

* Use lognormal() not "lognormal"

* Stop with brms::bf and use bf

* Remove more calls to brms::lognormal that can be lognormal

* We are also exporting stats::Gamma

* Another one

* Document

* Use predictions in test of sex effect

* Can do this without predict_delay_pars

* Change to link function here

Former-commit-id: 8b6f99d3c05117cc2e5c8be1afc3627fb3619870 [formerly 7e594460374bbeef99ff031663befa07fe579e80]
Former-commit-id: 0f4a99d8a8b5e1e3be0d6a8e806e68597c05d7ca
seabbs pushed a commit that referenced this pull request Jan 21, 2025
@athowes
Issue #438: Use class as default for family and reexport common famil…
cc3f47c 
…ies and formula function (#449)

* Add 3 families and bf as reexports

* Use lognormal() as default and document it

* Use lognormal() not "lognormal"

* Stop with brms::bf and use bf

* Remove more calls to brms::lognormal that can be lognormal

* We are also exporting stats::Gamma

* Another one

* Document

* Use predictions in test of sex effect

* Can do this without predict_delay_pars

* Change to link function here

Former-commit-id: 8b6f99d3c05117cc2e5c8be1afc3627fb3619870 [formerly 7e594460374bbeef99ff031663befa07fe579e80]
Former-commit-id: 0f4a99d8a8b5e1e3be0d6a8e806e68597c05d7ca
Former-commit-id: 09f93b1
seabbs pushed a commit that referenced this pull request Jan 21, 2025
@athowes
Issue #438: Use class as default for family and reexport common famil…
b4acfb4 
…ies and formula function (#449)

* Add 3 families and bf as reexports

* Use lognormal() as default and document it

* Use lognormal() not "lognormal"

* Stop with brms::bf and use bf

* Remove more calls to brms::lognormal that can be lognormal

* We are also exporting stats::Gamma

* Another one

* Document

* Use predictions in test of sex effect

* Can do this without predict_delay_pars

* Change to link function here

Former-commit-id: 3991f2f
Former-commit-id: ff40773bd7e215f5bea27216f841f2212a34b971
Former-commit-id: a4f827363f07f786eb8f3516a2b0b0b2030f3dfa [formerly 15b81cd]
Former-commit-id: 599a0c65a82aea0c82030dbb8a91dbd5d585041d
seabbs pushed a commit that referenced this pull request Jan 21, 2025
@athowes
Issue #438: Use class as default for family and reexport common famil…
4dcdd97 
…ies and formula function (#449)

* Add 3 families and bf as reexports

* Use lognormal() as default and document it

* Use lognormal() not "lognormal"

* Stop with brms::bf and use bf

* Remove more calls to brms::lognormal that can be lognormal

* We are also exporting stats::Gamma

* Another one

* Document

* Use predictions in test of sex effect

* Can do this without predict_delay_pars

* Change to link function here

Former-commit-id: 3991f2f
Former-commit-id: ff40773bd7e215f5bea27216f841f2212a34b971
Former-commit-id: a4f827363f07f786eb8f3516a2b0b0b2030f3dfa [formerly 15b81cd]
Former-commit-id: 599a0c65a82aea0c82030dbb8a91dbd5d585041d
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Revert to using family as family class rather than string
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@athowes @seabbs