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Issue 234: Allow prior passing and overwrite functionality #242

Merged

athowes merged 26 commits into main from prior-interface

Aug 21, 2024

Collaborator

athowes commented Aug 13, 2024

Description

This draft PR will close issue #234.

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.


          replace_brms_prior function from dropped PR

0bc7bf7

athowes changed the title ~~234: Allow prior passing and overwrite functionality~~ Issue 234: Allow prior passing and overwrite functionality

athowes added 13 commits

August 13, 2024 08:52


          Pseudocode for the new epidist_prior set-up

cf342bc


          Transfer location of existing prior

b439ad7


          Edits to epidist::epidist required for inputing priors

d5b68c1


          Add import statement

f4a4da8


          Move useful parts of prior into relevant places

31eeabf


          Start setting up testing

7f22f03


          The fiddling required for the problem now to be the helper function

f48b59d


          Write a working join based version of replace_brms_prior

3cd46ef


          Reduce simplification

b0c6ab3


          Document and clean up

b72ea48


          More clean up and linting

b616865


          Unit tests for replace_brms_prior

d1633bb


          Rename as replace_prior rather than replace_brms_prior

0d4c0cb

athowes marked this pull request as ready for review

August 13, 2024 10:10


          Find bug with < and <- and move prior test to right place

47fbf48

athowes commented

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athowes added 2 commits

August 13, 2024 11:59


          Try to fix check

5d10388


          Well it's horrible but it works

a34e5bb

athowes commented

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athowes added 3 commits

August 13, 2024 12:19


          Lint and document again

a506bad


          Website fix

03e14ac


          More ugly code for this to be passing

f4201fa

athowes added 4 commits

August 13, 2024 13:53


          Move posterior to suggests

0bc775b


          I think this has been exposed now

be0b0bf


          Fix to R CMD CHECK warning

e7ca80f


          Fix test to use prep_obs as data

287e3b3

athowes requested a review from seabbs

August 14, 2024 12:17

seabbs previously approved these changes

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Contributor

seabbs left a comment

This overall looks really good. A few minor points.

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          Move dplyr to Imports

20b1792

athowes dismissed seabbs’s stale review via

20b1792

August 16, 2024 08:26

This was referenced Aug 16, 2024

Replace dplyr use with data.table (or vice versa) #246

Closed

Functionality to allow users to set within-model priors (for latent individual) #199

Closed

Collaborator Author

athowes commented Aug 16, 2024

For some reason I couldn't reply directly to the comment "could you touch more on the problems you see?". I've added a comment here: #199 (comment)


          Move classing of family inside epidist_prior

6d656fa

This was referenced Aug 16, 2024

Within-code clarity on what e.g. family refers to #198

Closed

More verbose to user about priors used? #249

Open

athowes requested a review from seabbs

August 16, 2024 09:42

athowes mentioned this pull request

Build favicons error #251

Closed

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Contributor

seabbs left a comment

This looks good and I think we can merge it. This needs to be added to the discussion about data.table vs dplyr.

Collaborator Author

athowes commented Aug 21, 2024

This needs to be added to the discussion about data.table vs dplyr.

I've updated the existing comment #246 (comment) to be more explicit.

athowes merged commit eb2fe4c into main

6 of 7 checks passed

athowes deleted the prior-interface branch

August 21, 2024 09:23

This was referenced Aug 25, 2024

Allow for prior overwriting by the user #196

Closed

Alter design of priors towards family specific? #197

Closed

Default priors across families #172

Closed

Update epidist_prior to return all priors including defaults for additional parameters #108

Closed

This was referenced Oct 10, 2024

epidist_prior accepting a family or an epidist_family #298

Closed

Add option to pass custom additional priors #123

Closed

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