Open
Conversation
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Previously the _missing datasets had 12 monthly rows with NA measurement columns per unobserved year. The model expects one placeholder row per year — the data pipeline uses these to set Annual factor levels, then strips them before building the likelihood. Random effects for unobserved years are estimated purely from the hierarchical prior. Also simplifies validation: chk_whole_numeric and chk_gte pass with all-NA values, so only chk_range, chk_not_any_na, and check_key need to be gated by allow_missing. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Wider staggering: ~35% latent year-population combos (was ~15%) - Internal gaps: B missing 2008-2009 (surv) / 2009-2010 (recruit) - Unobserved year placeholder rows: 2015 (surv) / 2016 (recruit) - bbousurv_annual now multi-population (A + C, staggered years) - Tests can filter to single pop or remove placeholders as needed - Updated tests to use both multi_population and allow_missing flags Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…easurement cols missing data)
sebdalgarno
changed the title
joethorley
requested changes
Mar 12, 2026
Member
joethorley
left a comment
joethorley
left a comment
There was a problem hiding this comment.
Looks great - I have one minor question
There was a problem hiding this comment.
Pull request overview
Updates bboudata to support bboutools 1.3.0 by adding new example datasets (including multi-population and missing-year placeholder patterns) and extending the survival/recruitment validation helpers to accept these new structures via opt-in flags.
Changes:
- Added new datasets (
bbousurv_multi,bbousurv_missing,bbousurv_annual,bbourecruit_multi,bbourecruit_missing) plus pkgdown/man documentation updates. - Extended
bbd_chk_data_survival()/bbd_chk_data_recruitment()withmulti_populationandallow_missingarguments and new placeholder-row validation. - Added/updated test coverage for the new flags and placeholder-row behavior.
Reviewed changes
Copilot reviewed 20 out of 32 changed files in this pull request and generated 9 comments.
Show a summary per file
| File | Description |
|---|---|
| R/chk-data-survival.R | Adds multi_population / allow_missing behavior to survival validation. |
| R/chk-data-recruitment.R | Adds multi_population / allow_missing behavior to recruitment validation. |
| R/functions.R | Updates internal validation helpers and adds placeholder-row helper. |
| tests/testthat/test-chk-data-survival.R | Adds tests for multi-population and placeholder-row validation. |
| tests/testthat/test-chk-data-recruitment.R | Adds tests for multi-population/missing datasets and placeholder-row validation. |
| data-raw/data-raw.R | Builds the new datasets from raw spreadsheets. |
| data/*.rda | Adds the new serialized datasets and re-saves existing ones. |
| R/bbousurv.R, R/bbourecruit.R | Adds roxygen dataset documentation blocks for new datasets. |
| man/*.Rd | Adds generated documentation for new datasets and updated function docs. |
| _pkgdown.yml | Adds new datasets to the reference index. |
| DESCRIPTION | Bumps package version and updates metadata. |
| NEWS.md | Adds a new release section describing the updates. |
| .gitignore, .Rbuildignore | Ignores Claude-related artifacts. |
| R/licensing.R | Removes an @examples tag from an internal helper doc block. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Co-authored-by: Joe Thorley <joe@poissonconsulting.ca>
Member
Author
|
I've implemented the changes suggested by copilot |
joethorley
approved these changes
Mar 12, 2026
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Member
Author
|
Updated licensing: added |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Updates bboudata for bboutools 1.3.0 extensions (ECCC contract).
New datasets
bbousurv_multi/bbourecruit_multi— multi-population (A, B, C) with staggered year ranges, internal data gaps, and unobserved year placeholder rowsbbousurv_missing/bbourecruit_missing— single-population with unobserved year placeholder rowsbbousurv_annual— multi-population aggregate annual survival dataUpdated validation
bbd_chk_data_survival()andbbd_chk_data_recruitment()gainedmulti_populationandallow_missingargumentsallow_missing = TRUE(all measurement columns must be NA, not just some)🤖 Generated with Claude Code