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_ in type for data and change to data_big#1293

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kellijohnson-NOAA merged 9 commits into
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dev-data_big
Mar 13, 2026
Merged

_ in type for data and change to data_big#1293
kellijohnson-NOAA merged 9 commits into
devfrom
dev-data_big

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@kellijohnson-NOAA kellijohnson-NOAA commented Mar 12, 2026

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What is the feature?

  • Change all type names to use underscores in the stored data, e.g., weight_at_age
  • Use a stored object fims_input_types to check the validity of input types that are present
  • Change data1 to data_big because Andrea will have a data_limited later for the surplus production model and Ian has a data_small in PR Add data_small dataset and associated test and documentation #958
  • Add test coverage for R/fimsframe.R

Does the PR impact any other area of the project, maybe another repo?

  • Yes, the case studies will need to be updated
  • @iantaylor-NOAA function for converting SS3 data in {r4ss} will need to be updated to produce type names with underscores

Close #1247


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@kellijohnson-NOAA kellijohnson-NOAA linked an issue Mar 12, 2026 that may be closed by this pull request
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Codecov Report

❌ Patch coverage is 92.95775% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.91%. Comparing base (ab0b19f) to head (c57b896).
⚠️ Report is 3 commits behind head on dev.

Files with missing lines Patch % Lines
R/fimsframe.R 92.64% 5 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##              dev    #1293      +/-   ##
==========================================
+ Coverage   86.87%   88.91%   +2.04%     
==========================================
  Files          81       80       -1     
  Lines        7803     7923     +120     
  Branches      496      538      +42     
==========================================
+ Hits         6779     7045     +266     
+ Misses       1019      854     -165     
- Partials        5       24      +19     

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Comment thread tests/testthat/test-fimsframe.R Outdated
Comment thread R/fimsframe.R Outdated
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Comment thread tests/testthat/test-fimsframe.R Outdated
Comment thread tests/testthat/test-fimsframe.R Outdated
Comment thread pkgdown/_pkgdown.yml
Comment thread pkgdown/_pkgdown.yml
Comment thread tests/testthat/test-fimsframe.R Outdated
Comment thread tests/testthat/test-fimsframe.R
@kellijohnson-NOAA kellijohnson-NOAA force-pushed the dev-data_big branch 7 times, most recently from 23579a1 to a081f58 Compare March 12, 2026 21:46
* scales is not used anywhere
* Adds alt text for the logo in the pkgdown site
@kellijohnson-NOAA kellijohnson-NOAA merged commit d410b9e into dev Mar 13, 2026
18 of 19 checks passed
@kellijohnson-NOAA kellijohnson-NOAA deleted the dev-data_big branch March 13, 2026 03:55
kellijohnson-NOAA added a commit that referenced this pull request Mar 13, 2026
The following changes were made to data1, which is now named data_big.

* Changes to "-" to "_" for type in FIMSFrame
* Renames data1 to data_big and adds fims_input_types
* Fix cli output to naturally create a list
* Adds tests and logic checks for FIMSFrame
* fix: use the stored fims_input_types object for validating
* chore: Ignores usethis R functions from codecoverage
* fix(plot(FIMSFrame)): Use tibble instead of S4 object
* Use plot of data in the fims-demo
* fix package loading errors
* scales is not used anywhere so remove from DESCRIPTION
* Adds alt text for the logo in the pkgdown site
* Adds test for age or length compositions that do not sum to one for a given grouping
kellijohnson-NOAA added a commit that referenced this pull request Mar 16, 2026
The following changes were made to data1, which is now named data_big.

* Changes to "-" to "_" for type in FIMSFrame
* Renames data1 to data_big and adds fims_input_types
* Fix cli output to naturally create a list
* Adds tests and logic checks for FIMSFrame
* fix: use the stored fims_input_types object for validating
* chore: Ignores usethis R functions from codecoverage
* fix(plot(FIMSFrame)): Use tibble instead of S4 object
* Use plot of data in the fims-demo
* fix package loading errors
* scales is not used anywhere so remove from DESCRIPTION
* Adds alt text for the logo in the pkgdown site
* Adds test for age or length compositions that do not sum to one for a given grouping
e-perl-NOAA pushed a commit to e-perl-NOAA/FIMS that referenced this pull request Apr 13, 2026
The following changes were made to data1, which is now named data_big.

* Changes to "-" to "_" for type in FIMSFrame
* Renames data1 to data_big and adds fims_input_types
* Fix cli output to naturally create a list
* Adds tests and logic checks for FIMSFrame
* fix: use the stored fims_input_types object for validating
* chore: Ignores usethis R functions from codecoverage
* fix(plot(FIMSFrame)): Use tibble instead of S4 object
* Use plot of data in the fims-demo
* fix package loading errors
* scales is not used anywhere so remove from DESCRIPTION
* Adds alt text for the logo in the pkgdown site
* Adds test for age or length compositions that do not sum to one for a given grouping
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[Developer Issue]: inconsistent formatting of data-type names

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