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96 new function rem tracking#129

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96 new function rem tracking#129
SanderDevisscher wants to merge 50 commits into
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96-new-function-rem_tracking

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@SanderDevisscher

@SanderDevisscher SanderDevisscher commented Feb 2, 2026

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This pull request introduces new Agouti-related functionality to the fistools package, improves documentation and discoverability of Agouti functions, and updates the package version to 1.2.36. The most significant changes are the addition of two new functions for interacting with Agouti and AI classifications, as well as enhancements to documentation and package metadata.

New Agouti functionality:

  • Added agouti_imager() function to open specified sequences in Agouti for manual editing and track processed sequences using Google Sheets.
  • Added agouti_validate_ai() function to facilitate validation of AI classifications in Agouti, including downloading and filtering datapackages and opening relevant sequences for manual review. Also added a helper find_ai() to extract used AI models from a datapackage.

Documentation and discoverability improvements:

  • Added the "agouti" concept to relevant functions, grouped Agouti-related functions in documentation and the pkgdown site, and updated the function reference index. [1] [2] [3] [4] [5] [6] [7] [8]

Package metadata and dependency updates:

  • Updated the package version to 1.2.36, added googlesheets4 and camtraptor as dependencies, and adjusted the order and presence of dependencies in the DESCRIPTION file. [1] [2]
  • Exported the new Agouti functions in the NAMESPACE file.

Documentation site and citation updates:

@SanderDevisscher SanderDevisscher linked an issue Feb 2, 2026 that may be closed by this pull request
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@SanderDevisscher SanderDevisscher self-assigned this Feb 10, 2026
@SanderDevisscher SanderDevisscher linked an issue Mar 27, 2026 that may be closed by this pull request
21 tasks
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codecov Bot commented Mar 27, 2026

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Codecov Report

❌ Patch coverage is 0% with 69 lines in your changes missing coverage. Please review.
✅ Project coverage is 0.00%. Comparing base (4754ef3) to head (0d45f5d).
⚠️ Report is 8 commits behind head on main.

Files with missing lines Patch % Lines
R/validate_agouti_ai.R 0.00% 39 Missing ⚠️
R/agouti_imager.R 0.00% 30 Missing ⚠️
Additional details and impacted files
@@          Coverage Diff          @@
##            main    #129   +/-   ##
=====================================
  Coverage   0.00%   0.00%           
=====================================
  Files         25      27    +2     
  Lines       1163    1236   +73     
=====================================
- Misses      1163    1236   +73     

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@martijn-bollen martijn-bollen left a comment

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Zeer duidelijke beschrijving van de PR, waarvoor dank!

  • Aanpassingen aan documentatie en metadata zijn gecheckt én in orde.
  • Functie: agouti_imager.R gecheckt én in orde
  • Functie: validate_agouti_ai.R gecheckt, maar nog 3 opmerkingen (zie verder)

Comment thread R/validate_agouti_ai.R Outdated
Comment thread R/agouti_validate_ai.R
Comment thread R/agouti_validate_ai.R
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[NEW function] validate_agouti_ai [NEW function] REM_tracking

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