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Update and improve roxygen2 documentation#7

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lcgodoy merged 1 commit intodevfrom
drmr-docs-update-12729099472964578122
Feb 24, 2026
Merged

Update and improve roxygen2 documentation#7
lcgodoy merged 1 commit intodevfrom
drmr-docs-update-12729099472964578122

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@lcgodoy lcgodoy commented Feb 24, 2026

This pull request updates the roxygen2 documentation across several R files in the drmr package.

Changes include:

  • R/model-run.R: Fixed typos, clarified init parameter options, and improved return value descriptions for fit_drm and fit_sdm.
  • R/make-data.R: Corrected grammar in parameter descriptions and fixed typos in .toggles documentation. Removed inapplicable toggles from make_data_sdm documentation.
  • R/predict.R: Fixed typos and clarified new_data and past_data usage. Updated predict.sdm documentation to accurately reflect its arguments.
  • R/methods.R: Cleaned up documentation for S3 methods (update, print, summary, draws), including removing duplicate author tags and fixing parameter descriptions.
  • R/generics.R: Corrected the description of sdm in new_sdm (Species Distribution Model).
  • R/defaults.R: Replaced placeholder return value descriptions with meaningful text.
  • R/utils.R: Improved return value descriptions and clarified the alpha parameter in int_score.

These changes aim to improve the correctness, clarity, and conciseness of the package documentation. Note that the documentation (man/ files) needs to be regenerated using roxygen2::roxygenize() as the environment did not support running R.


PR created automatically by Jules for task 12729099472964578122 started by @lcgodoy

- Corrected typos and grammar in `R/model-run.R`, `R/make-data.R`, `R/predict.R`, `R/methods.R`, `R/generics.R`, `R/defaults.R`, and `R/utils.R`.
- Clarified parameter descriptions, particularly for `init`, `.toggles`, `new_data`, and `past_data`.
- Updated return value descriptions to be more specific, including class names where appropriate (`adrm`, `sdm`, `CmdStanGQ`).
- Fixed incorrect documentation for `fit_sdm` toggles and `@seealso` links.
- Standardized documentation for S3 methods and internal helper functions.
- Addressed placeholder documentation in `R/defaults.R`.
- Clarified `int_score` documentation regarding the `alpha` parameter.

Co-authored-by: lcgodoy <24809942+lcgodoy@users.noreply.github.com>
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@lcgodoy lcgodoy merged commit 97af27b into dev Feb 24, 2026
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@lcgodoy lcgodoy deleted the drmr-docs-update-12729099472964578122 branch February 25, 2026 16:09
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