fix docs for diann converter

[tonywu1999]

Motivation and Context

This PR addresses documentation inconsistencies and updates in the MSstatsConvert package. The changes focus on correcting typos in parameter documentation, updating maintainer information, and synchronizing documentation to match the actual implementation of the intensity parameter in the Spectronaut converter.

Changes

• Fixed typo in DIANN converter documentation: Corrected the description of the useUniquePeptide parameter from "pepties" to "peptides" in both the R source file and the generated .Rd documentation file for DIANNtoMSstatsFormat.

• Updated package maintainer and authors: Modified the MSstatsConvert.Rd documentation to reflect the package maintenance structure:

  • Changed Maintainer from Anthony Wu to Mateusz Staniak with corresponding email (mtst@mstaniak.pl)
  • Added Mateusz Staniak to the Authors list
  • Removed Anthony Wu from the Authors list (now appears only as Maintainer)

• Updated SpectronauttoMSstatsFormat documentation: Modified the intensity parameter documentation in the .Rd file to reflect the actual implementation, changing from a single default value "PeakArea" to a vector of options c("PeakArea", "NormalizedPeakArea", "MS1Quantity"). This aligns the documentation with the function implementation which already supports multiple intensity measurement types.

Testing

No new unit tests were added or modified to verify these documentation changes. Existing tests in the repository continue to verify the expected behavior of the converter functions through output validation of data structure and content.

[coderabbitai]

📝 Walkthrough

Walkthrough

Documentation updates across multiple files including typo corrections in DIANN converter documentation, maintainer and author changes in the main MSstatsConvert documentation, and an API signature update for the intensity parameter in the Spectronaut converter function.

Changes

Cohort / File(s)	Summary
DIANN Documentation Fixes R/converters_DIANNtoMSstatsFormat.R, man/DIANNtoMSstatsFormat.Rd	Corrected typo in useUniquePeptide parameter description: "pepties" → "peptides"
MSstatsConvert Metadata man/MSstatsConvert.Rd	Updated maintainer from Mateusz Staniak to Anthony Wu; added Mateusz Staniak to authors list and removed Anthony Wu from authors
Spectronaut Intensity Parameter man/SpectronauttoMSstatsFormat.Rd	Broadened intensity parameter default from single string "PeakArea" to vector of options: c("PeakArea", "NormalizedPeakArea", "MS1Quantity")

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

• feat(diann): Add support for DIANN 2.0 #109: Expands DIANN-related parameter documentation and examples alongside the typo fix in this PR's DIANN converter docs.
• Add option to use MS1Quantity for quantifications for Spectronaut #117: Implements runtime support and testing for the "MS1Quantity" intensity option that is documented in this PR's Spectronaut Rd file signature update.

Suggested reviewers

• mstaniak

Poem

🐰 A hop through docs, a typo's gone away,
Peptides spelled right, pepties had their day,
New authors rise, while maintainers shift and sway,
Intensity options bloom in brilliant array,
Clean docs, clean hearts—let's celebrate today! 📚✨

🚥 Pre-merge checks | ✅ 1 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Description check	⚠️ Warning	The pull request description is completely empty; only the template structure is present with no content filled in any required sections.	Fill in all required sections: provide motivation and context, detailed list of changes, testing information, and confirm the pre-review checklist items have been addressed.
Title check	❓ Inconclusive	The title 'fix docs for diann converter' is vague and generic, lacking specificity about which documentation issues were fixed.	Clarify the title with specific details about the changes, such as 'Fix typo in DIANN converter documentation' or 'Update DIANN converter docs and maintainer information'.

✅ Passed checks (1 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing Touches

• 📝 Generate docstrings (stacked PR)
• 📝 Generate docstrings (commit on current branch)

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix-docs

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

R/converters_DIANNtoMSstatsFormat.R (1)

18-18: Clarify useUniquePeptide wording to avoid inverted meaning.

Line 18 currently says unique peptides are removed, but this flag corresponds to removing shared/non-unique peptides. Please update the text to prevent misuse.

✏️ Suggested wording

-#' `@param` useUniquePeptide should unique peptides be removed
+#' `@param` useUniquePeptide should shared (non-unique) peptides be removed

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@R/converters_DIANNtoMSstatsFormat.R` at line 18, The param description for
useUniquePeptide is misleading (it currently says "should unique peptides be
removed")—update the roxygen `@param` text in converters_DIANNtoMSstatsFormat.R to
clearly state the flag's behavior (e.g., whether TRUE means retain only unique
peptides or TRUE means remove non-unique/shared peptides) so users cannot invert
the meaning; locate the useUniquePeptide parameter in the function's
documentation and replace the ambiguous sentence with explicit wording that maps
TRUE/FALSE to the intended action.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@man/SpectronauttoMSstatsFormat.Rd`:
- Line 10: The function exposes an intensity parameter documented as a single
choice but currently accepts a vector; call match.arg(intensity) near the start
of the function body (e.g., inside SpectronauttoMSstatsFormat) so intensity
becomes a single selected value before being passed to MSstatsClean; update any
subsequent uses (including the call to MSstatsClean) to use this matched
intensity.

---

Nitpick comments:
In `@R/converters_DIANNtoMSstatsFormat.R`:
- Line 18: The param description for useUniquePeptide is misleading (it
currently says "should unique peptides be removed")—update the roxygen `@param`
text in converters_DIANNtoMSstatsFormat.R to clearly state the flag's behavior
(e.g., whether TRUE means retain only unique peptides or TRUE means remove
non-unique/shared peptides) so users cannot invert the meaning; locate the
useUniquePeptide parameter in the function's documentation and replace the
ambiguous sentence with explicit wording that maps TRUE/FALSE to the intended
action.

---

ℹ️ Review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between dc0dfbb and 58ee3cf.

📒 Files selected for processing (4)

• R/converters_DIANNtoMSstatsFormat.R
• man/DIANNtoMSstatsFormat.Rd
• man/MSstatsConvert.Rd
• man/SpectronauttoMSstatsFormat.Rd