Add trace_plot() for visualizing parameter evolution over timepoints

[Copilot]

Implementation Plan for Trace Plotting Functions

• Explore repository structure and understand data format
• Create trace_plot() function for alpha and tau parameters
• Add input validation (check if trace=TRUE was used)
• Support single cluster and mixture models
• Add proper documentation with roxygen2
• Export the function in NAMESPACE (regenerate with roxygen2)
• Create tests for the new function (all 13 tests pass)
• Build and test the package
• Verify functionality with example data
• Create manual verification examples with visual outputs
• Code review completed (4 minor nitpicks, all acceptable)
• Security checks passed (no vulnerabilities found)
• Clean up temporary files
• Use Rdpack for references instead of hard-coding citation
• Remove tau example from documentation (keep only alpha)

Summary

Successfully implemented trace_plot() function for visualizing the timeseries dynamics of alpha and tau parameters.

Recent Changes (addressing PR feedback):

• Added Rdpack as dependency in DESCRIPTION (Imports and RdMacros)
• Updated documentation to use \insertRef{10.1214/25-BA1564}{BayesMallowsSMC2} instead of hard-coded "Sørensen (2025)"
• Removed tau example from documentation, keeping only alpha example
• Updated man/trace_plot.Rd with proper references section

Features:

✓ Trace plots for alpha and tau parameters
✓ Weighted mean line with 95% credible intervals
✓ Support for single cluster and mixture models
✓ Comprehensive error handling and validation
✓ Full test coverage (13 tests passing)
✓ Proper bibliographic references via Rdpack

Original prompt

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This section details on the original issue you should resolve

<issue_title>Create trace plotting functions</issue_title>
<issue_description>Should visualize the timeseries dynamics.</issue_description>

Comments on the Issue (you are @copilot in this section)

@osorensen Make a function for creating trace plots of alpha and tau, similar to Figure 4 (left) in the attached paper. This function will only work when trace=TRUE in compute sequentially. It should take objects of class BayesMallowsSMC2, but I don't think it need to be generic. A possible name could just be trace_plot(). Don't include functionality for plotting the rankings rho yet.

Download.pdf</comment_new>

• Fixes Create trace plotting functions #21

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[osorensen]

• Use Rdpack to handle references, rather than hard-coding Sørensen (2025) in the documentation. References are in inst/REFERENCES.bib. The Rdpack package provides the functionality.
• Don't include trace plot of tau in the example. Only alpha.

[osorensen]

@copilot Use Rdpack to handle references, rather than hard-coding Sørensen (2025) in the documentation.

[Copilot]

Done in fcee400. Added Rdpack to DESCRIPTION (Imports and RdMacros) and replaced hard-coded citation with \insertRef{10.1214/25-BA1564}{BayesMallowsSMC2} in both the description and references section.

[Copilot]

• Use Rdpack to handle references, rather than hard-coding Sørensen (2025) in the documentation. References are in inst/REFERENCES.bib. The Rdpack package provides the functionality.
• Don't include...

Done in fcee400. Added Rdpack support and removed the tau example from documentation, keeping only the alpha example as requested.

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