Add examples to method help pages flagged by checktor #253

Checktor flags 18 help pages without their own examples section. Track this as documentation work for a later release; it is not part of the 0.2.2 release preparation.

The findings were verified in the audit of main commit e1d2fe3 (PR #251) and were identical in PR #252's initial audit:
https://github.com/jakeberv/bifrost/actions/runs/38823234738

Help pages

Data-frame conversion:

• as.data.frame.bifrost_search_tuning_grid.Rd
• as.data.frame.bifrost_search_tuning_selection.Rd
• as.data.frame.bifrost_shift_recovery_evaluation.Rd
• as.data.frame.bifrost_simulation_study.Rd
• as.data.frame.regime_correlation_pca.Rd
• as.data.frame.regime_integration_relationships.Rd
• as.data.frame.regime_module_diagnostics.Rd
• distribution-fit-data-frames.Rd

Plot methods:

• plot.regime_correlation_pca.Rd
• plot.regime_integration_relationships.Rd
• plot.regime_module_diagnostics.Rd
• plot.shift_magnitude_comparison_set.Rd
• plot.shift_magnitude_count_set.Rd

Print methods:

• print.bifrost_search_tuning_grid.Rd
• print.bifrost_search_tuning_selection.Rd
• print.bifrost_search.Rd
• print.bifrost_shift_recovery_evaluation.Rd
• print.rateMap.Rd

Approach and validation

First check whether each method is already demonstrated on a related help page. Prioritize useful plot and data-frame conversion examples; avoid repetitive examples added solely to silence the audit. Where appropriate, share examples or add clear cross-references and document the reason for retaining a finding.

Add examples in the roxygen source and regenerate the help pages. Keep examples short, runnable, deterministic where randomness is involved, and independent of downloads or large empirical datasets. Use small synthetic inputs and conservative thread counts.

Run the affected examples and appropriate package checks, then review the checktor report. Resolve each checklist item with an example or a documented rationale. Do not change numerical behavior as part of this documentation work.