1 Drawing the pedigree | 1.1 A simple pedigree graph | 1.1.1 Highlighting specific individuals | 1.1.2 Showing inbreeding coefficients | 1.2 A reduced pedigree graph | 1.3 An outlined pedigree graph | 1.4 How to use this package in a selective breeding program | 1.4.1 An analysis of founders for an individual | 1.4.2 The contribution of different families in a selective breeding program

1. Installation of the visPedigree package | 2. Pedigree format specification | 3. Checking and tidying pedigree | 3.1 Introduction | 3.2 Pedigree loop detection | 3.3 Tracing the pedigree of a specific individual | 3.4 Creating an integer pedigree | 3.5 Calculating inbreeding coefficients | 3.6 Customizing generation assignment | 3.7 Summarizing the pedigree | 3.8 Splitting large pedigrees

1. Class identity | 2. Core design goals | 3. The head invariant: IndNum == row index | 4. Column contract | 4.1 Minimal structural columns | 4.2 Integer pedigree columns | 4.3 Other common columns | 4.4 Column naming convention | 5. Metadata layer | 6. Structural invariants | 7. Constructor pipeline | 7.1 Full path: tidyped(raw_input) | 7.2 Fast path: tidyped(tp, cand = ids) | 7.3 new_tidyped() — internal constructor | 8. Three-tier guard system | 8.1 validate_tidyped() — visualization guard | 8.2 ensure_tidyped() — structure-light guard | 8.3 ensure_complete_tidyped() — complete-pedigree guard | 8.4 Choosing the right guard | 9. Safe subsetting contract | 9.1 := operations | 9.2 Column-only selections | 9.3 Row subsets | 10. Computational boundaries: C++ vs igraph | 10.1 C++ — core computation path | 10.2 igraph — graph-specific tasks | 11. Extension rules | 11.1 Do not add new pedigree-level attributes | 11.2 Keep computed state derivable | 11.3 Preserve data.table semantics | 11.4 Respect downgrade semantics | 11.5 Document C++ assumptions | 12. User-facing inspection helpers | 13. Maintenance checklist | 14. Recommended workflow

1. Setup and Data Preparation | 2. Pedigree Overview with pedstats() | 3. Pedigree Completeness with pedecg() | 4. Generation Intervals with pedgenint() | 5. Subpopulation Structure with pedsubpop() | 6. Diversity Indicators with pediv() | 6.1 fe, fa, and fg: what do they measure? | Effective number of founders (fe) | Effective number of ancestors (fa) | Founder genome equivalents (fg) | Retained genetic diversity (GeneDiv) | 6.2 Shannon-entropy effective numbers: feH and faH | Metric guide | Interpreting the ratio $f_e^{(H)} / f_e$ | Management implications | 7. Diversity Dynamics over Time with pedhalflife() | 7.1 Column guide for $timeseries | 7.2 Interpreting the $\lambda$ components | 7.3 Interpreting $T_{1/2}$ | 8. Effective Population Size with pedne() and pediv() | 8.1 Demographic Ne | 8.2 Inbreeding Ne | 8.3 Coancestry Ne | 9. Average Relationship Trends with pedrel() | 9.1 Mean additive relationship (scale = "relationship") | 9.2 Corrected mean coancestry (scale = "coancestry") | 10. Inbreeding Trends with inbreed() and pedfclass() | 11. Gene Flow and Partial Inbreeding | 11.1 pedancestry(): founder-line proportions | 11.2 pedpartial(): which ancestors explain inbreeding? | 12. Practical Interpretation | References

1. Calculating Relationship Matrices with pedmat() | 1.1 Supported Methods | 1.2 Basic Usage | 1.3 Sparse Matrix Representation | 2. Inspecting the Matrix | 2.1 Summary Statistics | 2.2 Querying Specific Relationships | 3. Compact Mode for Large Pedigrees | 3.1 Using compact = TRUE | 3.2 Expanding and Querying Compacted Matrices | 3.3 When to Use Compact Mode | 4. Visualizing Relationship Matrices with vismat() | 4.1 Relationship Heatmaps | Compact Matrix — Direct Visualization | Preserve Pedigree Order | Display a Subset of Individuals | Grouping by Pedigree Column | 4.2 Inbreeding and Kinship Histograms | 5. Performance Considerations

1. Load packages and example data | 2. Tidy once, reuse many times | 3. Fast repeated tracing from an existing tidyped | 4. Safe data.table usage on tidyped | 4.1 Adding new columns is safe | 4.2 Incomplete row subsetting now degrades safely | 4.3 Use explicit tracing when you need a valid sub-pedigree | 5. splitped() versus pedsubpop() | 6. Use accessors instead of manual attribute checks | 7. Recommended high-efficiency workflow | 8. Practical rules of thumb