Package: BGmisc 1.8.0

Introduction | Prerequisites | Data Requirements at a Glance | Pedigree data frame | Relatedness matrices | Phenotype data format | Missing phenotypes | Part 1: Single-Family Model | Step 1: Subset to one family and inspect | Step 2: Compute relatedness matrices | Step 3: Prepare the phenotype data | Step 4: Subset matrices to observed individuals | Step 5: Check model identification | Step 6: Build and fit the model | Part 2: Two-Family Multi-Group Model | Family 2: matrices | Family 2: phenotype data | Family 2: subset matrices | Check identification across both families | Build and fit the two-family model | Part 3: Scaling Up — Many Families and Parameter Recovery | Simulate pedigrees and data | Build and fit the multi-family model | Compare estimates to true values | Using the high-level wrapper | Understanding the Covariance Structure | Summary

Introduction | Summarizing Pedigrees | Plotting Pedigree | Single Pedigree Visualization | Visualizing Multiple Pedigrees Side-by-Side

Introduction | Relatedness Coefficient | Inferring r from Observed Phenotypic Correlation | Computing Relatedness from Pedigree Data | Hazard Data Example | Introducing Missingness: Remove a Parent | Removing the Father Instead | Inbreeding Dataset: Family-Level Evaluation | Example: Family r famIDs[1] | Summary

Introduction | Loading Required Libraries | Working with Variance Component Models | Using comp2vech Function | Using identifyComponentModel Function | Extended Pedigrees

Introduction | Load Packages and Data | Prepare and Validate Sex Codes | Compute Relatedness Matrices | Convert to Pairwise Format | Locate Jon and Daenerys | Plotting the Pedigree with Incomplete Parental Information | Visualize the Pedigree | Conclusion

Introduction | Loading Required Libraries and Data | Finding Extended Families | Computing Relatedness | Other relatedness measures | Computing mitochondrial relatedness | Computing relatedness through common nuclear environment | Computing relatedness through common extended family environment | Subsetting Pedigrees

Introduction | Identifying and Repairing ID Issues | A Clean Dataset | What checkIDs() Reports | A Tale of Two Duplicates | Repairing Between-Row Duplicates | Oedipus ID | Identifying and Repairing Sex Coding Issues | Best Practices for Pedigree Validation