Introduction | Who is RcppTskit for? | State of the tree sequence ecosystem | Aims for RcppTskit | Data and class model | API mirroring across the languages | Four typical use cases | 1) Load a tree sequence into R and summarise it | 2) Pass a tree sequence between R and reticulate or standard Python | 3) Call the tskit C API from C++ in an R session or script | 4) Call the tskit C API from C++ in another R package | Conclusion | Session information

Example Breeding Program | Creating Founder Haplotypes | Setting Simulation Parameters | Modeling the Breeding Program | Examining the Results | Full Code | References

Introduction | Option 1: Cross a single virgin queen/colony | Option2: Cross with drone packages (pre-selecting drone populations) | Option 3: Cross according to a provided cross plan | Options 4 and 5: Cross according to an internally created cross plan | Special cases | Cross virgin queens at a mating station | Cross colonies with varying methods

Introduction | Swarming | Split | Supersedure | Collapse | References

Introduction | Initiating simulation with founder genomes and global parameters | Creating and building up a colony | Colony structure | Complementary sex determining locus | References

Introduction | Why aren't drones removed from colonies when creating a DCA?

Introduction | Obtaining genomic information | Pooling genotypic information | Computing Genomic Relationship Matrices | References

Introduction | Initial settings | Creating a MultiColony object | MultiColony operations | Crossing a MultiColony | Working with multiple MultiColony objects

Introduction | Honey yield | Base population quantitative genetic parameters | Individual values in the base population | Individual values in a colony | Colony value | MultiColony values | Selection on colony values | Honey yield and Calmness | Strength and honey yield

Introduction | Functions to sample numbers | Functions that sample proportions

Loading packages | Loading datafile | Partitioning trends in genetic mean and variance | Example of plots to analyse the results

AlphaPart

Genotype Dosage Scaling | Additive Effects | Dominance Effects | Epistatic Effects | Genotype-by-Environment Effects | Adding Environmental Variance | Relationship to Finlay-Wilkinson Regression | User Interaction | References