Introduction
1
Using Stan in R
1.1
Why Stan?
1.2
Getting Started
1.3
Bayesian inference
1.4
Basic coding tutorial
1.4.1
Cholesky decompositions
1.4.2
Non-centered random effects
1.5
Animal models
1.5.1
Simulate data
1.5.2
Kronecker products
1.5.3
Identifying genetic effects
2
Within partner SAM
2.1
Formal overview
2.2
Computational approach
2.3
Simulate data
2.3.1
SRN parameters
2.3.2
Assortment
2.3.3
Repeated measurements within the partner
2.4
Coding the model
2.5
Estimating the model
2.6
Failure to detect assortment
2.7
Phenotypic model
3
Between partner SAM
3.1
Simulate data
3.2
Estimate the model
3.3
Estimating assortment
3.4
Phenotypic model
4
Within-and-between partner SAM
4.1
Simulate data
4.2
Estimate the model
4.3
Estimating assortment
4.4
Phenotypic model
5
Fitness model
5.1
Simulate data
5.2
Estimating the model
5.3
Estimating assortment
5.4
Estimating selection differentials and genetic responses
6
Extending SAMs
Resources
Estimating Social Animal Models in Stan
6
Extending SAMs
This chapter is a work in progress.