Indri

Indri is an R package for estimating additive genetic covariance matrices for large sets of traits. Following the approach of LiMMBo, it fits models to small, overlapping trait subsets instead of one large multivariate animal model, then assembles their estimates into a single covariance matrix with uncertainty estimates for its entries.

The subset models can be fitted using Bayesian sampling with Stanimal or REML with sommer or ASReml. Indri also uses the estimated genetic and residual covariances for multi-trait and single-trait genome-wide association scans, with options including dominance effects and permutation tests.

Indri is under active development. The documentation includes examples and guides to using the package.