Stanimal

Stanimal is an R package for fitting Bayesian animal models in Stan. Given a pedigree or genomic relationship matrix, it estimates genetic and residual variation for one or more traits, including the additive genetic covariance matrix (G).

The package supports univariate and multivariate models, with unstructured and factor-based covariance models for larger trait sets. Fits use CmdStan through cmdstanr or, alternatively, rstan. Stanimal is designed particularly for many traits measured on a moderate number of individuals.

Stanimal can also be used as an engine for Indri, which combines estimates from smaller trait subsets to estimate covariance matrices for larger sets of traits.