10 Constraint Transforms
To avoid having to deal with constraints while simulating the Hamiltonian dynamics during sampling, every (multivariate) parameter in a Stan model is transformed to an unconstrained variable behind the scenes by the model compiler. The transform is based on the constraints, if any, in the parameter’s definition. Scalars or the scalar values in vectors, row vectors or matrices may be constrained with lower and/or upper bounds. Vectors may alternatively be constrained to be ordered, positive ordered, or simplexes. Matrices may be constrained to be correlation matrices or covariance matrices. This chapter provides a definition of the transforms used for each type of variable.
Stan converts models to C++ classes which define probability functions with support on all of \(\mathbb{R}^K\), where \(K\) is the number of unconstrained parameters needed to define the constrained parameters defined in the program. The C++ classes also include code to transform the parameters from unconstrained to constrained and apply the appropriate Jacobians.