  boost | Reimplementing boost functionality |
  math | Reimplmeneting boost functionality for stan::agrad::var and and bugs in classification of integer types |
| Eigen | (Expert) Numerical traits for algorithmic differentiation variables |
 internal | (Expert) Product traits for algorithmic differentiation variables |
  significant_decimals_default_impl< stan::agrad::var, false > | Implemented this for printing to stream |
| scalar_product_traits< stan::agrad::var, double > | Scalar product traits override for Eigen for automatic gradient variables |
| scalar_product_traits< double, stan::agrad::var > | Scalar product traits override for Eigen for automatic gradient variables |
| general_matrix_vector_product< Index, stan::agrad::var, ColMajor, ConjugateLhs, stan::agrad::var, ConjugateRhs > | Override matrix-vector and matrix-matrix products to use more efficient implementation |
| general_matrix_vector_product< Index, stan::agrad::var, RowMajor, ConjugateLhs, stan::agrad::var, ConjugateRhs > | |
| general_matrix_matrix_product< Index, stan::agrad::var, LhsStorageOrder, ConjugateLhs, stan::agrad::var, RhsStorageOrder, ConjugateRhs, ColMajor > | |
| NumTraits< stan::agrad::var > | Numerical traits template override for Eigen for automatic gradient variables |
| stan | Probability, optimization and sampling library |
| agrad | Function gradients via reverse-mode automatic differentiation |
| var_to_vi | |
| var_to_vi< stan::agrad::var > | |
| chainable | Abstract base class for variable implementations that handles memory management and applying the chain rule |
| vari | The variable implementation base class |
| var | Independent (input) and dependent (output) variables for gradients |
| gevv_vvv_vari | |
| needs_promotion | |
| assigner | |
| assigner< false, LHS, RHS > | |
| assigner< true, LHS, RHS > | |
| partials_vari | |
| OperandsAndPartials | A variable implementation that stores operands and derivatives with respect to the variable |
| gm | Directed graphical model compiler |
| nil | Placeholder struct for boost::variant default ctors |
| expr_type | |
| function_signatures | |
| statements | |
| distribution | |
| expression_type_vis | |
| expression | |
| printable | |
| is_nil_op | |
| variable_dims | |
| int_literal | |
| double_literal | |
| variable | |
| fun | |
| index_op | |
| binary_op | |
| unary_op | |
| range | |
| base_var_decl | |
| variable_map | |
| int_var_decl | |
| double_var_decl | |
| simplex_var_decl | |
| ordered_var_decl | |
| positive_ordered_var_decl | |
| vector_var_decl | |
| row_vector_var_decl | |
| matrix_var_decl | |
| cov_matrix_var_decl | |
| corr_matrix_var_decl | |
| name_vis | |
| var_decl | |
| statement | |
| for_statement | |
| print_statement | |
| no_op_statement | |
| program | |
| sample | |
| assignment | |
| visgen | Generic visitor with output for extension |
| expression_visgen | |
| printable_visgen | |
| var_resizing_visgen | |
| init_local_var_visgen | |
| validate_var_decl_visgen | |
| member_var_decl_visgen | |
| local_var_decl_visgen | |
| generate_init_vars_visgen | |
| validate_transformed_params_visgen | |
| statement_visgen | |
| dump_member_var_visgen | |
| generate_init_visgen | |
| write_dims_visgen | |
| write_param_names_visgen | |
| write_csv_header_visgen | |
| write_csv_visgen | |
| write_csv_vars_visgen | |
| write_array_visgen | |
| write_array_vars_visgen | |
| set_param_ranges_visgen | |
| expression_grammar | |
| program_grammar | |
| statement_grammar | |
| var_decls_grammar | |
| whitespace_grammar | |
| io | Input/output utilities |
| cmd_line | Parses and stores command-line arguments |
| csv_writer | Writes Stan variables in comma-separated-value format to an output stream |
| dump_writer | Writes data into the S-plus dump format |
| dump_reader | Reads data from S-plus dump format |
| dump | Represents named arrays with dimensions |
| reader | A stream-based reader for integer, scalar, vector, matrix and array data types, with Jacobian calculations |
| var_context | A var_reader reads array variables of integer and floating point type by name and dimension |
| writer | A stream-based writer for integer, scalar, vector, matrix and array data types, which transforms from constrained to a sequence of constrained variables |
| math | Matrices and templated mathematical functions |
| policies | Extending boost functionality |
| detail | Reimplementing boost::math::policies::detail::raise_domain_error |
| EigenType | This is a traits structure for Eigen matrix types |
| mcmc | Markov chain Monte Carlo samplers |
| adaptive_cdhmc | Adaptive "constant distance" Hamiltonian Monte Carlo (CDHMC) sampler |
| adaptive_hmc | Adaptive Hamiltonian Monte Carlo (HMC) sampler |
| adaptive_sampler | An abstract base class for adaptive samplers |
| chains | An mcmc::chains object stores parameter names and dimensionalities along with samples from multiple chains |
| DualAverage | Implements Nesterov's dual average algorithm |
| hmc | Hamiltonian Monte Carlo (HMC) sampler |
| hmc_base | |
| nuts | No-U-Turn Sampler (NUTS) |
| nuts_diag | No-U-Turn Sampler (NUTS) with varying step sizes |
| sample | Representation of a MCMC sample |
| memory | (Expert) Allocate, free, and manage underlying system memory |
| chunk_alloc | |
| stack_alloc | An instance of this class provides a memory pool through which blocks of raw memory may be allocated and then collected simultaneously |
| model | For compiling models |
| prob_grad | The prob_grad class represents densities with fixed numbers of discrete and scalar parameters and the gradient with respet to the scalar parameters |
| prob_grad_ad | |
| stanc_model | The abstract base class for models generated by the Stan compiler stanc |
| prob | Templated probability distributions |
| include_summand | Template metaprogram to calculate whether a summand needs to be included in a proportional (log) probability calculation |
| is_constant | Metaprogramming struct to detect whether a given type is constant in the mathematical sense (not the C++ const sense) |
| is_constant_struct | Metaprogram to determine if a type has a base scalar type that can be assigned to type double |
| is_constant_struct< std::vector< T > > | |
| is_constant_struct< Eigen::Matrix< T, R, C > > | |
| is_vector | |
| is_vector< const T > | |
| is_vector< std::vector< T > > | |
| is_vector< Eigen::Matrix< T, Eigen::Dynamic, 1 > > | |
| is_vector< Eigen::Matrix< T, 1, Eigen::Dynamic > > | |
| scalar_type | Metaprogram structure to determine the base scalar type of a template argument |
| size_of_helper | |
| size_of_helper< T, true > | |
| VectorView | |
| VectorView< T *, false > | |
| VectorView< T, true > | |
| VectorView< T *, true > | |
| VectorView< const T, true > | |
| DoubleVectorView | |
| DoubleVectorView< true, T, false > | |
| DoubleVectorView< true, T, true > | |
| return_type | Metaprogram to calculate the base scalar return type resulting from promoting all the scalar types of the template parameters |
 std | Template specification of functions in std for Stan |
 numeric_limits< stan::agrad::var > | Specialization of numeric limits for var objects |
