include what you use

[bob-carpenter]

Get help from Ben on setting up the include-what-you-use tool, then listen to it.

[syclik]

@bgoodri, what tool is this? How do I set it up?

[bgoodri]

There is nothing to set up; you just have to install it

http://code.google.com/p/include-what-you-use/

On Thu, May 22, 2014 at 6:35 PM, Daniel Lee notifications@github.comwrote:

@bgoodri https://github.com/bgoodri, what tool is this? How do I set it up?

— Reply to this email directly or view it on GitHubhttps://github.com/stan-dev/stan/issues/225#issuecomment-43952448 .

[syclik]

Ha! I didn't realize it was called "include what you use." Thanks!

On Thu, May 22, 2014 at 6:52 PM, bgoodri notifications@github.com wrote:

There is nothing to set up; you just have to install it

http://code.google.com/p/include-what-you-use/

On Thu, May 22, 2014 at 6:35 PM, Daniel Lee notifications@github.comwrote:

@bgoodri https://github.com/bgoodri, what tool is this? How do I set it up?

— Reply to this email directly or view it on GitHub< https://github.com/stan-dev/stan/issues/225#issuecomment-43952448> .

— Reply to this email directly or view it on GitHubhttps://github.com/stan-dev/stan/issues/225#issuecomment-43953707 .

[syclik]

Ben, I'm having a little trouble installing. Any suggestions? Or is there some way we can use the output from a working system?

[bgoodri]

I have never tried to install it on a Mac. Attached is the output from my laptop. However, iwyu still gets confused by Eigen sometimes.

Ben

On Sat, Aug 9, 2014 at 10:39 PM, Daniel Lee notifications@github.com wrote:

Ben, I'm having a little trouble installing. Any suggestions? Or is there some way we can use the output from a working system?

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51704370.

25541 total 461 ./optimization/newton.hpp_iwyu.txt 416 ./mcmc/chains.hpp_iwyu.txt 368 ./agrad/fwd/matrix/to_fvar.hpp_iwyu.txt 276 ./prob/distributions/multivariate/continuous/lkj_corr.hpp_iwyu.txt 219 ./common/command.hpp_iwyu.txt 212 ./math/matrix/containers_conversion.hpp_iwyu.txt 206 ./agrad/rev/matrix/to_var.hpp_iwyu.txt 204 ./command/print.hpp_iwyu.txt 204 ./agrad/autodiff.hpp_iwyu.txt 180 ./math/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 175 ./io/dump.hpp_iwyu.txt 166 ./agrad/rev/matrix/softmax.hpp_iwyu.txt 163 ./agrad/rev/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 163 ./agrad/rev/matrix/log_softmax.hpp_iwyu.txt 162 ./prob/distributions/multivariate/continuous/wishart.hpp_iwyu.txt 162 ./agrad/rev/matrix/tcrossprod.hpp_iwyu.txt 153 ./math/matrix/tcrossprod.hpp_iwyu.txt 143 ./prob/distributions/multivariate/continuous/multi_student_t.hpp_iwyu.txt 142 ./prob/distributions/multivariate/continuous/inv_wishart.hpp_iwyu.txt 132 ./prob/welford_covar_estimator.hpp_iwyu.txt 131 ./prob/distributions/univariate/discrete/ordered_logistic.hpp_iwyu.txt 127 ./prob/distributions/multivariate/discrete/categorical.hpp_iwyu.txt 124 ./gm/ast.hpp_iwyu.txt 123 ./math/matrix.hpp_iwyu.txt 123 ./gm/parser.hpp_iwyu.txt 122 ./prob/distributions/multivariate/continuous/multi_normal_cholesky.hpp_iwyu.txt 120 ./agrad/rev/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 117 ./prob/distributions/multivariate/continuous/multi_normal.hpp_iwyu.txt 115 ./mcmc/hmc/nuts/diag_e_nuts.hpp_iwyu.txt 115 ./mcmc/hmc/nuts/dense_e_nuts.hpp_iwyu.txt 111 ./prob/distributions/multivariate/continuous/dirichlet.hpp_iwyu.txt 111 ./mcmc/hmc/nuts/unit_e_nuts.hpp_iwyu.txt 110 ./io/mcmc_writer.hpp_iwyu.txt 109 ./optimization/bfgs.hpp_iwyu.txt 106 ./agrad/rev/matrix/dot_product.hpp_iwyu.txt 105 ./mcmc/hmc/hamiltonians/dense_e_metric.hpp_iwyu.txt 102 ./mcmc/hmc/hamiltonians/diag_e_metric.hpp_iwyu.txt 101 ./prob/transform.hpp_iwyu.txt 101 ./agrad/rev/matrix/crossprod.hpp_iwyu.txt 98 ./model/util.hpp_iwyu.txt 98 ./mcmc/hmc/hamiltonians/unit_e_metric.hpp_iwyu.txt 98 ./agrad/rev/matrix/multiply.hpp_iwyu.txt 95 ./mcmc/hmc/nuts/base_nuts.hpp_iwyu.txt 94 ./agrad/rev/functions.hpp_iwyu.txt 94 ./agrad/fwd/functions.hpp_iwyu.txt 87 ./prob/welford_var_estimator.hpp_iwyu.txt 87 ./math/matrix/crossprod.hpp_iwyu.txt 85 ./gm/grammars/program_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/term_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/statement_grammar_def.hpp_iwyu.txt 77 ./agrad/rev/functions/cbrt.hpp_iwyu.txt 76 ./gm/grammars/functions_grammar_def.hpp_iwyu.txt 74 ./gm/grammars/var_decls_grammar_def.hpp_iwyu.txt 74 ./gm/grammars/bare_type_grammar_def.hpp_iwyu.txt 73 ./math/functions.hpp_iwyu.txt 71 ./agrad/rev/functions/digamma.hpp_iwyu.txt 69 ./prob/distributions/multivariate/continuous/multi_gp.hpp_iwyu.txt 69 ./prob/distributions/multivariate/continuous/gaussian_dlm_obs.hpp_iwyu.txt 69 ./io/reader.hpp_iwyu.txt 68 ./model/model_header.hpp_iwyu.txt 67 ./mcmc.hpp_iwyu.txt 66 ./agrad/rev/functions/ibeta.hpp_iwyu.txt 65 ./prob/distributions/univariate/continuous/double_exponential.hpp_iwyu.txt 65 ./gm/grammars/expression07_grammar_def.hpp_iwyu.txt 64 ./prob/distributions/univariate/continuous/inv_gamma.hpp_iwyu.txt 64 ./prob/distributions/univariate/continuous/gamma.hpp_iwyu.txt 64 ./prob/distributions/multivariate/continuous/matrix_normal.hpp_iwyu.txt 64 ./common.hpp_iwyu.txt 63 ./prob/distributions/multivariate/continuous/multi_normal_prec.hpp_iwyu.txt 63 ./gm/grammars/expression_grammar_def.hpp_iwyu.txt 62 ./prob/distributions/univariate/discrete/neg_binomial.hpp_iwyu.txt 62 ./prob/distributions/univariate/continuous/skew_normal.hpp_iwyu.txt 62 ./gm/grammars/statement_2_grammar_def.hpp_iwyu.txt 61 ./prob/distributions/univariate/continuous/gumbel.hpp_iwyu.txt 61 ./prob/distributions/univariate/continuous/beta.hpp_iwyu.txt 61 ./prob/distributions/multivariate/continuous/lkj_cov.hpp_iwyu.txt 61 ./agrad/rev/internal.hpp_iwyu.txt 60 ./prob/distributions/univariate/discrete/beta_binomial.hpp_iwyu.txt 60 ./prob/distributions/univariate/continuous/student_t.hpp_iwyu.txt 60 ./prob/distributions/univariate/continuous/inv_chi_square.hpp_iwyu.txt 60 ./prob/distributions/univariate/continuous/exp_mod_normal.hpp_iwyu.txt 60 ./agrad/rev/functions/atanh.hpp_iwyu.txt 59 ./prob/distributions/univariate/discrete/neg_binomial_2.hpp_iwyu.txt 59 ./prob/distributions/univariate/discrete/binomial.hpp_iwyu.txt 59 ./prob/distributions/univariate/continuous/scaled_inv_chi_square.hpp_iwyu.txt 59 ./agrad/rev/matrix.hpp_iwyu.txt 58 ./prob.hpp_iwyu.txt 58 ./prob/distributions/univariate/continuous/chi_square.hpp_iwyu.txt 57 ./prob/distributions/univariate/discrete/hypergeometric.hpp_iwyu.txt 57 ./prob/distributions/multivariate/discrete/multinomial.hpp_iwyu.txt 57 ./io/writer.hpp_iwyu.txt 57 ./io/stan_csv_reader.hpp_iwyu.txt 56 ./prob/distributions/univariate/continuous/von_mises.hpp_iwyu.txt 56 ./prob/distributions/univariate/continuous/cauchy.hpp_iwyu.txt 56 ./agrad/rev/matrix/Eigen_NumTraits.hpp_iwyu.txt 56 ./agrad/rev/functions/trunc.hpp_iwyu.txt 56 ./agrad/rev/functions/round.hpp_iwyu.txt 55 ./prob/distributions/univariate/continuous/rayleigh.hpp_iwyu.txt 55 ./prob/distributions/univariate/continuous/pareto.hpp_iwyu.txt 55 ./prob/distributions/univariate/continuous/lognormal.hpp_iwyu.txt 55 ./prob/distributions/multivariate/continuous.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/normal.hpp_iwyu.txt 54 ./common/warmup.hpp_iwyu.txt 54 ./common/sample.hpp_iwyu.txt 53 ./prob/traits.hpp_iwyu.txt 53 ./prob/distributions/univariate/discrete/poisson.hpp_iwyu.txt 53 ./math/matrix_error_handling.hpp_iwyu.txt 52 ./prob/distributions/univariate/discrete/bernoulli.hpp_iwyu.txt 52 ./prob/distributions/univariate/continuous/weibull.hpp_iwyu.txt 52 ./io/json/json_data.hpp_iwyu.txt 52 ./io/json/json_data_handler.hpp_iwyu.txt 52 ./common/run_markov_chain.hpp_iwyu.txt 52 ./agrad/rev/matrix/sd.hpp_iwyu.txt 52 ./agrad/fwd/matrix.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/exponential.hpp_iwyu.txt 51 ./agrad/rev/matrix/log_sum_exp.hpp_iwyu.txt 50 ./prob/constants.hpp_iwyu.txt 50 ./agrad/rev/functions/log_sum_exp.hpp_iwyu.txt 49 ./prob/distributions/multivariate.hpp_iwyu.txt 49 ./agrad/rev/matrix/variance.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/uniform.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/logistic.hpp_iwyu.txt 48 ./agrad/rev/matrix/mdivide_left_tri.hpp_iwyu.txt 48 ./agrad/rev/functions/gamma_q.hpp_iwyu.txt 48 ./agrad/fwd/functions/trunc.hpp_iwyu.txt 48 ./agrad/fwd/functions/round.hpp_iwyu.txt 47 ./prob/autocovariance.hpp_iwyu.txt 47 ./agrad/rev/matrix/log_determinant_spd.hpp_iwyu.txt 47 ./agrad/rev/functions/gamma_p.hpp_iwyu.txt 47 ./agrad/rev/functions/bessel_second_kind.hpp_iwyu.txt 47 ./agrad/rev/functions/bessel_first_kind.hpp_iwyu.txt 47 ./agrad/fwd/matrix/log_sum_exp.hpp_iwyu.txt 46 ./prob/distributions.hpp_iwyu.txt 46 ./math/constants.hpp_iwyu.txt 46 ./io.hpp_iwyu.txt 46 ./agrad/rev/matrix/mdivide_left_spd.hpp_iwyu.txt 46 ./agrad/rev/matrix/mdivide_left.hpp_iwyu.txt 46 ./agrad/fwd/matrix/mdivide_right_tri_low.hpp_iwyu.txt 46 ./agrad/fwd/matrix/mdivide_right.hpp_iwyu.txt 45 ./math/functions/digamma.hpp_iwyu.txt 45 ./agrad/rev/functions/rising_factorial.hpp_iwyu.txt 45 ./agrad/rev/functions/log_rising_factorial.hpp_iwyu.txt 45 ./agrad/rev/functions/log_falling_factorial.hpp_iwyu.txt 45 ./agrad/rev/functions/falling_factorial.hpp_iwyu.txt 44 ./agrad/rev/matrix/mdivide_left_ldlt.hpp_iwyu.txt 44 ./agrad/fwd/matrix/mdivide_left_tri_low.hpp_iwyu.txt 44 ./agrad/fwd/matrix/inverse.hpp_iwyu.txt 43 ./math/error_handling/matrix/check_corr_matrix.hpp_iwyu.txt 43 ./agrad/rev/functions/asinh.hpp_iwyu.txt 43 ./agrad/rev/functions/acosh.hpp_iwyu.txt 42 ./prob/autocorrelation.hpp_iwyu.txt 42 ./meta/traits.hpp_iwyu.txt 42 ./math/error_handling.hpp_iwyu.txt 42 ./io/csv_writer.hpp_iwyu.txt 42 ./agrad/fwd/prob/univariate/continuous/normal.hpp_iwyu.txt 41 ./prob/distributions/multivariate/discrete/categorical_logit.hpp_iwyu.txt 41 ./mcmc/hmc/static/adapt_diag_e_static_hmc.hpp_iwyu.txt 41 ./mcmc/hmc/static/adapt_dense_e_static_hmc.hpp_iwyu.txt 41 ./mcmc/hmc/nuts/adapt_diag_e_nuts.hpp_iwyu.txt 41 ./mcmc/hmc/nuts/adapt_dense_e_nuts.hpp_iwyu.txt 41 ./agrad/rev/matrix/dot_self.hpp_iwyu.txt 41 ./agrad/rev/functions/log_diff_exp.hpp_iwyu.txt 41 ./agrad/rev/functions/lmgamma.hpp_iwyu.txt 41 ./agrad/rev/functions/lgamma.hpp_iwyu.txt 41 ./agrad/fwd/matrix/mdivide_left.hpp_iwyu.txt 40 ./model/prob_grad.hpp_iwyu.txt 40 ./model.hpp_iwyu.txt 40 ./io/json.hpp_iwyu.txt 40 ./agrad/rev/operators.hpp_iwyu.txt 40 ./agrad/rev/matrix/trace_gen_quad_form.hpp_iwyu.txt 40 ./agrad/rev/matrix/squared_distance.hpp_iwyu.txt 40 ./agrad/rev/matrix/log_determinant.hpp_iwyu.txt 40 ./agrad/rev/matrix/determinant.hpp_iwyu.txt 40 ./agrad/rev/functions/modified_bessel_first_kind.hpp_iwyu.txt 39 ./mcmc/hmc/static/adapt_unit_e_static_hmc.hpp_iwyu.txt 39 ./mcmc/hmc/nuts/adapt_unit_e_nuts.hpp_iwyu.txt 39 ./math/matrix/dot_product.hpp_iwyu.txt 39 ./agrad/rev/functions/fma.hpp_iwyu.txt 38 ./prob/distributions/univariate/discrete.hpp_iwyu.txt 38 ./agrad/rev/matrix/trace_quad_form.hpp_iwyu.txt 38 ./agrad/rev/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 38 ./agrad/rev/matrix/quad_form.hpp_iwyu.txt 38 ./agrad/rev/functions/tgamma.hpp_iwyu.txt 38 ./agrad/rev/functions/multiply_log.hpp_iwyu.txt 38 ./agrad/rev/functions/modified_bessel_second_kind.hpp_iwyu.txt 38 ./agrad/fwd/matrix/log_softmax.hpp_iwyu.txt 37 ./prob/distributions/univariate/continuous/johnson.hpp_iwyu.txt 37 ./mcmc/hmc/static/unit_e_static_hmc.hpp_iwyu.txt 37 ./mcmc/hmc/static/diag_e_static_hmc.hpp_iwyu.txt 37 ./mcmc/hmc/static/dense_e_static_hmc.hpp_iwyu.txt 37 ./mcmc/hmc/hamiltonians/base_hamiltonian.hpp_iwyu.txt 37 ./math/matrix/qr_R.hpp_iwyu.txt 37 ./math/matrix/qr_Q.hpp_iwyu.txt 37 ./math/error_handling/dom_err_vec.hpp_iwyu.txt 37 ./agrad/rev/matrix/LDLT_factor.hpp_iwyu.txt 37 ./agrad/rev/functions/owens_t.hpp_iwyu.txt 37 ./agrad/fwd/matrix/multiply.hpp_iwyu.txt 37 ./agrad/fwd/matrix/dot_product.hpp_iwyu.txt 37 ./agrad/fwd/matrix/divide.hpp_iwyu.txt 36 ./math/matrix/sd.hpp_iwyu.txt 36 ./math/matrix/mdivide_right_tri.hpp_iwyu.txt 36 ./math/matrix/assign.hpp_iwyu.txt 36 ./agrad/rev/matrix/grad.hpp_iwyu.txt 36 ./agrad/fwd/matrix/rows_dot_self.hpp_iwyu.txt 36 ./agrad/fwd/matrix/qr_R.hpp_iwyu.txt 36 ./agrad/fwd/matrix/qr_Q.hpp_iwyu.txt 36 ./agrad/fwd/matrix/columns_dot_self.hpp_iwyu.txt 35 ./prob/distributions/univariate.hpp_iwyu.txt 35 ./math/matrix/segment.hpp_iwyu.txt 35 ./math/matrix/quad_form_diag.hpp_iwyu.txt 35 ./math/matrix/mdivide_right_tri_low.hpp_iwyu.txt 35 ./math/matrix/mdivide_right_ldlt.hpp_iwyu.txt 35 ./math/matrix/log_softmax.hpp_iwyu.txt 35 ./math/error_handling/matrix/check_spsd_matrix.hpp_iwyu.txt 35 ./math/error_handling/matrix/check_cov_matrix.hpp_iwyu.txt 35 ./math/error_handling/matrix/check_cholesky_factor_corr.hpp_iwyu.txt 35 ./agrad/rev/matrix/sum.hpp_iwyu.txt 35 ./agrad/fwd/matrix/trace_quad_form.hpp_iwyu.txt 35 ./agrad/fwd/matrix/trace_gen_quad_form.hpp_iwyu.txt 35 ./agrad/fwd/matrix/determinant.hpp_iwyu.txt 34 ./prob/distributions/multivariate/discrete.hpp_iwyu.txt 34 ./math/matrix/variance.hpp_iwyu.txt 34 ./math/matrix/row.hpp_iwyu.txt 34 ./math/matrix/quad_form.hpp_iwyu.txt 34 ./math/matrix/mdivide_left_tri_low.hpp_iwyu.txt 34 ./math/matrix/inverse_spd.hpp_iwyu.txt 34 ./math/error_handling/matrix/check_symmetric.hpp_iwyu.txt 34 ./agrad/rev/functions/pow.hpp_iwyu.txt 34 ./agrad/rev/functions/atan2.hpp_iwyu.txt 34 ./agrad/fwd/operators.hpp_iwyu.txt 34 ./agrad/fwd/matrix/softmax.hpp_iwyu.txt 33 ./math/matrix/mdivide_right_spd.hpp_iwyu.txt 33 ./math/matrix/mdivide_right.hpp_iwyu.txt 33 ./math/matrix/distance.hpp_iwyu.txt 33 ./math.hpp_iwyu.txt 33 ./math/error_handling/matrix/check_cholesky_factor.hpp_iwyu.txt 33 ./agrad/rev/matrix/log_determinant_ldlt.hpp_iwyu.txt 33 ./agrad/rev/matrix/LDLT_alloc.hpp_iwyu.txt 33 ./agrad/fwd/matrix/typedefs.hpp_iwyu.txt 33 ./agrad/fwd/functions/gamma_p.hpp_iwyu.txt 32 ./math/rep_vector.hpp_iwyu.txt 32 ./math/rep_row_vector.hpp_iwyu.txt 32 ./math/rep_matrix.hpp_iwyu.txt 32 ./math/matrix/softmax.hpp_iwyu.txt 32 ./math/matrix/multiply.hpp_iwyu.txt 32 ./math/matrix/mdivide_left_tri.hpp_iwyu.txt 32 ./math/matrix/eigenvectors_sym.hpp_iwyu.txt 32 ./math/matrix/eigenvalues_sym.hpp_iwyu.txt 32 ./math/matrix/cholesky_decompose.hpp_iwyu.txt 32 ./agrad/rev/matrix/sort.hpp_iwyu.txt 32 ./agrad/rev/functions/fmod.hpp_iwyu.txt 32 ./agrad/fwd/matrix/rows_dot_product.hpp_iwyu.txt 32 ./agrad/fwd/matrix/log_determinant.hpp_iwyu.txt 32 ./agrad/fwd/matrix/columns_dot_product.hpp_iwyu.txt 32 ./agrad/fwd/functions/pow.hpp_iwyu.txt 32 ./agrad/fwd/functions/log_sum_exp.hpp_iwyu.txt 32 ./agrad/fwd/functions/gamma_q.hpp_iwyu.txt 31 ./mcmc/var_adaptation.hpp_iwyu.txt 31 ./math/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 31 ./math/matrix/mean.hpp_iwyu.txt 31 ./math/error_handling/matrix/check_positive_ordered.hpp_iwyu.txt 31 ./math/error_handling/matrix/check_ordered.hpp_iwyu.txt 31 ./math/error_handling/matrix/check_lower_triangular.hpp_iwyu.txt 31 ./gm/grammars/common_adaptors_def.hpp_iwyu.txt 31 ./agrad/rev/operators/operator_subtraction.hpp_iwyu.txt 31 ./agrad/rev/operators/operator_division.hpp_iwyu.txt 31 ./agrad/partials_vari.hpp_iwyu.txt 31 ./agrad/fwd/matrix/tcrossprod.hpp_iwyu.txt 31 ./agrad/fwd/matrix/sort.hpp_iwyu.txt 31 ./agrad/fwd/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 31 ./agrad/fwd/matrix/dot_self.hpp_iwyu.txt 31 ./agrad/fwd/matrix/crossprod.hpp_iwyu.txt 31 ./agrad/fwd/functions/owens_t.hpp_iwyu.txt 30 ./math/matrix/trace_quad_form.hpp_iwyu.txt 30 ./math/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 30 ./math/matrix/trace_gen_quad_form.hpp_iwyu.txt 30 ./math/matrix/mdivide_left_spd.hpp_iwyu.txt 30 ./math/matrix/mdivide_left_ldlt.hpp_iwyu.txt 30 ./math/matrix/mdivide_left.hpp_iwyu.txt 30 ./math/error_handling/check_consistent_sizes.hpp_iwyu.txt 30 ./math/error_handling/check_bounded.hpp_iwyu.txt 30 ./agrad/rev/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 30 ./agrad/rev/functions/Phi.hpp_iwyu.txt 30 ./agrad/rev/functions/log1m_exp.hpp_iwyu.txt 30 ./agrad/rev/functions/hypot.hpp_iwyu.txt 30 ./agrad/rev/functions/erf.hpp_iwyu.txt 30 ./agrad/rev/functions/erfc.hpp_iwyu.txt 30 ./agrad/rev/functions/binary_log_loss.hpp_iwyu.txt 30 ./agrad/fwd/functions/log1m_exp.hpp_iwyu.txt 30 ./agrad/fwd/functions/erf.hpp_iwyu.txt 30 ./agrad/fwd/functions/erfc.hpp_iwyu.txt 30 ./agrad/fwd/functions/acosh.hpp_iwyu.txt 29 ./mcmc/covar_adaptation.hpp_iwyu.txt 29 ./math/error_handling/matrix/check_vector.hpp_iwyu.txt 29 ./math/error_handling/check_positive.hpp_iwyu.txt 29 ./math/error_handling/check_not_nan.hpp_iwyu.txt 29 ./math/error_handling/check_nonnegative.hpp_iwyu.txt 29 ./math/error_handling/check_less_or_equal.hpp_iwyu.txt 29 ./math/error_handling/check_less.hpp_iwyu.txt 29 ./math/error_handling/check_greater_or_equal.hpp_iwyu.txt 29 ./math/error_handling/check_greater.hpp_iwyu.txt 29 ./math/error_handling/check_finite.hpp_iwyu.txt 29 ./math/error_handling/check_equal.hpp_iwyu.txt 29 ./agrad/rev/print_stack.hpp_iwyu.txt 29 ./agrad/rev/matrix/typedefs.hpp_iwyu.txt 29 ./agrad/rev/functions/inv_sqrt.hpp_iwyu.txt 29 ./agrad/rev/functions/expm1.hpp_iwyu.txt 29 ./agrad/rev/functions/exp2.hpp_iwyu.txt 29 ./agrad/fwd/functions/Phi.hpp_iwyu.txt 29 ./agrad/fwd/functions/log_diff_exp.hpp_iwyu.txt 29 ./agrad/fwd/functions/log2.hpp_iwyu.txt 29 ./agrad/fwd/functions/lmgamma.hpp_iwyu.txt 29 ./agrad/fwd/functions/hypot.hpp_iwyu.txt 29 ./agrad/fwd/functions/exp2.hpp_iwyu.txt 29 ./agrad/fwd/functions/binomial_coefficient_log.hpp_iwyu.txt 29 ./agrad/fwd/functions/asinh.hpp_iwyu.txt 28 ./math/matrix/squared_distance.hpp_iwyu.txt 28 ./math/matrix/rows_dot_product.hpp_iwyu.txt 28 ./math/matrix/columns_dot_product.hpp_iwyu.txt 28 ./agrad/rev/operators/operator_multiplication.hpp_iwyu.txt 28 ./agrad/rev/operators/operator_addition.hpp_iwyu.txt 28 ./agrad/rev/matrix/divide.hpp_iwyu.txt 28 ./agrad/rev/internal/matrix_vari.hpp_iwyu.txt 28 ./agrad/rev/functions/sinh.hpp_iwyu.txt 28 ./agrad/rev/functions/log1p.hpp_iwyu.txt 28 ./agrad/rev/functions/inv_cloglog.hpp_iwyu.txt 28 ./agrad/rev/functions/fdim.hpp_iwyu.txt 28 ./agrad/rev/functions/cosh.hpp_iwyu.txt 28 ./agrad/rev/functions/atan.hpp_iwyu.txt 28 ./agrad/rev/functions/acos.hpp_iwyu.txt 28 ./agrad/fwd/functions/sqrt.hpp_iwyu.txt 28 ./agrad/fwd/functions/multiply_log.hpp_iwyu.txt 28 ./agrad/fwd/functions/log_inv_logit.hpp_iwyu.txt 28 ./agrad/fwd/functions/log.hpp_iwyu.txt 28 ./agrad/fwd/functions/log1p_exp.hpp_iwyu.txt 28 ./agrad/fwd/functions/log1m_inv_logit.hpp_iwyu.txt 28 ./agrad/fwd/functions/log10.hpp_iwyu.txt 28 ./agrad/fwd/functions/inv_sqrt.hpp_iwyu.txt 28 ./agrad/fwd/functions/inv_logit.hpp_iwyu.txt 28 ./agrad/fwd/functions/inv_cloglog.hpp_iwyu.txt 28 ./agrad/fwd/functions/expm1.hpp_iwyu.txt 28 ./agrad/fwd/functions/asin.hpp_iwyu.txt 28 ./agrad/fwd/functions/acos.hpp_iwyu.txt 27 ./prob/internal_math.hpp_iwyu.txt 27 ./math/matrix/dot_self.hpp_iwyu.txt 27 ./agrad/rev/vari.hpp_iwyu.txt 27 ./agrad/rev/internal/precomp_v_vari.hpp_iwyu.txt 27 ./agrad/rev/functions/log2.hpp_iwyu.txt 27 ./agrad/rev/functions/log1p_exp.hpp_iwyu.txt 27 ./agrad/rev/functions/log10.hpp_iwyu.txt 27 ./agrad/rev/functions/inv_square.hpp_iwyu.txt 27 ./agrad/rev/functions/inv.hpp_iwyu.txt 27 ./agrad/fwd.hpp_iwyu.txt 27 ./agrad/fwd/functions/tan.hpp_iwyu.txt 27 ./agrad/fwd/functions/tanh.hpp_iwyu.txt 27 ./agrad/fwd/functions/sin.hpp_iwyu.txt 27 ./agrad/fwd/functions/sinh.hpp_iwyu.txt 27 ./agrad/fwd/functions/exp.hpp_iwyu.txt 27 ./agrad/fwd/functions/cos.hpp_iwyu.txt 27 ./agrad/fwd/functions/cosh.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_multiplicable.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_matching_sizes.hpp_iwyu.txt 26 ./gm/grammars/functions_grammar.hpp_iwyu.txt 26 ./agrad/rev/var.hpp_iwyu.txt 26 ./agrad/rev/matrix/stored_gradient_vari.hpp_iwyu.txt 26 ./agrad/rev/matrix/initialize_variable.hpp_iwyu.txt 26 ./agrad/rev.hpp_iwyu.txt 26 ./agrad/rev/functions/tan.hpp_iwyu.txt 26 ./agrad/rev/functions/tanh.hpp_iwyu.txt 26 ./agrad/rev/functions/sqrt.hpp_iwyu.txt 26 ./agrad/rev/functions/sin.hpp_iwyu.txt 26 ./agrad/rev/functions/Phi_approx.hpp_iwyu.txt 26 ./agrad/rev/functions/log.hpp_iwyu.txt 26 ./agrad/rev/functions/log1m.hpp_iwyu.txt 26 ./agrad/rev/functions/inv_logit.hpp_iwyu.txt 26 ./agrad/rev/functions/floor.hpp_iwyu.txt 26 ./agrad/rev/functions/fabs.hpp_iwyu.txt 26 ./agrad/rev/functions/exp.hpp_iwyu.txt 26 ./agrad/rev/functions/cos.hpp_iwyu.txt 26 ./agrad/rev/functions/ceil.hpp_iwyu.txt 26 ./agrad/rev/functions/asin.hpp_iwyu.txt 26 ./agrad/rev/chainable.hpp_iwyu.txt 26 ./agrad/fwd/functions/tgamma.hpp_iwyu.txt 26 ./agrad/fwd/functions/logit.hpp_iwyu.txt 26 ./agrad/fwd/functions/lgamma.hpp_iwyu.txt 26 ./agrad/fwd/functions/fmin.hpp_iwyu.txt 26 ./agrad/fwd/functions/fmax.hpp_iwyu.txt 26 ./agrad/fwd/functions/fdim.hpp_iwyu.txt 26 ./agrad/fwd/functions/atan.hpp_iwyu.txt 26 ./agrad/fwd/functions/atan2.hpp_iwyu.txt 25 ./math/matrix/LDLT_factor.hpp_iwyu.txt 25 ./math/error_handling/matrix/check_nonzero_size.hpp_iwyu.txt 25 ./math/error_handling/check_consistent_size.hpp_iwyu.txt 25 ./io/json/json_parser.hpp_iwyu.txt 25 ./gm/grammars/program_grammar.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_unary_negative.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_unary_increment.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_unary_decrement.hpp_iwyu.txt 25 ./agrad/rev/matrix/value_of.hpp_iwyu.txt 25 ./agrad/rev/functions/square.hpp_iwyu.txt 25 ./agrad/hessian.hpp_iwyu.txt 25 ./agrad/fwd/operators/operator_not_equal.hpp_iwyu.txt 25 ./agrad/fwd/operators/operator_less_than_or_equal.hpp_iwyu.txt 25 ./agrad/fwd/operators/operator_less_than.hpp_iwyu.txt 25 ./agrad/fwd/operators/operator_greater_than_or_equal.hpp_iwyu.txt 25 ./agrad/fwd/operators/operator_greater_than.hpp_iwyu.txt 25 ./agrad/fwd/operators/operator_equal.hpp_iwyu.txt 25 ./agrad/fwd/numeric_limits.hpp_iwyu.txt 25 ./agrad/fwd/functions/rising_factorial.hpp_iwyu.txt 25 ./agrad/fwd/functions/log_rising_factorial.hpp_iwyu.txt 25 ./agrad/fwd/functions/log_falling_factorial.hpp_iwyu.txt 25 ./agrad/fwd/functions/log1p.hpp_iwyu.txt 25 ./agrad/fwd/functions/log1m.hpp_iwyu.txt 25 ./agrad/fwd/functions/lbeta.hpp_iwyu.txt 25 ./agrad/fwd/functions/fmod.hpp_iwyu.txt 25 ./agrad/fwd/functions/floor.hpp_iwyu.txt 25 ./agrad/fwd/functions/falling_factorial.hpp_iwyu.txt 25 ./agrad/fwd/functions/digamma.hpp_iwyu.txt 25 ./agrad/fwd/functions/ceil.hpp_iwyu.txt 25 ./agrad/fwd/functions/cbrt.hpp_iwyu.txt 25 ./agrad/fwd/functions/atanh.hpp_iwyu.txt 24 ./mcmc/hmc/base_hmc.hpp_iwyu.txt 24 ./gm/grammars/term_grammar.hpp_iwyu.txt 24 ./gm/grammars/statement_grammar.hpp_iwyu.txt 24 ./gm/grammars/expression_grammar.hpp_iwyu.txt 24 ./agrad/rev/internal/vector_vari.hpp_iwyu.txt 24 ./agrad/rev/internal/precomputed_gradients.hpp_iwyu.txt 24 ./agrad/rev/functions/abs.hpp_iwyu.txt 24 ./agrad/fwd/functions/square.hpp_iwyu.txt 24 ./agrad/fwd/functions/modified_bessel_second_kind.hpp_iwyu.txt 24 ./agrad/fwd/functions/modified_bessel_first_kind.hpp_iwyu.txt 24 ./agrad/fwd/functions/inv_square.hpp_iwyu.txt 24 ./agrad/fwd/functions/inv.hpp_iwyu.txt 24 ./agrad/fwd/functions/fabs.hpp_iwyu.txt 24 ./agrad/fwd/functions/binary_log_loss.hpp_iwyu.txt 24 ./agrad/fwd/functions/bessel_second_kind.hpp_iwyu.txt 24 ./agrad/fwd/functions/bessel_first_kind.hpp_iwyu.txt 24 ./agrad/fwd/functions/abs.hpp_iwyu.txt 23 ./gm/grammars/var_decls_grammar.hpp_iwyu.txt 23 ./gm/grammars/expression07_grammar.hpp_iwyu.txt 23 ./common/init_adapt.hpp_iwyu.txt 23 ./command/stanc_helper.hpp_iwyu.txt 23 ./agrad/rev/numeric_limits.hpp_iwyu.txt 23 ./agrad/rev/functions/is_uninitialized.hpp_iwyu.txt 23 ./agrad/rev/boost_fpclassify.hpp_iwyu.txt 23 ./agrad/fwd/operators/operator_unary_minus.hpp_iwyu.txt 23 ./agrad/fwd/operators/operator_subtraction.hpp_iwyu.txt 23 ./agrad/fwd/operators/operator_multiplication.hpp_iwyu.txt 23 ./agrad/fwd/operators/operator_division.hpp_iwyu.txt 23 ./agrad/fwd/operators/operator_addition.hpp_iwyu.txt 22 ./meta.hpp_iwyu.txt 22 ./mcmc/hmc/hamiltonians/ps_point.hpp_iwyu.txt 22 ./math/functions/ibeta.hpp_iwyu.txt 22 ./gm/grammars/bare_type_grammar.hpp_iwyu.txt 22 ./gm/generator.hpp_iwyu.txt 22 ./agrad/rev/functions/value_of.hpp_iwyu.txt 22 ./agrad/rev/functions/step.hpp_iwyu.txt 22 ./agrad/rev/functions/fmin.hpp_iwyu.txt 22 ./agrad/rev/functions/fmax.hpp_iwyu.txt 22 ./agrad/rev/functions/as_bool.hpp_iwyu.txt 22 ./agrad/rev/error_handling/matrix.hpp_iwyu.txt 21 ./optimization/lbfgs_update.hpp_iwyu.txt 21 ./mcmc/hmc/static/base_static_hmc.hpp_iwyu.txt 21 ./math/matrix/accumulator.hpp_iwyu.txt 21 ./math/error_handling/dom_err.hpp_iwyu.txt 21 ./gm/grammars/statement_2_grammar.hpp_iwyu.txt 21 ./common/init_windowed_adapt.hpp_iwyu.txt 21 ./agrad/rev/jacobian.hpp_iwyu.txt 20 ./math/rep_array.hpp_iwyu.txt 20 ./math/functions/lgamma.hpp_iwyu.txt 20 ./math/functions/gamma_q.hpp_iwyu.txt 20 ./math/functions/gamma_p.hpp_iwyu.txt 20 ./gm/arguments/argument_parser.hpp_iwyu.txt 20 ./gm/arguments/arg_adapt.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_unit_vector.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_simplex.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_semidefinite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 19 ./agrad/rev/var_stack.hpp_iwyu.txt 19 ./agrad/fwd/matrix/normalize.hpp_iwyu.txt 18 ./mcmc/hmc/hamiltonians/dense_e_point.hpp_iwyu.txt 18 ./math/matrix/tail.hpp_iwyu.txt 18 ./math/matrix/resize.hpp_iwyu.txt 18 ./math/matrix/log_sum_exp.hpp_iwyu.txt 18 ./math/matrix/head.hpp_iwyu.txt 18 ./math/matrix/get_base1_lhs.hpp_iwyu.txt 18 ./gm/arguments/singleton_argument.hpp_iwyu.txt 18 ./gm/arguments/list_argument.hpp_iwyu.txt 18 ./gm/arguments/arg_sample.hpp_iwyu.txt 18 ./agrad/rev/internal/vvv_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vv_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vvd_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/v_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vdv_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vd_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vdd_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/dvv_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/dv_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/dvd_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/ddv_vari.hpp_iwyu.txt 17 ./mcmc/hmc/integrators/expl_leapfrog.hpp_iwyu.txt 17 ./io/cmd_line.hpp_iwyu.txt 16 ./memory/chunk_alloc.hpp_iwyu.txt 16 ./mcmc/hmc/hamiltonians/diag_e_point.hpp_iwyu.txt 16 ./math/matrix/typedefs.hpp_iwyu.txt 16 ./math/matrix/sub_row.hpp_iwyu.txt 16 ./math/matrix/sub_col.hpp_iwyu.txt 16 ./math/matrix/min.hpp_iwyu.txt 16 ./math/matrix/max.hpp_iwyu.txt 16 ./math/matrix/get_base1.hpp_iwyu.txt 16 ./math/matrix/block.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_row_index.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_column_index.hpp_iwyu.txt 16 ./gm/arguments/arg_hmc.hpp_iwyu.txt 16 ./agrad/fwd/functions/fma.hpp_iwyu.txt 15 ./memory/stack_alloc.hpp_iwyu.txt 15 ./math/seq_view.hpp_iwyu.txt 15 ./math/matrix/stan_print.hpp_iwyu.txt 15 ./math/matrix/initialize.hpp_iwyu.txt 15 ./math/matrix/col.hpp_iwyu.txt 15 ./math/functions/log_sum_exp.hpp_iwyu.txt 15 ./math/error_handling/matrix/check_ldlt_factor.hpp_iwyu.txt 15 ./gm/arguments/arg_output.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize_algo.hpp_iwyu.txt 15 ./gm/arguments/arg_metric.hpp_iwyu.txt 15 ./gm/arguments/arg_method.hpp_iwyu.txt 15 ./common/do_bfgs_optimize.hpp_iwyu.txt 14 ./optimization/bfgs_linesearch.hpp_iwyu.txt 14 ./mcmc/sample.hpp_iwyu.txt 14 ./math/matrix/singular_values.hpp_iwyu.txt 14 ./math/matrix/rank.hpp_iwyu.txt 14 ./math/matrix/log_determinant_spd.hpp_iwyu.txt 14 ./math/functions/log2.hpp_iwyu.txt 14 ./math/functions/log1m_exp.hpp_iwyu.txt 14 ./math/functions/inverse_softmax.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_std_vector_index.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_square.hpp_iwyu.txt 14 ./gm/arguments/arg_test_gradient.hpp_iwyu.txt 14 ./gm/arguments/arg_sample_algo.hpp_iwyu.txt 14 ./gm/arguments/arg_engine.hpp_iwyu.txt 14 ./gm/arguments/arg_bfgs.hpp_iwyu.txt 14 ./common/recorder/filtered_values.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_unary_plus.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_unary_not.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_plus_equal.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_not_equal.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_multiply_equal.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_minus_equal.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_less_than_or_equal.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_less_than.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_greater_than_or_equal.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_greater_than.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_equal.hpp_iwyu.txt 14 ./agrad/rev/operators/operator_divide_equal.hpp_iwyu.txt 14 ./agrad/rev/matrix/stan_print.hpp_iwyu.txt 14 ./agrad/rev/functions/if_else.hpp_iwyu.txt 14 ./agrad/agrad_thread_safe.hpp_iwyu.txt 13 ./math/matrix/sum.hpp_iwyu.txt 13 ./math/matrix/sort.hpp_iwyu.txt 13 ./math/matrix/promoter.hpp_iwyu.txt 13 ./math/matrix/prod.hpp_iwyu.txt 13 ./math/matrix/inverse.hpp_iwyu.txt 13 ./math/matrix/fill.hpp_iwyu.txt 13 ./math/matrix/cumulative_sum.hpp_iwyu.txt 13 ./math/functions/log_diff_exp.hpp_iwyu.txt 13 ./math/functions/binomial_coefficient_log.hpp_iwyu.txt 13 ./math/error_handling/matrix/check_matching_dims.hpp_iwyu.txt 13 ./io/var_context.hpp_iwyu.txt 13 ./gm/grammars/whitespace_grammar_def.hpp_iwyu.txt 13 ./gm/arguments/categorical_argument.hpp_iwyu.txt 13 ./gm/arguments/argument.hpp_iwyu.txt 13 ./gm/arguments/arg_tolerance.hpp_iwyu.txt 13 ./gm/arguments/arg_test.hpp_iwyu.txt 13 ./gm/arguments/arg_static.hpp_iwyu.txt 13 ./gm/arguments/arg_random.hpp_iwyu.txt 13 ./gm/arguments/arg_nuts.hpp_iwyu.txt 13 ./gm/arguments/arg_lbfgs.hpp_iwyu.txt 13 ./gm/arguments/arg_diagnose.hpp_iwyu.txt 13 ./gm/arguments/arg_data.hpp_iwyu.txt 13 ./common/recorder/values.hpp_iwyu.txt 13 ./common/recorder.hpp_iwyu.txt 13 ./common/print_progress.hpp_iwyu.txt 13 ./common/init_static_hmc.hpp_iwyu.txt 13 ./common/init_nuts.hpp_iwyu.txt 12 ./optimization/bfgs_update.hpp_iwyu.txt 12 ./mcmc/stepsize_var_adapter.hpp_iwyu.txt 12 ./mcmc/stepsize_covar_adapter.hpp_iwyu.txt 12 ./mcmc/base_mcmc.hpp_iwyu.txt 12 ./math/matrix/trace.hpp_iwyu.txt 12 ./math/matrix/subtract.hpp_iwyu.txt 12 ./math/matrix/rows.hpp_iwyu.txt 12 ./math/matrix/elt_multiply.hpp_iwyu.txt 12 ./math/matrix/elt_divide.hpp_iwyu.txt 12 ./math/matrix/divide.hpp_iwyu.txt 12 ./math/matrix/diag_pre_multiply.hpp_iwyu.txt 12 ./math/matrix/diag_post_multiply.hpp_iwyu.txt 12 ./math/matrix/diagonal.hpp_iwyu.txt 12 ./math/matrix/diag_matrix.hpp_iwyu.txt 12 ./math/matrix/common_type.hpp_iwyu.txt 12 ./math/matrix/cols.hpp_iwyu.txt 12 ./math/matrix/add.hpp_iwyu.txt 12 ./math/functions/trigamma.hpp_iwyu.txt 12 ./math/error_handling/matrix/check_size_match.hpp_iwyu.txt 12 ./gm/grammars/whitespace_grammar.hpp_iwyu.txt 12 ./gm/arguments/valued_argument.hpp_iwyu.txt 12 ./gm/arguments/unvalued_argument.hpp_iwyu.txt 12 ./common/recorder/sum_values.hpp_iwyu.txt 12 ./agrad/fwd/matrix/sum.hpp_iwyu.txt 11 ./math/matrix/sort_indices.hpp_iwyu.txt 11 ./math/matrix/log_determinant.hpp_iwyu.txt 11 ./math/matrix/dims.hpp_iwyu.txt 11 ./math/matrix/determinant.hpp_iwyu.txt 11 ./math/matrix/check_range.hpp_iwyu.txt 11 ./math/functions/Phi_approx.hpp_iwyu.txt 11 ./math/functions/log1p.hpp_iwyu.txt 11 ./math/functions/log1p_exp.hpp_iwyu.txt 11 ./math/error_handling/matrix/validate_non_negative_index.hpp_iwyu.txt 11 ./gm/grammars/iterator_typedefs.hpp_iwyu.txt 11 ./gm/arguments/argument_probe.hpp_iwyu.txt 11 ./common/write_iteration.hpp_iwyu.txt 11 ./common/write_iteration_csv.hpp_iwyu.txt 11 ./common/write_error_msg.hpp_iwyu.txt 10 ./math/matrix/transpose.hpp_iwyu.txt 10 ./math/matrix/rows_dot_self.hpp_iwyu.txt 10 ./math/matrix/log.hpp_iwyu.txt 10 ./math/matrix/log_determinant_ldlt.hpp_iwyu.txt 10 ./math/matrix/exp.hpp_iwyu.txt 10 ./math/matrix/columns_dot_self.hpp_iwyu.txt 10 ./math/functions/rising_factorial.hpp_iwyu.txt 10 ./math/functions/multiply_log.hpp_iwyu.txt 10 ./math/functions/log_rising_factorial.hpp_iwyu.txt 10 ./math/functions/logit.hpp_iwyu.txt 10 ./math/functions/log_inv_logit.hpp_iwyu.txt 10 ./math/functions/log_falling_factorial.hpp_iwyu.txt 10 ./math/functions/log1m_inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_sqrt.hpp_iwyu.txt 10 ./math/functions/inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_cloglog.hpp_iwyu.txt 10 ./math/functions/falling_factorial.hpp_iwyu.txt 10 ./math/functions/exp2.hpp_iwyu.txt 10 ./math/functions/binary_log_loss.hpp_iwyu.txt 10 ./io/json/json_error.hpp_iwyu.txt 10 ./gm/arguments/arg_unit_e.hpp_iwyu.txt 10 ./gm/arguments/arg_thin.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_err.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_eps.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize_jitter.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize.hpp_iwyu.txt 10 ./gm/arguments/arg_seed.hpp_iwyu.txt 10 ./gm/arguments/arg_save_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_save_iterations.hpp_iwyu.txt 10 ./gm/arguments/arg_rwm.hpp_iwyu.txt 10 ./gm/arguments/arg_refresh.hpp_iwyu.txt 10 ./gm/arguments/arg_output_file.hpp_iwyu.txt 10 ./gm/arguments/arg_num_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_num_samples.hpp_iwyu.txt 10 ./gm/arguments/arg_newton.hpp_iwyu.txt 10 ./gm/arguments/arg_max_depth.hpp_iwyu.txt 10 ./gm/arguments/arg_iter.hpp_iwyu.txt 10 ./gm/arguments/arg_int_time.hpp_iwyu.txt 10 ./gm/arguments/arg_init.hpp_iwyu.txt 10 ./gm/arguments/arg_init_alpha.hpp_iwyu.txt 10 ./gm/arguments/arg_id.hpp_iwyu.txt 10 ./gm/arguments/arg_history_size.hpp_iwyu.txt 10 ./gm/arguments/arg_fixed_param.hpp_iwyu.txt 10 ./gm/arguments/arg_fail.hpp_iwyu.txt 10 ./gm/arguments/arg_diagnostic_file.hpp_iwyu.txt 10 ./gm/arguments/arg_diag_e.hpp_iwyu.txt 10 ./gm/arguments/arg_dense_e.hpp_iwyu.txt 10 ./gm/arguments/arg_data_file.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_window.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_term_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_t0.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_kappa.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_init_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_gamma.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_engaged.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_delta.hpp_iwyu.txt 10 ./common/recorder/no_op.hpp_iwyu.txt 10 ./agrad/rev/calculate_chain.hpp_iwyu.txt 9 ./math/matrix/Eigen.hpp_iwyu.txt 8 ./memory.hpp_iwyu.txt 8 ./gm.hpp_iwyu.txt 5 ./math/error_handling/matrix/constraint_tolerance.hpp_iwyu.txt 2 ./version.hpp_iwyu.txt 2 ./mcmc/windowed_adaptation.hpp_iwyu.txt 2 ./mcmc/stepsize_adapter.hpp_iwyu.txt 2 ./mcmc/stepsize_adaptation.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_leapfrog.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_integrator.hpp_iwyu.txt 2 ./mcmc/hmc/hamiltonians/unit_e_point.hpp_iwyu.txt 2 ./mcmc/fixed_param_sampler.hpp_iwyu.txt 2 ./mcmc/base_adapter.hpp_iwyu.txt 2 ./mcmc/base_adaptation.hpp_iwyu.txt 2 ./math/matrix/size.hpp_iwyu.txt 2 ./math/matrix/promote_common.hpp_iwyu.txt 2 ./math/matrix/minus.hpp_iwyu.txt 2 ./math/matrix/array_builder.hpp_iwyu.txt 2 ./math/functions/value_of.hpp_iwyu.txt 2 ./math/functions/sum.hpp_iwyu.txt 2 ./math/functions/sub.hpp_iwyu.txt 2 ./math/functions/step.hpp_iwyu.txt 2 ./math/functions/square.hpp_iwyu.txt 2 ./math/functions/sign.hpp_iwyu.txt 2 ./math/functions/scaled_add.hpp_iwyu.txt 2 ./math/functions/Phi.hpp_iwyu.txt 2 ./math/functions/owens_t.hpp_iwyu.txt 2 ./math/functions/modified_bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/modified_bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/min.hpp_iwyu.txt 2 ./math/functions/max.hpp_iwyu.txt 2 ./math/functions/logical_or.hpp_iwyu.txt 2 ./math/functions/logical_neq.hpp_iwyu.txt 2 ./math/functions/logical_negation.hpp_iwyu.txt 2 ./math/functions/logical_lt.hpp_iwyu.txt 2 ./math/functions/logical_lte.hpp_iwyu.txt 2 ./math/functions/logical_gt.hpp_iwyu.txt 2 ./math/functions/logical_gte.hpp_iwyu.txt 2 ./math/functions/logical_eq.hpp_iwyu.txt 2 ./math/functions/logical_and.hpp_iwyu.txt 2 ./math/functions/log1m.hpp_iwyu.txt 2 ./math/functions/lmgamma.hpp_iwyu.txt 2 ./math/functions/lbeta.hpp_iwyu.txt 2 ./math/functions/is_uninitialized.hpp_iwyu.txt 2 ./math/functions/inv_square.hpp_iwyu.txt 2 ./math/functions/inv.hpp_iwyu.txt 2 ./math/functions/int_step.hpp_iwyu.txt 2 ./math/functions/if_else.hpp_iwyu.txt 2 ./math/functions/fma.hpp_iwyu.txt 2 ./math/functions/fdim.hpp_iwyu.txt 2 ./math/functions/dot_self.hpp_iwyu.txt 2 ./math/functions/dot.hpp_iwyu.txt 2 ./math/functions/dist.hpp_iwyu.txt 2 ./math/functions/bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/as_bool.hpp_iwyu.txt 2 ./math/functions/abs.hpp_iwyu.txt 2 ./io/util.hpp_iwyu.txt 2 ./io/json/json_handler.hpp_iwyu.txt 2 ./gm/error_codes.hpp_iwyu.txt 2 ./gm/compiler.hpp_iwyu.txt 2 ./common/write_stan.hpp_iwyu.txt 2 ./common/write_model.hpp_iwyu.txt 2 ./common/recorder/messages.hpp_iwyu.txt 2 ./common/recorder/csv.hpp_iwyu.txt 2 ./common/do_print.hpp_iwyu.txt 2 ./agrad/rev/error_handling.hpp_iwyu.txt 2 ./agrad.hpp_iwyu.txt 2 ./agrad/fwd/fvar.hpp_iwyu.txt

[bgoodri]

Sorry, I forgot to pull before running it. The attached is up to date with develop.

Ben

On Sat, Aug 9, 2014 at 11:06 PM, Ben Goodrich goodrich.ben@gmail.com wrote:

I have never tried to install it on a Mac. Attached is the output from my laptop. However, iwyu still gets confused by Eigen sometimes.

Ben

On Sat, Aug 9, 2014 at 10:39 PM, Daniel Lee notifications@github.com wrote:

Ben, I'm having a little trouble installing. Any suggestions? Or is there some way we can use the output from a working system?

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51704370.

22297 total 452 ./optimization/newton.hpp_iwyu.txt 406 ./mcmc/chains.hpp_iwyu.txt 361 ./agrad/fwd/matrix/to_fvar.hpp_iwyu.txt 265 ./prob/distributions/multivariate/continuous/lkj_corr.hpp_iwyu.txt 208 ./common/command.hpp_iwyu.txt 205 ./math/matrix/containers_conversion.hpp_iwyu.txt 200 ./agrad/rev/matrix/to_var.hpp_iwyu.txt 199 ./agrad/autodiff.hpp_iwyu.txt 193 ./command/print.hpp_iwyu.txt 180 ./math/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 165 ./io/dump.hpp_iwyu.txt 157 ./agrad/rev/matrix/softmax.hpp_iwyu.txt 157 ./agrad/rev/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 156 ./agrad/rev/matrix/tcrossprod.hpp_iwyu.txt 154 ./agrad/rev/matrix/log_softmax.hpp_iwyu.txt 153 ./math/matrix/tcrossprod.hpp_iwyu.txt 151 ./prob/distributions/multivariate/continuous/wishart.hpp_iwyu.txt 134 ./prob/distributions/multivariate/continuous/inv_wishart.hpp_iwyu.txt 133 ./prob/distributions/multivariate/continuous/multi_student_t.hpp_iwyu.txt 132 ./prob/welford_covar_estimator.hpp_iwyu.txt 125 ./gm/ast.hpp_iwyu.txt 123 ./gm/parser.hpp_iwyu.txt 122 ./prob/distributions/univariate/discrete/ordered_logistic.hpp_iwyu.txt 119 ./prob/distributions/multivariate/discrete/categorical.hpp_iwyu.txt 116 ./prob/distributions/multivariate/continuous/multi_normal_cholesky.hpp_iwyu.txt 115 ./math/matrix.hpp_iwyu.txt 114 ./agrad/rev/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 110 ./prob/distributions/multivariate/continuous/multi_normal.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/diag_e_nuts.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/dense_e_nuts.hpp_iwyu.txt 100 ./prob/distributions/multivariate/continuous/dirichlet.hpp_iwyu.txt 100 ./optimization/bfgs.hpp_iwyu.txt 100 ./mcmc/hmc/nuts/unit_e_nuts.hpp_iwyu.txt 98 ./io/mcmc_writer.hpp_iwyu.txt 98 ./agrad/rev/matrix/dot_product.hpp_iwyu.txt 95 ./mcmc/hmc/nuts/base_nuts.hpp_iwyu.txt 95 ./mcmc/hmc/hamiltonians/dense_e_metric.hpp_iwyu.txt 94 ./agrad/rev/matrix/crossprod.hpp_iwyu.txt 93 ./prob/transform.hpp_iwyu.txt 92 ./mcmc/hmc/hamiltonians/diag_e_metric.hpp_iwyu.txt 92 ./agrad/rev/matrix/multiply.hpp_iwyu.txt 90 ./model/util.hpp_iwyu.txt 88 ./mcmc/hmc/hamiltonians/unit_e_metric.hpp_iwyu.txt 87 ./prob/welford_var_estimator.hpp_iwyu.txt 87 ./math/matrix/crossprod.hpp_iwyu.txt 87 ./agrad/rev/functions.hpp_iwyu.txt 86 ./agrad/fwd/functions.hpp_iwyu.txt 85 ./gm/grammars/program_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/term_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/statement_grammar_def.hpp_iwyu.txt 76 ./gm/grammars/functions_grammar_def.hpp_iwyu.txt 75 ./math/functions.hpp_iwyu.txt 74 ./gm/grammars/var_decls_grammar_def.hpp_iwyu.txt 74 ./gm/grammars/bare_type_grammar_def.hpp_iwyu.txt 71 ./agrad/rev/functions/cbrt.hpp_iwyu.txt 65 ./gm/grammars/expression07_grammar_def.hpp_iwyu.txt 65 ./agrad/rev/functions/digamma.hpp_iwyu.txt 63 ./model/model_header.hpp_iwyu.txt 63 ./gm/grammars/expression_grammar_def.hpp_iwyu.txt 62 ./gm/grammars/statement_2_grammar_def.hpp_iwyu.txt 60 ./io/reader.hpp_iwyu.txt 60 ./agrad/rev/functions/ibeta.hpp_iwyu.txt 58 ./prob/distributions/multivariate/continuous/multi_normal_prec.hpp_iwyu.txt 58 ./prob/distributions/multivariate/continuous/gaussian_dlm_obs.hpp_iwyu.txt 57 ./prob/distributions/univariate/continuous/double_exponential.hpp_iwyu.txt 56 ./mcmc.hpp_iwyu.txt 55 ./agrad/rev/internal.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/inv_gamma.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/gamma.hpp_iwyu.txt 54 ./prob/distributions/multivariate/continuous/multi_gp.hpp_iwyu.txt 54 ./agrad/rev/functions/atanh.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/skew_normal.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/gumbel.hpp_iwyu.txt 53 ./prob/distributions/multivariate/continuous/matrix_normal.hpp_iwyu.txt 52 ./prob/distributions/univariate/discrete/neg_binomial.hpp_iwyu.txt 52 ./prob/distributions/univariate/continuous/student_t.hpp_iwyu.txt 52 ./common.hpp_iwyu.txt 52 ./agrad/rev/matrix.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/neg_binomial_2.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/binomial.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/exp_mod_normal.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/beta.hpp_iwyu.txt 51 ./prob/distributions/multivariate/continuous/lkj_cov.hpp_iwyu.txt 50 ./prob/distributions/univariate/continuous/inv_chi_square.hpp_iwyu.txt 50 ./prob/constants.hpp_iwyu.txt 50 ./agrad/rev/matrix/Eigen_NumTraits.hpp_iwyu.txt 50 ./agrad/rev/functions/trunc.hpp_iwyu.txt 50 ./agrad/rev/functions/round.hpp_iwyu.txt 49 ./prob/distributions/univariate/discrete/beta_binomial.hpp_iwyu.txt 49 ./prob/distributions/univariate/continuous/scaled_inv_chi_square.hpp_iwyu.txt 49 ./prob/distributions/multivariate/discrete/multinomial.hpp_iwyu.txt 48 ./prob/distributions/univariate/discrete/hypergeometric.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/von_mises.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/chi_square.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/cauchy.hpp_iwyu.txt 48 ./io/writer.hpp_iwyu.txt 47 ./prob/distributions/univariate/continuous/lognormal.hpp_iwyu.txt 47 ./io/stan_csv_reader.hpp_iwyu.txt 46 ./prob/traits.hpp_iwyu.txt 46 ./prob.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/normal.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/frechet.hpp_iwyu.txt 46 ./math/constants.hpp_iwyu.txt 45 ./prob/distributions/univariate/discrete/poisson.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/rayleigh.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/pareto.hpp_iwyu.txt 45 ./math/functions/digamma.hpp_iwyu.txt 45 ./agrad/rev/matrix/log_sum_exp.hpp_iwyu.txt 44 ./prob/distributions/univariate/discrete/bernoulli.hpp_iwyu.txt 44 ./prob/distributions/univariate/continuous/weibull.hpp_iwyu.txt 44 ./prob/distributions/multivariate/continuous/multi_gp_cholesky.hpp_iwyu.txt 44 ./prob/distributions/multivariate/continuous.hpp_iwyu.txt 44 ./math/matrix_error_handling.hpp_iwyu.txt 44 ./agrad/rev/functions/log_sum_exp.hpp_iwyu.txt 44 ./agrad/fwd/matrix.hpp_iwyu.txt 43 ./prob/distributions/univariate/continuous.hpp_iwyu.txt 43 ./agrad/rev/matrix/sd.hpp_iwyu.txt 42 ./io/json/json_data.hpp_iwyu.txt 42 ./io/json/json_data_handler.hpp_iwyu.txt 42 ./agrad/rev/functions/gamma_q.hpp_iwyu.txt 41 ./prob/distributions/univariate/continuous/exponential.hpp_iwyu.txt 41 ./common/warmup.hpp_iwyu.txt 41 ./common/sample.hpp_iwyu.txt 41 ./agrad/rev/matrix/log_determinant_spd.hpp_iwyu.txt 41 ./agrad/rev/functions/gamma_p.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_second_kind.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_first_kind.hpp_iwyu.txt 41 ./agrad/fwd/functions/trunc.hpp_iwyu.txt 41 ./agrad/fwd/functions/round.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/uniform.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/logistic.hpp_iwyu.txt 40 ./agrad/rev/matrix/variance.hpp_iwyu.txt 40 ./agrad/rev/matrix/mdivide_left_tri.hpp_iwyu.txt 39 ./common/run_markov_chain.hpp_iwyu.txt 39 ./agrad/rev/functions/rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_falling_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/falling_factorial.hpp_iwyu.txt 39 ./agrad/fwd/matrix/log_sum_exp.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_spd.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_ldlt.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left.hpp_iwyu.txt 37 ./prob/distributions/univariate/continuous/johnson.hpp_iwyu.txt 37 ./agrad/rev/functions/asinh.hpp_iwyu.txt 37 ./agrad/rev/functions/acosh.hpp_iwyu.txt 36 ./prob/distributions/multivariate.hpp_iwyu.txt 36 ./prob/autocovariance.hpp_iwyu.txt 36 ./meta/traits.hpp_iwyu.txt 36 ./math/error_handling.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right_tri_low.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right.hpp_iwyu.txt 35 ./prob/distributions.hpp_iwyu.txt 35 ./io.hpp_iwyu.txt 35 ./agrad/rev/functions/log_diff_exp.hpp_iwyu.txt 35 ./agrad/rev/functions/lmgamma.hpp_iwyu.txt 35 ./agrad/rev/functions/lgamma.hpp_iwyu.txt 35 ./agrad/fwd/matrix/mdivide_left_tri_low.hpp_iwyu.txt 35 ./agrad/fwd/matrix/inverse.hpp_iwyu.txt 34 ./math/error_handling/matrix/check_corr_matrix.hpp_iwyu.txt 34 ./agrad/rev/matrix/log_determinant.hpp_iwyu.txt 34 ./agrad/rev/matrix/determinant.hpp_iwyu.txt 34 ./agrad/rev/functions/modified_bessel_first_kind.hpp_iwyu.txt 34 ./agrad/fwd/prob/univariate/continuous/normal.hpp_iwyu.txt 33 ./prob/distributions/multivariate/discrete/categorical_logit.hpp_iwyu.txt 33 ./agrad/rev/operators.hpp_iwyu.txt 33 ./agrad/rev/matrix/trace_gen_quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/dot_self.hpp_iwyu.txt 33 ./agrad/rev/functions/fma.hpp_iwyu.txt 33 ./agrad/fwd/matrix/mdivide_left.hpp_iwyu.txt 32 ./prob/autocorrelation.hpp_iwyu.txt 32 ./io/csv_writer.hpp_iwyu.txt 32 ./agrad/rev/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 32 ./agrad/rev/matrix/squared_distance.hpp_iwyu.txt 32 ./agrad/rev/functions/tgamma.hpp_iwyu.txt 32 ./agrad/rev/functions/multiply_log.hpp_iwyu.txt 32 ./agrad/rev/functions/modified_bessel_second_kind.hpp_iwyu.txt 31 ./mcmc/var_adaptation.hpp_iwyu.txt 31 ./math/matrix/dot_product.hpp_iwyu.txt 31 ./gm/grammars/common_adaptors_def.hpp_iwyu.txt 31 ./agrad/rev/matrix/trace_quad_form.hpp_iwyu.txt 31 ./agrad/rev/matrix/LDLT_factor.hpp_iwyu.txt 31 ./agrad/rev/functions/owens_t.hpp_iwyu.txt 30 ./math/error_handling/dom_err_vec.hpp_iwyu.txt 29 ./prob/distributions/univariate/discrete.hpp_iwyu.txt 29 ./model/prob_grad.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_diag_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_dense_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_diag_e_nuts.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_dense_e_nuts.hpp_iwyu.txt 29 ./mcmc/covar_adaptation.hpp_iwyu.txt 29 ./io/json.hpp_iwyu.txt 29 ./agrad/rev/matrix/sum.hpp_iwyu.txt 29 ./agrad/rev/matrix/grad.hpp_iwyu.txt 29 ./agrad/fwd/matrix/multiply.hpp_iwyu.txt 29 ./agrad/fwd/matrix/dot_product.hpp_iwyu.txt 28 ./model.hpp_iwyu.txt 28 ./mcmc/hmc/hamiltonians/base_hamiltonian.hpp_iwyu.txt 28 ./math/matrix/qr_R.hpp_iwyu.txt 28 ./math/matrix/qr_Q.hpp_iwyu.txt 28 ./math/matrix/assign.hpp_iwyu.txt 28 ./agrad/rev/functions/pow.hpp_iwyu.txt 28 ./agrad/rev/functions/atan2.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_R.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_Q.hpp_iwyu.txt 28 ./agrad/fwd/matrix/log_softmax.hpp_iwyu.txt 28 ./agrad/fwd/matrix/divide.hpp_iwyu.txt 28 ./agrad/fwd/matrix/determinant.hpp_iwyu.txt 27 ./prob/internal_math.hpp_iwyu.txt 27 ./mcmc/hmc/static/adapt_unit_e_static_hmc.hpp_iwyu.txt 27 ./mcmc/hmc/nuts/adapt_unit_e_nuts.hpp_iwyu.txt 27 ./math/matrix/mdivide_right_tri.hpp_iwyu.txt 27 ./math/matrix/log_softmax.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_symmetric.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_simplex.hpp_iwyu.txt 27 ./agrad/rev/matrix/log_determinant_ldlt.hpp_iwyu.txt 27 ./agrad/rev/matrix/LDLT_alloc.hpp_iwyu.txt 27 ./agrad/fwd/matrix/typedefs.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_gen_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/rows_dot_self.hpp_iwyu.txt 27 ./agrad/fwd/matrix/columns_dot_self.hpp_iwyu.txt 26 ./mcmc/hmc/static/unit_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/diag_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/dense_e_static_hmc.hpp_iwyu.txt 26 ./math/matrix/segment.hpp_iwyu.txt 26 ./math/matrix/sd.hpp_iwyu.txt 26 ./math/matrix/quad_form.hpp_iwyu.txt 26 ./math/matrix/quad_form_diag.hpp_iwyu.txt 26 ./math/matrix/mdivide_right_ldlt.hpp_iwyu.txt 26 ./math/matrix/inverse_spd.hpp_iwyu.txt 26 ./math/matrix/distance.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_spsd_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cov_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cholesky_factor_corr.hpp_iwyu.txt 26 ./gm/grammars/functions_grammar.hpp_iwyu.txt 26 ./agrad/rev/matrix/sort.hpp_iwyu.txt 26 ./agrad/rev/functions/fmod.hpp_iwyu.txt 26 ./agrad/fwd/operators.hpp_iwyu.txt 26 ./agrad/fwd/functions/gamma_p.hpp_iwyu.txt 25 ./prob/distributions/univariate.hpp_iwyu.txt 25 ./prob/distributions/multivariate/discrete.hpp_iwyu.txt 25 ./math/matrix/variance.hpp_iwyu.txt 25 ./math/matrix/row.hpp_iwyu.txt 25 ./math/matrix/mdivide_right_tri_low.hpp_iwyu.txt 25 ./math/matrix/mdivide_left_tri_low.hpp_iwyu.txt 25 ./math/matrix/LDLT_factor.hpp_iwyu.txt 25 ./io/json/json_parser.hpp_iwyu.txt 25 ./gm/grammars/program_grammar.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_subtraction.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_division.hpp_iwyu.txt 25 ./agrad/fwd/matrix/softmax.hpp_iwyu.txt 25 ./agrad/fwd/matrix/rows_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/matrix/log_determinant.hpp_iwyu.txt 25 ./agrad/fwd/matrix/columns_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/functions/pow.hpp_iwyu.txt 25 ./agrad/fwd/functions/log_sum_exp.hpp_iwyu.txt 25 ./agrad/fwd/functions/gamma_q.hpp_iwyu.txt 24 ./mcmc/hmc/base_hmc.hpp_iwyu.txt 24 ./math/matrix/softmax.hpp_iwyu.txt 24 ./math/matrix/multiply.hpp_iwyu.txt 24 ./math/matrix/mdivide_right_spd.hpp_iwyu.txt 24 ./math/matrix/mdivide_right.hpp_iwyu.txt 24 ./math/matrix/mdivide_left_tri.hpp_iwyu.txt 24 ./math/matrix/eigenvectors_sym.hpp_iwyu.txt 24 ./math/matrix/eigenvalues_sym.hpp_iwyu.txt 24 ./math/matrix/cholesky_decompose.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_positive_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_lower_triangular.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_cholesky_factor.hpp_iwyu.txt 24 ./gm/grammars/term_grammar.hpp_iwyu.txt 24 ./gm/grammars/statement_grammar.hpp_iwyu.txt 24 ./gm/grammars/expression_grammar.hpp_iwyu.txt 24 ./agrad/rev/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 24 ./agrad/rev/functions/Phi.hpp_iwyu.txt 24 ./agrad/rev/functions/log1m_exp.hpp_iwyu.txt 24 ./agrad/rev/functions/hypot.hpp_iwyu.txt 24 ./agrad/rev/functions/erf.hpp_iwyu.txt 24 ./agrad/rev/functions/erfc.hpp_iwyu.txt 24 ./agrad/rev/functions/binary_log_loss.hpp_iwyu.txt 24 ./agrad/partials_vari.hpp_iwyu.txt 24 ./agrad/fwd/matrix/tcrossprod.hpp_iwyu.txt 24 ./agrad/fwd/matrix/sort.hpp_iwyu.txt 24 ./agrad/fwd/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 24 ./agrad/fwd/matrix/crossprod.hpp_iwyu.txt 24 ./agrad/fwd/functions/owens_t.hpp_iwyu.txt 23 ./math/rep_vector.hpp_iwyu.txt 23 ./math/rep_row_vector.hpp_iwyu.txt 23 ./math/rep_matrix.hpp_iwyu.txt 23 ./math/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 23 ./math/matrix/mean.hpp_iwyu.txt 23 ./math.hpp_iwyu.txt 23 ./gm/grammars/var_decls_grammar.hpp_iwyu.txt 23 ./gm/grammars/expression07_grammar.hpp_iwyu.txt 23 ./common/init_adapt.hpp_iwyu.txt 23 ./command/stanc_helper.hpp_iwyu.txt 23 ./agrad/rev/matrix/typedefs.hpp_iwyu.txt 23 ./agrad/rev/functions/inv_sqrt.hpp_iwyu.txt 23 ./agrad/rev/functions/expm1.hpp_iwyu.txt 23 ./agrad/rev/functions/exp2.hpp_iwyu.txt 23 ./agrad/fwd/matrix/dot_self.hpp_iwyu.txt 23 ./agrad/fwd/functions/log1m_exp.hpp_iwyu.txt 23 ./agrad/fwd/functions/erf.hpp_iwyu.txt 23 ./agrad/fwd/functions/erfc.hpp_iwyu.txt 23 ./agrad/fwd/functions/acosh.hpp_iwyu.txt 22 ./mcmc/hmc/hamiltonians/ps_point.hpp_iwyu.txt 22 ./math/matrix/trace_quad_form.hpp_iwyu.txt 22 ./math/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 22 ./math/matrix/trace_gen_quad_form.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_spd.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_ldlt.hpp_iwyu.txt 22 ./math/matrix/mdivide_left.hpp_iwyu.txt 22 ./math/matrix/append_row.hpp_iwyu.txt 22 ./math/matrix/append_col.hpp_iwyu.txt 22 ./math/functions/ibeta.hpp_iwyu.txt 22 ./math/error_handling/matrix/check_vector.hpp_iwyu.txt 22 ./math/error_handling/check_consistent_sizes.hpp_iwyu.txt 22 ./math/error_handling/check_bounded.hpp_iwyu.txt 22 ./gm/grammars/bare_type_grammar.hpp_iwyu.txt 22 ./gm/generator.hpp_iwyu.txt 22 ./agrad/rev/print_stack.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_multiplication.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_addition.hpp_iwyu.txt 22 ./agrad/rev/matrix/divide.hpp_iwyu.txt 22 ./agrad/rev/internal/matrix_vari.hpp_iwyu.txt 22 ./agrad/rev.hpp_iwyu.txt 22 ./agrad/rev/functions/sinh.hpp_iwyu.txt 22 ./agrad/rev/functions/log1p.hpp_iwyu.txt 22 ./agrad/rev/functions/inv_cloglog.hpp_iwyu.txt 22 ./agrad/rev/functions/fdim.hpp_iwyu.txt 22 ./agrad/rev/functions/cosh.hpp_iwyu.txt 22 ./agrad/rev/functions/atan.hpp_iwyu.txt 22 ./agrad/rev/functions/acos.hpp_iwyu.txt 22 ./agrad/fwd/functions/Phi.hpp_iwyu.txt 22 ./agrad/fwd/functions/log_diff_exp.hpp_iwyu.txt 22 ./agrad/fwd/functions/log2.hpp_iwyu.txt 22 ./agrad/fwd/functions/lmgamma.hpp_iwyu.txt 22 ./agrad/fwd/functions/hypot.hpp_iwyu.txt 22 ./agrad/fwd/functions/exp2.hpp_iwyu.txt 22 ./agrad/fwd/functions/binomial_coefficient_log.hpp_iwyu.txt 22 ./agrad/fwd/functions/asinh.hpp_iwyu.txt 21 ./optimization/lbfgs_update.hpp_iwyu.txt 21 ./mcmc/hmc/static/base_static_hmc.hpp_iwyu.txt 21 ./math/matrix/accumulator.hpp_iwyu.txt 21 ./math/error_handling/dom_err.hpp_iwyu.txt 21 ./math/error_handling/check_positive.hpp_iwyu.txt 21 ./math/error_handling/check_not_nan.hpp_iwyu.txt 21 ./math/error_handling/check_nonnegative.hpp_iwyu.txt 21 ./math/error_handling/check_less_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_less.hpp_iwyu.txt 21 ./math/error_handling/check_greater_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_greater.hpp_iwyu.txt 21 ./math/error_handling/check_finite.hpp_iwyu.txt 21 ./math/error_handling/check_equal.hpp_iwyu.txt 21 ./gm/grammars/statement_2_grammar.hpp_iwyu.txt 21 ./common/init_windowed_adapt.hpp_iwyu.txt 21 ./agrad/rev/var.hpp_iwyu.txt 21 ./agrad/rev/functions/log2.hpp_iwyu.txt 21 ./agrad/rev/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/rev/functions/log10.hpp_iwyu.txt 21 ./agrad/rev/functions/inv_square.hpp_iwyu.txt 21 ./agrad/rev/functions/inv.hpp_iwyu.txt 21 ./agrad/fwd/functions/sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/multiply_log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1m_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log10.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_cloglog.hpp_iwyu.txt 21 ./agrad/fwd/functions/expm1.hpp_iwyu.txt 21 ./agrad/fwd/functions/asin.hpp_iwyu.txt 21 ./agrad/fwd/functions/acos.hpp_iwyu.txt 20 ./math/matrix/squared_distance.hpp_iwyu.txt 20 ./math/matrix/rows_dot_product.hpp_iwyu.txt 20 ./math/matrix/columns_dot_product.hpp_iwyu.txt 20 ./math/functions/lgamma.hpp_iwyu.txt 20 ./math/functions/gamma_q.hpp_iwyu.txt 20 ./math/functions/gamma_p.hpp_iwyu.txt 20 ./gm/arguments/argument_parser.hpp_iwyu.txt 20 ./gm/arguments/arg_adapt.hpp_iwyu.txt 20 ./agrad/rev/vari.hpp_iwyu.txt 20 ./agrad/rev/matrix/initialize_variable.hpp_iwyu.txt 20 ./agrad/rev/functions/tan.hpp_iwyu.txt 20 ./agrad/rev/functions/tanh.hpp_iwyu.txt 20 ./agrad/rev/functions/sqrt.hpp_iwyu.txt 20 ./agrad/rev/functions/sin.hpp_iwyu.txt 20 ./agrad/rev/functions/Phi_approx.hpp_iwyu.txt 20 ./agrad/rev/functions/log.hpp_iwyu.txt 20 ./agrad/rev/functions/log1m.hpp_iwyu.txt 20 ./agrad/rev/functions/inv_logit.hpp_iwyu.txt 20 ./agrad/rev/functions/floor.hpp_iwyu.txt 20 ./agrad/rev/functions/fabs.hpp_iwyu.txt 20 ./agrad/rev/functions/exp.hpp_iwyu.txt 20 ./agrad/rev/functions/cos.hpp_iwyu.txt 20 ./agrad/rev/functions/ceil.hpp_iwyu.txt 20 ./agrad/rev/functions/asin.hpp_iwyu.txt 20 ./agrad/hessian.hpp_iwyu.txt 20 ./agrad/fwd/functions/tan.hpp_iwyu.txt 20 ./agrad/fwd/functions/tanh.hpp_iwyu.txt 20 ./agrad/fwd/functions/sin.hpp_iwyu.txt 20 ./agrad/fwd/functions/sinh.hpp_iwyu.txt 20 ./agrad/fwd/functions/exp.hpp_iwyu.txt 20 ./agrad/fwd/functions/cos.hpp_iwyu.txt 20 ./agrad/fwd/functions/cosh.hpp_iwyu.txt 19 ./math/matrix/dot_self.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_unit_vector.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_semidefinite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_multiplicable.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_matching_sizes.hpp_iwyu.txt 19 ./agrad/rev/var_stack.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_negative.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_increment.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_decrement.hpp_iwyu.txt 19 ./agrad/rev/matrix/value_of.hpp_iwyu.txt 19 ./agrad/rev/internal/precomp_v_vari.hpp_iwyu.txt 19 ./agrad/rev/internal/precomputed_gradients.hpp_iwyu.txt 19 ./agrad/rev/functions/square.hpp_iwyu.txt 19 ./agrad/rev/chainable.hpp_iwyu.txt 19 ./agrad/fwd/matrix/normalize.hpp_iwyu.txt 19 ./agrad/fwd.hpp_iwyu.txt 19 ./agrad/fwd/functions/tgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/logit.hpp_iwyu.txt 19 ./agrad/fwd/functions/lgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmin.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmax.hpp_iwyu.txt 19 ./agrad/fwd/functions/fdim.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan2.hpp_iwyu.txt 18 ./mcmc/hmc/hamiltonians/dense_e_point.hpp_iwyu.txt 18 ./math/matrix/tail.hpp_iwyu.txt 18 ./math/matrix/resize.hpp_iwyu.txt 18 ./math/matrix/log_sum_exp.hpp_iwyu.txt 18 ./math/matrix/head.hpp_iwyu.txt 18 ./math/matrix/get_base1_lhs.hpp_iwyu.txt 18 ./math/error_handling/matrix/check_nonzero_size.hpp_iwyu.txt 18 ./math/error_handling/check_consistent_size.hpp_iwyu.txt 18 ./gm/arguments/singleton_argument.hpp_iwyu.txt 18 ./gm/arguments/list_argument.hpp_iwyu.txt 18 ./gm/arguments/arg_sample.hpp_iwyu.txt 18 ./agrad/rev/matrix/stored_gradient_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vector_vari.hpp_iwyu.txt 18 ./agrad/rev/boost_fpclassify.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_not_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_equal.hpp_iwyu.txt 18 ./agrad/fwd/numeric_limits.hpp_iwyu.txt 18 ./agrad/fwd/functions/rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1p.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1m.hpp_iwyu.txt 18 ./agrad/fwd/functions/lbeta.hpp_iwyu.txt 18 ./agrad/fwd/functions/fmod.hpp_iwyu.txt 18 ./agrad/fwd/functions/floor.hpp_iwyu.txt 18 ./agrad/fwd/functions/falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/digamma.hpp_iwyu.txt 18 ./agrad/fwd/functions/ceil.hpp_iwyu.txt 18 ./agrad/fwd/functions/cbrt.hpp_iwyu.txt 18 ./agrad/fwd/functions/atanh.hpp_iwyu.txt 17 ./mcmc/hmc/integrators/expl_leapfrog.hpp_iwyu.txt 17 ./io/cmd_line.hpp_iwyu.txt 17 ./agrad/rev/numeric_limits.hpp_iwyu.txt 17 ./agrad/rev/functions/is_uninitialized.hpp_iwyu.txt 17 ./agrad/rev/functions/abs.hpp_iwyu.txt 17 ./agrad/fwd/functions/square.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv_square.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv.hpp_iwyu.txt 17 ./agrad/fwd/functions/fabs.hpp_iwyu.txt 17 ./agrad/fwd/functions/binary_log_loss.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/abs.hpp_iwyu.txt 16 ./memory/chunk_alloc.hpp_iwyu.txt 16 ./mcmc/hmc/hamiltonians/diag_e_point.hpp_iwyu.txt 16 ./math/matrix/typedefs.hpp_iwyu.txt 16 ./math/matrix/sub_row.hpp_iwyu.txt 16 ./math/matrix/sub_col.hpp_iwyu.txt 16 ./math/matrix/min.hpp_iwyu.txt 16 ./math/matrix/max.hpp_iwyu.txt 16 ./math/matrix/get_base1.hpp_iwyu.txt 16 ./math/matrix/block.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_row_index.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_column_index.hpp_iwyu.txt 16 ./gm/arguments/arg_hmc.hpp_iwyu.txt 16 ./agrad/rev/functions/value_of.hpp_iwyu.txt 16 ./agrad/rev/functions/step.hpp_iwyu.txt 16 ./agrad/rev/functions/fmin.hpp_iwyu.txt 16 ./agrad/rev/functions/fmax.hpp_iwyu.txt 16 ./agrad/rev/functions/as_bool.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_unary_minus.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_subtraction.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_multiplication.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_division.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_addition.hpp_iwyu.txt 15 ./meta.hpp_iwyu.txt 15 ./memory/stack_alloc.hpp_iwyu.txt 15 ./math/seq_view.hpp_iwyu.txt 15 ./math/matrix/stan_print.hpp_iwyu.txt 15 ./math/matrix/initialize.hpp_iwyu.txt 15 ./math/matrix/col.hpp_iwyu.txt 15 ./math/functions/log_sum_exp.hpp_iwyu.txt 15 ./math/error_handling/matrix/check_ldlt_factor.hpp_iwyu.txt 15 ./gm/arguments/arg_output.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize_algo.hpp_iwyu.txt 15 ./gm/arguments/arg_metric.hpp_iwyu.txt 15 ./gm/arguments/arg_method.hpp_iwyu.txt 15 ./common/do_bfgs_optimize.hpp_iwyu.txt 15 ./agrad/rev/jacobian.hpp_iwyu.txt 15 ./agrad/rev/error_handling/matrix.hpp_iwyu.txt 14 ./optimization/bfgs_linesearch.hpp_iwyu.txt 14 ./mcmc/sample.hpp_iwyu.txt 14 ./math/matrix/singular_values.hpp_iwyu.txt 14 ./math/matrix/rank.hpp_iwyu.txt 14 ./math/matrix/log_determinant_spd.hpp_iwyu.txt 14 ./math/functions/log2.hpp_iwyu.txt 14 ./math/functions/log1m_exp.hpp_iwyu.txt 14 ./math/functions/inverse_softmax.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_std_vector_index.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_square.hpp_iwyu.txt 14 ./gm/arguments/arg_test_gradient.hpp_iwyu.txt 14 ./gm/arguments/arg_sample_algo.hpp_iwyu.txt 14 ./gm/arguments/arg_engine.hpp_iwyu.txt 14 ./gm/arguments/arg_bfgs.hpp_iwyu.txt 14 ./common/recorder/filtered_values.hpp_iwyu.txt 14 ./agrad/agrad_thread_safe.hpp_iwyu.txt 13 ./math/matrix/sum.hpp_iwyu.txt 13 ./math/matrix/sort.hpp_iwyu.txt 13 ./math/matrix/promoter.hpp_iwyu.txt 13 ./math/matrix/prod.hpp_iwyu.txt 13 ./math/matrix/inverse.hpp_iwyu.txt 13 ./math/matrix/fill.hpp_iwyu.txt 13 ./math/matrix/cumulative_sum.hpp_iwyu.txt 13 ./math/functions/log_diff_exp.hpp_iwyu.txt 13 ./math/functions/binomial_coefficient_log.hpp_iwyu.txt 13 ./math/error_handling/matrix/check_matching_dims.hpp_iwyu.txt 13 ./io/var_context.hpp_iwyu.txt 13 ./gm/grammars/whitespace_grammar_def.hpp_iwyu.txt 13 ./gm/arguments/categorical_argument.hpp_iwyu.txt 13 ./gm/arguments/argument.hpp_iwyu.txt 13 ./gm/arguments/arg_tolerance.hpp_iwyu.txt 13 ./gm/arguments/arg_test.hpp_iwyu.txt 13 ./gm/arguments/arg_static.hpp_iwyu.txt 13 ./gm/arguments/arg_random.hpp_iwyu.txt 13 ./gm/arguments/arg_nuts.hpp_iwyu.txt 13 ./gm/arguments/arg_lbfgs.hpp_iwyu.txt 13 ./gm/arguments/arg_diagnose.hpp_iwyu.txt 13 ./gm/arguments/arg_data.hpp_iwyu.txt 13 ./common/recorder/values.hpp_iwyu.txt 13 ./common/recorder.hpp_iwyu.txt 13 ./common/print_progress.hpp_iwyu.txt 13 ./common/init_static_hmc.hpp_iwyu.txt 13 ./common/init_nuts.hpp_iwyu.txt 12 ./optimization/bfgs_update.hpp_iwyu.txt 12 ./mcmc/stepsize_var_adapter.hpp_iwyu.txt 12 ./mcmc/stepsize_covar_adapter.hpp_iwyu.txt 12 ./mcmc/base_mcmc.hpp_iwyu.txt 12 ./math/matrix/trace.hpp_iwyu.txt 12 ./math/matrix/subtract.hpp_iwyu.txt 12 ./math/matrix/rows.hpp_iwyu.txt 12 ./math/matrix/elt_multiply.hpp_iwyu.txt 12 ./math/matrix/elt_divide.hpp_iwyu.txt 12 ./math/matrix/divide.hpp_iwyu.txt 12 ./math/matrix/diag_pre_multiply.hpp_iwyu.txt 12 ./math/matrix/diag_post_multiply.hpp_iwyu.txt 12 ./math/matrix/diagonal.hpp_iwyu.txt 12 ./math/matrix/diag_matrix.hpp_iwyu.txt 12 ./math/matrix/common_type.hpp_iwyu.txt 12 ./math/matrix/cols.hpp_iwyu.txt 12 ./math/matrix/add.hpp_iwyu.txt 12 ./math/functions/trigamma.hpp_iwyu.txt 12 ./math/error_handling/matrix/check_size_match.hpp_iwyu.txt 12 ./gm/grammars/whitespace_grammar.hpp_iwyu.txt 12 ./gm/arguments/valued_argument.hpp_iwyu.txt 12 ./gm/arguments/unvalued_argument.hpp_iwyu.txt 12 ./common/recorder/sum_values.hpp_iwyu.txt 12 ./agrad/fwd/matrix/sum.hpp_iwyu.txt 11 ./math/rep_array.hpp_iwyu.txt 11 ./math/matrix/sort_indices.hpp_iwyu.txt 11 ./math/matrix/log_determinant.hpp_iwyu.txt 11 ./math/matrix/dims.hpp_iwyu.txt 11 ./math/matrix/determinant.hpp_iwyu.txt 11 ./math/functions/Phi_approx.hpp_iwyu.txt 11 ./math/functions/log1p.hpp_iwyu.txt 11 ./math/functions/log1p_exp.hpp_iwyu.txt 11 ./math/error_handling/matrix/validate_non_negative_index.hpp_iwyu.txt 11 ./math/error_handling/matrix/check_range.hpp_iwyu.txt 11 ./math/error_handling/check_positive_finite.hpp_iwyu.txt 11 ./gm/grammars/iterator_typedefs.hpp_iwyu.txt 11 ./gm/arguments/argument_probe.hpp_iwyu.txt 11 ./common/write_iteration.hpp_iwyu.txt 11 ./common/write_iteration_csv.hpp_iwyu.txt 11 ./common/write_error_msg.hpp_iwyu.txt 10 ./math/matrix/transpose.hpp_iwyu.txt 10 ./math/matrix/rows_dot_self.hpp_iwyu.txt 10 ./math/matrix/log.hpp_iwyu.txt 10 ./math/matrix/log_determinant_ldlt.hpp_iwyu.txt 10 ./math/matrix/exp.hpp_iwyu.txt 10 ./math/matrix/columns_dot_self.hpp_iwyu.txt 10 ./math/functions/rising_factorial.hpp_iwyu.txt 10 ./math/functions/multiply_log.hpp_iwyu.txt 10 ./math/functions/modulus.hpp_iwyu.txt 10 ./math/functions/log_rising_factorial.hpp_iwyu.txt 10 ./math/functions/logit.hpp_iwyu.txt 10 ./math/functions/log_inv_logit.hpp_iwyu.txt 10 ./math/functions/log_falling_factorial.hpp_iwyu.txt 10 ./math/functions/log1m_inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_sqrt.hpp_iwyu.txt 10 ./math/functions/inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_cloglog.hpp_iwyu.txt 10 ./math/functions/falling_factorial.hpp_iwyu.txt 10 ./math/functions/exp2.hpp_iwyu.txt 10 ./math/functions/divide.hpp_iwyu.txt 10 ./math/functions/binary_log_loss.hpp_iwyu.txt 10 ./io/json/json_error.hpp_iwyu.txt 10 ./gm/arguments/arg_unit_e.hpp_iwyu.txt 10 ./gm/arguments/arg_thin.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_err.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_eps.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize_jitter.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize.hpp_iwyu.txt 10 ./gm/arguments/arg_seed.hpp_iwyu.txt 10 ./gm/arguments/arg_save_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_save_iterations.hpp_iwyu.txt 10 ./gm/arguments/arg_rwm.hpp_iwyu.txt 10 ./gm/arguments/arg_refresh.hpp_iwyu.txt 10 ./gm/arguments/arg_output_file.hpp_iwyu.txt 10 ./gm/arguments/arg_num_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_num_samples.hpp_iwyu.txt 10 ./gm/arguments/arg_newton.hpp_iwyu.txt 10 ./gm/arguments/arg_max_depth.hpp_iwyu.txt 10 ./gm/arguments/arg_iter.hpp_iwyu.txt 10 ./gm/arguments/arg_int_time.hpp_iwyu.txt 10 ./gm/arguments/arg_init.hpp_iwyu.txt 10 ./gm/arguments/arg_init_alpha.hpp_iwyu.txt 10 ./gm/arguments/arg_id.hpp_iwyu.txt 10 ./gm/arguments/arg_history_size.hpp_iwyu.txt 10 ./gm/arguments/arg_fixed_param.hpp_iwyu.txt 10 ./gm/arguments/arg_fail.hpp_iwyu.txt 10 ./gm/arguments/arg_diagnostic_file.hpp_iwyu.txt 10 ./gm/arguments/arg_diag_e.hpp_iwyu.txt 10 ./gm/arguments/arg_dense_e.hpp_iwyu.txt 10 ./gm/arguments/arg_data_file.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_window.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_term_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_t0.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_kappa.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_init_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_gamma.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_engaged.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_delta.hpp_iwyu.txt 10 ./common/recorder/no_op.hpp_iwyu.txt 10 ./agrad/rev/internal/vvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/v_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/ddv_vari.hpp_iwyu.txt 10 ./agrad/rev/calculate_chain.hpp_iwyu.txt 9 ./math/matrix/Eigen.hpp_iwyu.txt 9 ./agrad/fwd/functions/fma.hpp_iwyu.txt 8 ./memory.hpp_iwyu.txt 8 ./gm.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_plus.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_not.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_plus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_not_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_multiply_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_minus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_divide_equal.hpp_iwyu.txt 8 ./agrad/rev/matrix/stan_print.hpp_iwyu.txt 8 ./agrad/rev/functions/if_else.hpp_iwyu.txt 5 ./math/error_handling/matrix/constraint_tolerance.hpp_iwyu.txt 2 ./version.hpp_iwyu.txt 2 ./mcmc/windowed_adaptation.hpp_iwyu.txt 2 ./mcmc/stepsize_adapter.hpp_iwyu.txt 2 ./mcmc/stepsize_adaptation.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_leapfrog.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_integrator.hpp_iwyu.txt 2 ./mcmc/hmc/hamiltonians/unit_e_point.hpp_iwyu.txt 2 ./mcmc/fixed_param_sampler.hpp_iwyu.txt 2 ./mcmc/base_adapter.hpp_iwyu.txt 2 ./mcmc/base_adaptation.hpp_iwyu.txt 2 ./math/matrix/size.hpp_iwyu.txt 2 ./math/matrix/promote_common.hpp_iwyu.txt 2 ./math/matrix/minus.hpp_iwyu.txt 2 ./math/matrix/array_builder.hpp_iwyu.txt 2 ./math/functions/value_of.hpp_iwyu.txt 2 ./math/functions/sum.hpp_iwyu.txt 2 ./math/functions/sub.hpp_iwyu.txt 2 ./math/functions/step.hpp_iwyu.txt 2 ./math/functions/square.hpp_iwyu.txt 2 ./math/functions/sign.hpp_iwyu.txt 2 ./math/functions/scaled_add.hpp_iwyu.txt 2 ./math/functions/Phi.hpp_iwyu.txt 2 ./math/functions/owens_t.hpp_iwyu.txt 2 ./math/functions/modified_bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/modified_bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/min.hpp_iwyu.txt 2 ./math/functions/max.hpp_iwyu.txt 2 ./math/functions/logical_or.hpp_iwyu.txt 2 ./math/functions/logical_neq.hpp_iwyu.txt 2 ./math/functions/logical_negation.hpp_iwyu.txt 2 ./math/functions/logical_lt.hpp_iwyu.txt 2 ./math/functions/logical_lte.hpp_iwyu.txt 2 ./math/functions/logical_gt.hpp_iwyu.txt 2 ./math/functions/logical_gte.hpp_iwyu.txt 2 ./math/functions/logical_eq.hpp_iwyu.txt 2 ./math/functions/logical_and.hpp_iwyu.txt 2 ./math/functions/log1m.hpp_iwyu.txt 2 ./math/functions/lmgamma.hpp_iwyu.txt 2 ./math/functions/lbeta.hpp_iwyu.txt 2 ./math/functions/is_uninitialized.hpp_iwyu.txt 2 ./math/functions/inv_square.hpp_iwyu.txt 2 ./math/functions/inv.hpp_iwyu.txt 2 ./math/functions/int_step.hpp_iwyu.txt 2 ./math/functions/if_else.hpp_iwyu.txt 2 ./math/functions/fma.hpp_iwyu.txt 2 ./math/functions/fdim.hpp_iwyu.txt 2 ./math/functions/dot_self.hpp_iwyu.txt 2 ./math/functions/dot.hpp_iwyu.txt 2 ./math/functions/dist.hpp_iwyu.txt 2 ./math/functions/bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/as_bool.hpp_iwyu.txt 2 ./math/functions/abs.hpp_iwyu.txt 2 ./io/util.hpp_iwyu.txt 2 ./io/json/json_handler.hpp_iwyu.txt 2 ./gm/error_codes.hpp_iwyu.txt 2 ./gm/compiler.hpp_iwyu.txt 2 ./common/write_stan.hpp_iwyu.txt 2 ./common/write_model.hpp_iwyu.txt 2 ./common/recorder/messages.hpp_iwyu.txt 2 ./common/recorder/csv.hpp_iwyu.txt 2 ./common/do_print.hpp_iwyu.txt 2 ./agrad/rev/error_handling.hpp_iwyu.txt 2 ./agrad.hpp_iwyu.txt 2 ./agrad/fwd/fvar.hpp_iwyu.txt

[syclik]

Ben, github's issues swallowed the attachment. Can you either forward the attachment directly to me or to stan-dev?

On Sat, Aug 9, 2014 at 11:53 PM, bgoodri notifications@github.com wrote:

Sorry, I forgot to pull before running it. The attached is up to date with develop.

Ben

On Sat, Aug 9, 2014 at 11:06 PM, Ben Goodrich goodrich.ben@gmail.com wrote:

I have never tried to install it on a Mac. Attached is the output from my laptop. However, iwyu still gets confused by Eigen sometimes.

Ben

On Sat, Aug 9, 2014 at 10:39 PM, Daniel Lee notifications@github.com wrote:

Ben, I'm having a little trouble installing. Any suggestions? Or is there some way we can use the output from a working system?

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51704370.

22297 total 452 ./optimization/newton.hpp_iwyu.txt 406 ./mcmc/chains.hpp_iwyu.txt 361 ./agrad/fwd/matrix/to_fvar.hpp_iwyu.txt 265 ./prob/distributions/multivariate/continuous/lkj_corr.hpp_iwyu.txt 208 ./common/command.hpp_iwyu.txt 205 ./math/matrix/containers_conversion.hpp_iwyu.txt 200 ./agrad/rev/matrix/to_var.hpp_iwyu.txt 199 ./agrad/autodiff.hpp_iwyu.txt 193 ./command/print.hpp_iwyu.txt 180 ./math/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 165 ./io/dump.hpp_iwyu.txt 157 ./agrad/rev/matrix/softmax.hpp_iwyu.txt 157 ./agrad/rev/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 156 ./agrad/rev/matrix/tcrossprod.hpp_iwyu.txt 154 ./agrad/rev/matrix/log_softmax.hpp_iwyu.txt 153 ./math/matrix/tcrossprod.hpp_iwyu.txt 151 ./prob/distributions/multivariate/continuous/wishart.hpp_iwyu.txt 134 ./prob/distributions/multivariate/continuous/inv_wishart.hpp_iwyu.txt 133 ./prob/distributions/multivariate/continuous/multi_student_t.hpp_iwyu.txt 132 ./prob/welford_covar_estimator.hpp_iwyu.txt 125 ./gm/ast.hpp_iwyu.txt 123 ./gm/parser.hpp_iwyu.txt 122 ./prob/distributions/univariate/discrete/ordered_logistic.hpp_iwyu.txt 119 ./prob/distributions/multivariate/discrete/categorical.hpp_iwyu.txt 116 ./prob/distributions/multivariate/continuous/multi_normal_cholesky.hpp_iwyu.txt 115 ./math/matrix.hpp_iwyu.txt 114 ./agrad/rev/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 110 ./prob/distributions/multivariate/continuous/multi_normal.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/diag_e_nuts.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/dense_e_nuts.hpp_iwyu.txt 100 ./prob/distributions/multivariate/continuous/dirichlet.hpp_iwyu.txt 100 ./optimization/bfgs.hpp_iwyu.txt 100 ./mcmc/hmc/nuts/unit_e_nuts.hpp_iwyu.txt 98 ./io/mcmc_writer.hpp_iwyu.txt 98 ./agrad/rev/matrix/dot_product.hpp_iwyu.txt 95 ./mcmc/hmc/nuts/base_nuts.hpp_iwyu.txt 95 ./mcmc/hmc/hamiltonians/dense_e_metric.hpp_iwyu.txt 94 ./agrad/rev/matrix/crossprod.hpp_iwyu.txt 93 ./prob/transform.hpp_iwyu.txt 92 ./mcmc/hmc/hamiltonians/diag_e_metric.hpp_iwyu.txt 92 ./agrad/rev/matrix/multiply.hpp_iwyu.txt 90 ./model/util.hpp_iwyu.txt 88 ./mcmc/hmc/hamiltonians/unit_e_metric.hpp_iwyu.txt 87 ./prob/welford_var_estimator.hpp_iwyu.txt 87 ./math/matrix/crossprod.hpp_iwyu.txt 87 ./agrad/rev/functions.hpp_iwyu.txt 86 ./agrad/fwd/functions.hpp_iwyu.txt

85 ./gm/grammars/program_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/term_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/statement_grammar_def.hpp_iwyu.txt 76 ./gm/grammars/functions_grammar_def.hpp_iwyu.txt 75 ./math/functions.hpp_iwyu.txt 74 ./gm/grammars/var_decls_grammar_def.hpp_iwyu.txt 74 ./gm/grammars/bare_type_grammar_def.hpp_iwyu.txt 71 ./agrad/rev/functions/cbrt.hpp_iwyu.txt 65 ./gm/grammars/expression07_grammar_def.hpp_iwyu.txt 65 ./agrad/rev/functions/digamma.hpp_iwyu.txt 63 ./model/model_header.hpp_iwyu.txt 63 ./gm/grammars/expression_grammar_def.hpp_iwyu.txt 62 ./gm/grammars/statement_2_grammar_def.hpp_iwyu.txt 60 ./io/reader.hpp_iwyu.txt 60 ./agrad/rev/functions/ibeta.hpp_iwyu.txt 58 ./prob/distributions/multivariate/continuous/multi_normal_prec.hpp_iwyu.txt 58 ./prob/distributions/multivariate/continuous/gaussian_dlm_obs.hpp_iwyu.txt 57 ./prob/distributions/univariate/continuous/double_exponential.hpp_iwyu.txt 56 ./mcmc.hpp_iwyu.txt 55 ./agrad/rev/internal.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/inv_gamma.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/gamma.hpp_iwyu.txt 54 ./prob/distributions/multivariate/continuous/multi_gp.hpp_iwyu.txt 54 ./agrad/rev/functions/atanh.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/skew_normal.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/gumbel.hpp_iwyu.txt 53 ./prob/distributions/multivariate/continuous/matrix_normal.hpp_iwyu.txt 52 ./prob/distributions/univariate/discrete/neg_binomial.hpp_iwyu.txt 52 ./prob/distributions/univariate/continuous/student_t.hpp_iwyu.txt 52 ./common.hpp_iwyu.txt 52 ./agrad/rev/matrix.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/neg_binomial_2.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/binomial.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/exp_mod_normal.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/beta.hpp_iwyu.txt 51 ./prob/distributions/multivariate/continuous/lkj_cov.hpp_iwyu.txt 50 ./prob/distributions/univariate/continuous/inv_chi_square.hpp_iwyu.txt 50 ./prob/constants.hpp_iwyu.txt 50 ./agrad/rev/matrix/Eigen_NumTraits.hpp_iwyu.txt 50 ./agrad/rev/functions/trunc.hpp_iwyu.txt 50 ./agrad/rev/functions/round.hpp_iwyu.txt 49 ./prob/distributions/univariate/discrete/beta_binomial.hpp_iwyu.txt 49 ./prob/distributions/univariate/continuous/scaled_inv_chi_square.hpp_iwyu.txt 49 ./prob/distributions/multivariate/discrete/multinomial.hpp_iwyu.txt 48 ./prob/distributions/univariate/discrete/hypergeometric.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/von_mises.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/chi_square.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/cauchy.hpp_iwyu.txt 48 ./io/writer.hpp_iwyu.txt 47 ./prob/distributions/univariate/continuous/lognormal.hpp_iwyu.txt 47 ./io/stan_csv_reader.hpp_iwyu.txt 46 ./prob/traits.hpp_iwyu.txt 46 ./prob.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/normal.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/frechet.hpp_iwyu.txt 46 ./math/constants.hpp_iwyu.txt 45 ./prob/distributions/univariate/discrete/poisson.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/rayleigh.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/pareto.hpp_iwyu.txt 45 ./math/functions/digamma.hpp_iwyu.txt 45 ./agrad/rev/matrix/log_sum_exp.hpp_iwyu.txt 44 ./prob/distributions/univariate/discrete/bernoulli.hpp_iwyu.txt 44 ./prob/distributions/univariate/continuous/weibull.hpp_iwyu.txt 44 ./prob/distributions/multivariate/continuous/multi_gp_cholesky.hpp_iwyu.txt 44 ./prob/distributions/multivariate/continuous.hpp_iwyu.txt 44 ./math/matrix_error_handling.hpp_iwyu.txt 44 ./agrad/rev/functions/log_sum_exp.hpp_iwyu.txt 44 ./agrad/fwd/matrix.hpp_iwyu.txt 43 ./prob/distributions/univariate/continuous.hpp_iwyu.txt 43 ./agrad/rev/matrix/sd.hpp_iwyu.txt 42 ./io/json/json_data.hpp_iwyu.txt 42 ./io/json/json_data_handler.hpp_iwyu.txt 42 ./agrad/rev/functions/gamma_q.hpp_iwyu.txt 41 ./prob/distributions/univariate/continuous/exponential.hpp_iwyu.txt 41 ./common/warmup.hpp_iwyu.txt 41 ./common/sample.hpp_iwyu.txt 41 ./agrad/rev/matrix/log_determinant_spd.hpp_iwyu.txt 41 ./agrad/rev/functions/gamma_p.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_second_kind.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_first_kind.hpp_iwyu.txt 41 ./agrad/fwd/functions/trunc.hpp_iwyu.txt 41 ./agrad/fwd/functions/round.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/uniform.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/logistic.hpp_iwyu.txt 40 ./agrad/rev/matrix/variance.hpp_iwyu.txt 40 ./agrad/rev/matrix/mdivide_left_tri.hpp_iwyu.txt 39 ./common/run_markov_chain.hpp_iwyu.txt 39 ./agrad/rev/functions/rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_falling_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/falling_factorial.hpp_iwyu.txt 39 ./agrad/fwd/matrix/log_sum_exp.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_spd.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_ldlt.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left.hpp_iwyu.txt 37 ./prob/distributions/univariate/continuous/johnson.hpp_iwyu.txt 37 ./agrad/rev/functions/asinh.hpp_iwyu.txt 37 ./agrad/rev/functions/acosh.hpp_iwyu.txt 36 ./prob/distributions/multivariate.hpp_iwyu.txt 36 ./prob/autocovariance.hpp_iwyu.txt 36 ./meta/traits.hpp_iwyu.txt 36 ./math/error_handling.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right_tri_low.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right.hpp_iwyu.txt 35 ./prob/distributions.hpp_iwyu.txt 35 ./io.hpp_iwyu.txt 35 ./agrad/rev/functions/log_diff_exp.hpp_iwyu.txt 35 ./agrad/rev/functions/lmgamma.hpp_iwyu.txt 35 ./agrad/rev/functions/lgamma.hpp_iwyu.txt 35 ./agrad/fwd/matrix/mdivide_left_tri_low.hpp_iwyu.txt 35 ./agrad/fwd/matrix/inverse.hpp_iwyu.txt 34 ./math/error_handling/matrix/check_corr_matrix.hpp_iwyu.txt 34 ./agrad/rev/matrix/log_determinant.hpp_iwyu.txt 34 ./agrad/rev/matrix/determinant.hpp_iwyu.txt 34 ./agrad/rev/functions/modified_bessel_first_kind.hpp_iwyu.txt 34 ./agrad/fwd/prob/univariate/continuous/normal.hpp_iwyu.txt 33 ./prob/distributions/multivariate/discrete/categorical_logit.hpp_iwyu.txt 33 ./agrad/rev/operators.hpp_iwyu.txt 33 ./agrad/rev/matrix/trace_gen_quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/dot_self.hpp_iwyu.txt 33 ./agrad/rev/functions/fma.hpp_iwyu.txt 33 ./agrad/fwd/matrix/mdivide_left.hpp_iwyu.txt 32 ./prob/autocorrelation.hpp_iwyu.txt 32 ./io/csv_writer.hpp_iwyu.txt 32 ./agrad/rev/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 32 ./agrad/rev/matrix/squared_distance.hpp_iwyu.txt 32 ./agrad/rev/functions/tgamma.hpp_iwyu.txt 32 ./agrad/rev/functions/multiply_log.hpp_iwyu.txt 32 ./agrad/rev/functions/modified_bessel_second_kind.hpp_iwyu.txt 31 ./mcmc/var_adaptation.hpp_iwyu.txt 31 ./math/matrix/dot_product.hpp_iwyu.txt 31 ./gm/grammars/common_adaptors_def.hpp_iwyu.txt 31 ./agrad/rev/matrix/trace_quad_form.hpp_iwyu.txt 31 ./agrad/rev/matrix/LDLT_factor.hpp_iwyu.txt 31 ./agrad/rev/functions/owens_t.hpp_iwyu.txt 30 ./math/error_handling/dom_err_vec.hpp_iwyu.txt 29 ./prob/distributions/univariate/discrete.hpp_iwyu.txt 29 ./model/prob_grad.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_diag_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_dense_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_diag_e_nuts.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_dense_e_nuts.hpp_iwyu.txt 29 ./mcmc/covar_adaptation.hpp_iwyu.txt 29 ./io/json.hpp_iwyu.txt 29 ./agrad/rev/matrix/sum.hpp_iwyu.txt 29 ./agrad/rev/matrix/grad.hpp_iwyu.txt 29 ./agrad/fwd/matrix/multiply.hpp_iwyu.txt 29 ./agrad/fwd/matrix/dot_product.hpp_iwyu.txt 28 ./model.hpp_iwyu.txt 28 ./mcmc/hmc/hamiltonians/base_hamiltonian.hpp_iwyu.txt 28 ./math/matrix/qr_R.hpp_iwyu.txt 28 ./math/matrix/qr_Q.hpp_iwyu.txt 28 ./math/matrix/assign.hpp_iwyu.txt 28 ./agrad/rev/functions/pow.hpp_iwyu.txt 28 ./agrad/rev/functions/atan2.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_R.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_Q.hpp_iwyu.txt 28 ./agrad/fwd/matrix/log_softmax.hpp_iwyu.txt 28 ./agrad/fwd/matrix/divide.hpp_iwyu.txt 28 ./agrad/fwd/matrix/determinant.hpp_iwyu.txt 27 ./prob/internal_math.hpp_iwyu.txt 27 ./mcmc/hmc/static/adapt_unit_e_static_hmc.hpp_iwyu.txt 27 ./mcmc/hmc/nuts/adapt_unit_e_nuts.hpp_iwyu.txt 27 ./math/matrix/mdivide_right_tri.hpp_iwyu.txt 27 ./math/matrix/log_softmax.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_symmetric.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_simplex.hpp_iwyu.txt 27 ./agrad/rev/matrix/log_determinant_ldlt.hpp_iwyu.txt 27 ./agrad/rev/matrix/LDLT_alloc.hpp_iwyu.txt 27 ./agrad/fwd/matrix/typedefs.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_gen_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/rows_dot_self.hpp_iwyu.txt 27 ./agrad/fwd/matrix/columns_dot_self.hpp_iwyu.txt 26 ./mcmc/hmc/static/unit_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/diag_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/dense_e_static_hmc.hpp_iwyu.txt 26 ./math/matrix/segment.hpp_iwyu.txt 26 ./math/matrix/sd.hpp_iwyu.txt 26 ./math/matrix/quad_form.hpp_iwyu.txt 26 ./math/matrix/quad_form_diag.hpp_iwyu.txt 26 ./math/matrix/mdivide_right_ldlt.hpp_iwyu.txt 26 ./math/matrix/inverse_spd.hpp_iwyu.txt 26 ./math/matrix/distance.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_spsd_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cov_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cholesky_factor_corr.hpp_iwyu.txt 26 ./gm/grammars/functions_grammar.hpp_iwyu.txt 26 ./agrad/rev/matrix/sort.hpp_iwyu.txt 26 ./agrad/rev/functions/fmod.hpp_iwyu.txt 26 ./agrad/fwd/operators.hpp_iwyu.txt 26 ./agrad/fwd/functions/gamma_p.hpp_iwyu.txt 25 ./prob/distributions/univariate.hpp_iwyu.txt 25 ./prob/distributions/multivariate/discrete.hpp_iwyu.txt 25 ./math/matrix/variance.hpp_iwyu.txt 25 ./math/matrix/row.hpp_iwyu.txt 25 ./math/matrix/mdivide_right_tri_low.hpp_iwyu.txt 25 ./math/matrix/mdivide_left_tri_low.hpp_iwyu.txt 25 ./math/matrix/LDLT_factor.hpp_iwyu.txt 25 ./io/json/json_parser.hpp_iwyu.txt 25 ./gm/grammars/program_grammar.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_subtraction.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_division.hpp_iwyu.txt 25 ./agrad/fwd/matrix/softmax.hpp_iwyu.txt 25 ./agrad/fwd/matrix/rows_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/matrix/log_determinant.hpp_iwyu.txt 25 ./agrad/fwd/matrix/columns_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/functions/pow.hpp_iwyu.txt 25 ./agrad/fwd/functions/log_sum_exp.hpp_iwyu.txt 25 ./agrad/fwd/functions/gamma_q.hpp_iwyu.txt 24 ./mcmc/hmc/base_hmc.hpp_iwyu.txt 24 ./math/matrix/softmax.hpp_iwyu.txt 24 ./math/matrix/multiply.hpp_iwyu.txt 24 ./math/matrix/mdivide_right_spd.hpp_iwyu.txt 24 ./math/matrix/mdivide_right.hpp_iwyu.txt 24 ./math/matrix/mdivide_left_tri.hpp_iwyu.txt 24 ./math/matrix/eigenvectors_sym.hpp_iwyu.txt 24 ./math/matrix/eigenvalues_sym.hpp_iwyu.txt 24 ./math/matrix/cholesky_decompose.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_positive_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_lower_triangular.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_cholesky_factor.hpp_iwyu.txt

24 ./gm/grammars/term_grammar.hpp_iwyu.txt 24 ./gm/grammars/statement_grammar.hpp_iwyu.txt 24 ./gm/grammars/expression_grammar.hpp_iwyu.txt 24 ./agrad/rev/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 24 ./agrad/rev/functions/Phi.hpp_iwyu.txt 24 ./agrad/rev/functions/log1m_exp.hpp_iwyu.txt 24 ./agrad/rev/functions/hypot.hpp_iwyu.txt 24 ./agrad/rev/functions/erf.hpp_iwyu.txt 24 ./agrad/rev/functions/erfc.hpp_iwyu.txt 24 ./agrad/rev/functions/binary_log_loss.hpp_iwyu.txt 24 ./agrad/partials_vari.hpp_iwyu.txt 24 ./agrad/fwd/matrix/tcrossprod.hpp_iwyu.txt 24 ./agrad/fwd/matrix/sort.hpp_iwyu.txt 24 ./agrad/fwd/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 24 ./agrad/fwd/matrix/crossprod.hpp_iwyu.txt 24 ./agrad/fwd/functions/owens_t.hpp_iwyu.txt 23 ./math/rep_vector.hpp_iwyu.txt 23 ./math/rep_row_vector.hpp_iwyu.txt 23 ./math/rep_matrix.hpp_iwyu.txt 23 ./math/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 23 ./math/matrix/mean.hpp_iwyu.txt 23 ./math.hpp_iwyu.txt

23 ./gm/grammars/var_decls_grammar.hpp_iwyu.txt 23 ./gm/grammars/expression07_grammar.hpp_iwyu.txt 23 ./common/init_adapt.hpp_iwyu.txt 23 ./command/stanc_helper.hpp_iwyu.txt 23 ./agrad/rev/matrix/typedefs.hpp_iwyu.txt 23 ./agrad/rev/functions/inv_sqrt.hpp_iwyu.txt 23 ./agrad/rev/functions/expm1.hpp_iwyu.txt 23 ./agrad/rev/functions/exp2.hpp_iwyu.txt 23 ./agrad/fwd/matrix/dot_self.hpp_iwyu.txt 23 ./agrad/fwd/functions/log1m_exp.hpp_iwyu.txt 23 ./agrad/fwd/functions/erf.hpp_iwyu.txt 23 ./agrad/fwd/functions/erfc.hpp_iwyu.txt 23 ./agrad/fwd/functions/acosh.hpp_iwyu.txt 22 ./mcmc/hmc/hamiltonians/ps_point.hpp_iwyu.txt 22 ./math/matrix/trace_quad_form.hpp_iwyu.txt 22 ./math/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 22 ./math/matrix/trace_gen_quad_form.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_spd.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_ldlt.hpp_iwyu.txt 22 ./math/matrix/mdivide_left.hpp_iwyu.txt 22 ./math/matrix/append_row.hpp_iwyu.txt 22 ./math/matrix/append_col.hpp_iwyu.txt 22 ./math/functions/ibeta.hpp_iwyu.txt 22 ./math/error_handling/matrix/check_vector.hpp_iwyu.txt 22 ./math/error_handling/check_consistent_sizes.hpp_iwyu.txt 22 ./math/error_handling/check_bounded.hpp_iwyu.txt 22 ./gm/grammars/bare_type_grammar.hpp_iwyu.txt 22 ./gm/generator.hpp_iwyu.txt 22 ./agrad/rev/print_stack.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_multiplication.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_addition.hpp_iwyu.txt 22 ./agrad/rev/matrix/divide.hpp_iwyu.txt 22 ./agrad/rev/internal/matrix_vari.hpp_iwyu.txt 22 ./agrad/rev.hpp_iwyu.txt 22 ./agrad/rev/functions/sinh.hpp_iwyu.txt 22 ./agrad/rev/functions/log1p.hpp_iwyu.txt 22 ./agrad/rev/functions/inv_cloglog.hpp_iwyu.txt 22 ./agrad/rev/functions/fdim.hpp_iwyu.txt 22 ./agrad/rev/functions/cosh.hpp_iwyu.txt 22 ./agrad/rev/functions/atan.hpp_iwyu.txt 22 ./agrad/rev/functions/acos.hpp_iwyu.txt 22 ./agrad/fwd/functions/Phi.hpp_iwyu.txt 22 ./agrad/fwd/functions/log_diff_exp.hpp_iwyu.txt 22 ./agrad/fwd/functions/log2.hpp_iwyu.txt 22 ./agrad/fwd/functions/lmgamma.hpp_iwyu.txt 22 ./agrad/fwd/functions/hypot.hpp_iwyu.txt 22 ./agrad/fwd/functions/exp2.hpp_iwyu.txt 22 ./agrad/fwd/functions/binomial_coefficient_log.hpp_iwyu.txt 22 ./agrad/fwd/functions/asinh.hpp_iwyu.txt

21 ./optimization/lbfgs_update.hpp_iwyu.txt 21 ./mcmc/hmc/static/base_static_hmc.hpp_iwyu.txt 21 ./math/matrix/accumulator.hpp_iwyu.txt 21 ./math/error_handling/dom_err.hpp_iwyu.txt 21 ./math/error_handling/check_positive.hpp_iwyu.txt 21 ./math/error_handling/check_not_nan.hpp_iwyu.txt 21 ./math/error_handling/check_nonnegative.hpp_iwyu.txt 21 ./math/error_handling/check_less_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_less.hpp_iwyu.txt 21 ./math/error_handling/check_greater_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_greater.hpp_iwyu.txt 21 ./math/error_handling/check_finite.hpp_iwyu.txt 21 ./math/error_handling/check_equal.hpp_iwyu.txt 21 ./gm/grammars/statement_2_grammar.hpp_iwyu.txt 21 ./common/init_windowed_adapt.hpp_iwyu.txt 21 ./agrad/rev/var.hpp_iwyu.txt 21 ./agrad/rev/functions/log2.hpp_iwyu.txt 21 ./agrad/rev/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/rev/functions/log10.hpp_iwyu.txt 21 ./agrad/rev/functions/inv_square.hpp_iwyu.txt 21 ./agrad/rev/functions/inv.hpp_iwyu.txt 21 ./agrad/fwd/functions/sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/multiply_log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1m_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log10.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_cloglog.hpp_iwyu.txt 21 ./agrad/fwd/functions/expm1.hpp_iwyu.txt 21 ./agrad/fwd/functions/asin.hpp_iwyu.txt 21 ./agrad/fwd/functions/acos.hpp_iwyu.txt 20 ./math/matrix/squared_distance.hpp_iwyu.txt 20 ./math/matrix/rows_dot_product.hpp_iwyu.txt 20 ./math/matrix/columns_dot_product.hpp_iwyu.txt

20 ./math/functions/lgamma.hpp_iwyu.txt 20 ./math/functions/gamma_q.hpp_iwyu.txt 20 ./math/functions/gamma_p.hpp_iwyu.txt 20 ./gm/arguments/argument_parser.hpp_iwyu.txt 20 ./gm/arguments/arg_adapt.hpp_iwyu.txt 20 ./agrad/rev/vari.hpp_iwyu.txt 20 ./agrad/rev/matrix/initialize_variable.hpp_iwyu.txt 20 ./agrad/rev/functions/tan.hpp_iwyu.txt 20 ./agrad/rev/functions/tanh.hpp_iwyu.txt 20 ./agrad/rev/functions/sqrt.hpp_iwyu.txt 20 ./agrad/rev/functions/sin.hpp_iwyu.txt 20 ./agrad/rev/functions/Phi_approx.hpp_iwyu.txt 20 ./agrad/rev/functions/log.hpp_iwyu.txt 20 ./agrad/rev/functions/log1m.hpp_iwyu.txt 20 ./agrad/rev/functions/inv_logit.hpp_iwyu.txt 20 ./agrad/rev/functions/floor.hpp_iwyu.txt 20 ./agrad/rev/functions/fabs.hpp_iwyu.txt 20 ./agrad/rev/functions/exp.hpp_iwyu.txt 20 ./agrad/rev/functions/cos.hpp_iwyu.txt 20 ./agrad/rev/functions/ceil.hpp_iwyu.txt 20 ./agrad/rev/functions/asin.hpp_iwyu.txt 20 ./agrad/hessian.hpp_iwyu.txt 20 ./agrad/fwd/functions/tan.hpp_iwyu.txt 20 ./agrad/fwd/functions/tanh.hpp_iwyu.txt 20 ./agrad/fwd/functions/sin.hpp_iwyu.txt 20 ./agrad/fwd/functions/sinh.hpp_iwyu.txt 20 ./agrad/fwd/functions/exp.hpp_iwyu.txt 20 ./agrad/fwd/functions/cos.hpp_iwyu.txt 20 ./agrad/fwd/functions/cosh.hpp_iwyu.txt 19 ./math/matrix/dot_self.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_unit_vector.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_semidefinite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_multiplicable.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_matching_sizes.hpp_iwyu.txt 19 ./agrad/rev/var_stack.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_negative.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_increment.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_decrement.hpp_iwyu.txt 19 ./agrad/rev/matrix/value_of.hpp_iwyu.txt 19 ./agrad/rev/internal/precomp_v_vari.hpp_iwyu.txt 19 ./agrad/rev/internal/precomputed_gradients.hpp_iwyu.txt 19 ./agrad/rev/functions/square.hpp_iwyu.txt 19 ./agrad/rev/chainable.hpp_iwyu.txt 19 ./agrad/fwd/matrix/normalize.hpp_iwyu.txt 19 ./agrad/fwd.hpp_iwyu.txt 19 ./agrad/fwd/functions/tgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/logit.hpp_iwyu.txt 19 ./agrad/fwd/functions/lgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmin.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmax.hpp_iwyu.txt 19 ./agrad/fwd/functions/fdim.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan2.hpp_iwyu.txt

18 ./mcmc/hmc/hamiltonians/dense_e_point.hpp_iwyu.txt 18 ./math/matrix/tail.hpp_iwyu.txt 18 ./math/matrix/resize.hpp_iwyu.txt 18 ./math/matrix/log_sum_exp.hpp_iwyu.txt 18 ./math/matrix/head.hpp_iwyu.txt 18 ./math/matrix/get_base1_lhs.hpp_iwyu.txt 18 ./math/error_handling/matrix/check_nonzero_size.hpp_iwyu.txt 18 ./math/error_handling/check_consistent_size.hpp_iwyu.txt

18 ./gm/arguments/singleton_argument.hpp_iwyu.txt 18 ./gm/arguments/list_argument.hpp_iwyu.txt 18 ./gm/arguments/arg_sample.hpp_iwyu.txt 18 ./agrad/rev/matrix/stored_gradient_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vector_vari.hpp_iwyu.txt 18 ./agrad/rev/boost_fpclassify.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_not_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_equal.hpp_iwyu.txt 18 ./agrad/fwd/numeric_limits.hpp_iwyu.txt 18 ./agrad/fwd/functions/rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1p.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1m.hpp_iwyu.txt 18 ./agrad/fwd/functions/lbeta.hpp_iwyu.txt 18 ./agrad/fwd/functions/fmod.hpp_iwyu.txt 18 ./agrad/fwd/functions/floor.hpp_iwyu.txt 18 ./agrad/fwd/functions/falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/digamma.hpp_iwyu.txt 18 ./agrad/fwd/functions/ceil.hpp_iwyu.txt 18 ./agrad/fwd/functions/cbrt.hpp_iwyu.txt 18 ./agrad/fwd/functions/atanh.hpp_iwyu.txt 17 ./mcmc/hmc/integrators/expl_leapfrog.hpp_iwyu.txt 17 ./io/cmd_line.hpp_iwyu.txt 17 ./agrad/rev/numeric_limits.hpp_iwyu.txt 17 ./agrad/rev/functions/is_uninitialized.hpp_iwyu.txt 17 ./agrad/rev/functions/abs.hpp_iwyu.txt 17 ./agrad/fwd/functions/square.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv_square.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv.hpp_iwyu.txt 17 ./agrad/fwd/functions/fabs.hpp_iwyu.txt 17 ./agrad/fwd/functions/binary_log_loss.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/abs.hpp_iwyu.txt

16 ./memory/chunk_alloc.hpp_iwyu.txt 16 ./mcmc/hmc/hamiltonians/diag_e_point.hpp_iwyu.txt 16 ./math/matrix/typedefs.hpp_iwyu.txt 16 ./math/matrix/sub_row.hpp_iwyu.txt 16 ./math/matrix/sub_col.hpp_iwyu.txt 16 ./math/matrix/min.hpp_iwyu.txt 16 ./math/matrix/max.hpp_iwyu.txt 16 ./math/matrix/get_base1.hpp_iwyu.txt 16 ./math/matrix/block.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_row_index.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_column_index.hpp_iwyu.txt 16 ./gm/arguments/arg_hmc.hpp_iwyu.txt 16 ./agrad/rev/functions/value_of.hpp_iwyu.txt 16 ./agrad/rev/functions/step.hpp_iwyu.txt 16 ./agrad/rev/functions/fmin.hpp_iwyu.txt 16 ./agrad/rev/functions/fmax.hpp_iwyu.txt 16 ./agrad/rev/functions/as_bool.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_unary_minus.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_subtraction.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_multiplication.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_division.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_addition.hpp_iwyu.txt 15 ./meta.hpp_iwyu.txt

15 ./memory/stack_alloc.hpp_iwyu.txt 15 ./math/seq_view.hpp_iwyu.txt 15 ./math/matrix/stan_print.hpp_iwyu.txt 15 ./math/matrix/initialize.hpp_iwyu.txt 15 ./math/matrix/col.hpp_iwyu.txt 15 ./math/functions/log_sum_exp.hpp_iwyu.txt 15 ./math/error_handling/matrix/check_ldlt_factor.hpp_iwyu.txt 15 ./gm/arguments/arg_output.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize_algo.hpp_iwyu.txt 15 ./gm/arguments/arg_metric.hpp_iwyu.txt 15 ./gm/arguments/arg_method.hpp_iwyu.txt 15 ./common/do_bfgs_optimize.hpp_iwyu.txt 15 ./agrad/rev/jacobian.hpp_iwyu.txt 15 ./agrad/rev/error_handling/matrix.hpp_iwyu.txt

14 ./optimization/bfgs_linesearch.hpp_iwyu.txt 14 ./mcmc/sample.hpp_iwyu.txt 14 ./math/matrix/singular_values.hpp_iwyu.txt 14 ./math/matrix/rank.hpp_iwyu.txt 14 ./math/matrix/log_determinant_spd.hpp_iwyu.txt 14 ./math/functions/log2.hpp_iwyu.txt 14 ./math/functions/log1m_exp.hpp_iwyu.txt 14 ./math/functions/inverse_softmax.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_std_vector_index.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_square.hpp_iwyu.txt 14 ./gm/arguments/arg_test_gradient.hpp_iwyu.txt 14 ./gm/arguments/arg_sample_algo.hpp_iwyu.txt 14 ./gm/arguments/arg_engine.hpp_iwyu.txt 14 ./gm/arguments/arg_bfgs.hpp_iwyu.txt 14 ./common/recorder/filtered_values.hpp_iwyu.txt 14 ./agrad/agrad_thread_safe.hpp_iwyu.txt 13 ./math/matrix/sum.hpp_iwyu.txt 13 ./math/matrix/sort.hpp_iwyu.txt 13 ./math/matrix/promoter.hpp_iwyu.txt 13 ./math/matrix/prod.hpp_iwyu.txt 13 ./math/matrix/inverse.hpp_iwyu.txt 13 ./math/matrix/fill.hpp_iwyu.txt 13 ./math/matrix/cumulative_sum.hpp_iwyu.txt 13 ./math/functions/log_diff_exp.hpp_iwyu.txt 13 ./math/functions/binomial_coefficient_log.hpp_iwyu.txt 13 ./math/error_handling/matrix/check_matching_dims.hpp_iwyu.txt 13 ./io/var_context.hpp_iwyu.txt 13 ./gm/grammars/whitespace_grammar_def.hpp_iwyu.txt 13 ./gm/arguments/categorical_argument.hpp_iwyu.txt 13 ./gm/arguments/argument.hpp_iwyu.txt 13 ./gm/arguments/arg_tolerance.hpp_iwyu.txt 13 ./gm/arguments/arg_test.hpp_iwyu.txt 13 ./gm/arguments/arg_static.hpp_iwyu.txt 13 ./gm/arguments/arg_random.hpp_iwyu.txt 13 ./gm/arguments/arg_nuts.hpp_iwyu.txt 13 ./gm/arguments/arg_lbfgs.hpp_iwyu.txt 13 ./gm/arguments/arg_diagnose.hpp_iwyu.txt 13 ./gm/arguments/arg_data.hpp_iwyu.txt 13 ./common/recorder/values.hpp_iwyu.txt 13 ./common/recorder.hpp_iwyu.txt 13 ./common/print_progress.hpp_iwyu.txt 13 ./common/init_static_hmc.hpp_iwyu.txt 13 ./common/init_nuts.hpp_iwyu.txt 12 ./optimization/bfgs_update.hpp_iwyu.txt 12 ./mcmc/stepsize_var_adapter.hpp_iwyu.txt 12 ./mcmc/stepsize_covar_adapter.hpp_iwyu.txt 12 ./mcmc/base_mcmc.hpp_iwyu.txt 12 ./math/matrix/trace.hpp_iwyu.txt 12 ./math/matrix/subtract.hpp_iwyu.txt 12 ./math/matrix/rows.hpp_iwyu.txt 12 ./math/matrix/elt_multiply.hpp_iwyu.txt 12 ./math/matrix/elt_divide.hpp_iwyu.txt 12 ./math/matrix/divide.hpp_iwyu.txt 12 ./math/matrix/diag_pre_multiply.hpp_iwyu.txt 12 ./math/matrix/diag_post_multiply.hpp_iwyu.txt 12 ./math/matrix/diagonal.hpp_iwyu.txt 12 ./math/matrix/diag_matrix.hpp_iwyu.txt 12 ./math/matrix/common_type.hpp_iwyu.txt 12 ./math/matrix/cols.hpp_iwyu.txt 12 ./math/matrix/add.hpp_iwyu.txt 12 ./math/functions/trigamma.hpp_iwyu.txt 12 ./math/error_handling/matrix/check_size_match.hpp_iwyu.txt 12 ./gm/grammars/whitespace_grammar.hpp_iwyu.txt 12 ./gm/arguments/valued_argument.hpp_iwyu.txt 12 ./gm/arguments/unvalued_argument.hpp_iwyu.txt 12 ./common/recorder/sum_values.hpp_iwyu.txt 12 ./agrad/fwd/matrix/sum.hpp_iwyu.txt 11 ./math/rep_array.hpp_iwyu.txt

11 ./math/matrix/sort_indices.hpp_iwyu.txt 11 ./math/matrix/log_determinant.hpp_iwyu.txt 11 ./math/matrix/dims.hpp_iwyu.txt 11 ./math/matrix/determinant.hpp_iwyu.txt 11 ./math/functions/Phi_approx.hpp_iwyu.txt 11 ./math/functions/log1p.hpp_iwyu.txt 11 ./math/functions/log1p_exp.hpp_iwyu.txt 11 ./math/error_handling/matrix/validate_non_negative_index.hpp_iwyu.txt 11 ./math/error_handling/matrix/check_range.hpp_iwyu.txt 11 ./math/error_handling/check_positive_finite.hpp_iwyu.txt

11 ./gm/grammars/iterator_typedefs.hpp_iwyu.txt 11 ./gm/arguments/argument_probe.hpp_iwyu.txt 11 ./common/write_iteration.hpp_iwyu.txt 11 ./common/write_iteration_csv.hpp_iwyu.txt 11 ./common/write_error_msg.hpp_iwyu.txt 10 ./math/matrix/transpose.hpp_iwyu.txt 10 ./math/matrix/rows_dot_self.hpp_iwyu.txt 10 ./math/matrix/log.hpp_iwyu.txt 10 ./math/matrix/log_determinant_ldlt.hpp_iwyu.txt 10 ./math/matrix/exp.hpp_iwyu.txt 10 ./math/matrix/columns_dot_self.hpp_iwyu.txt 10 ./math/functions/rising_factorial.hpp_iwyu.txt 10 ./math/functions/multiply_log.hpp_iwyu.txt 10 ./math/functions/modulus.hpp_iwyu.txt

10 ./math/functions/log_rising_factorial.hpp_iwyu.txt 10 ./math/functions/logit.hpp_iwyu.txt 10 ./math/functions/log_inv_logit.hpp_iwyu.txt 10 ./math/functions/log_falling_factorial.hpp_iwyu.txt 10 ./math/functions/log1m_inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_sqrt.hpp_iwyu.txt 10 ./math/functions/inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_cloglog.hpp_iwyu.txt 10 ./math/functions/falling_factorial.hpp_iwyu.txt 10 ./math/functions/exp2.hpp_iwyu.txt 10 ./math/functions/divide.hpp_iwyu.txt

10 ./math/functions/binary_log_loss.hpp_iwyu.txt 10 ./io/json/json_error.hpp_iwyu.txt 10 ./gm/arguments/arg_unit_e.hpp_iwyu.txt 10 ./gm/arguments/arg_thin.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_err.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_eps.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize_jitter.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize.hpp_iwyu.txt 10 ./gm/arguments/arg_seed.hpp_iwyu.txt 10 ./gm/arguments/arg_save_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_save_iterations.hpp_iwyu.txt 10 ./gm/arguments/arg_rwm.hpp_iwyu.txt 10 ./gm/arguments/arg_refresh.hpp_iwyu.txt 10 ./gm/arguments/arg_output_file.hpp_iwyu.txt 10 ./gm/arguments/arg_num_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_num_samples.hpp_iwyu.txt 10 ./gm/arguments/arg_newton.hpp_iwyu.txt 10 ./gm/arguments/arg_max_depth.hpp_iwyu.txt 10 ./gm/arguments/arg_iter.hpp_iwyu.txt 10 ./gm/arguments/arg_int_time.hpp_iwyu.txt 10 ./gm/arguments/arg_init.hpp_iwyu.txt 10 ./gm/arguments/arg_init_alpha.hpp_iwyu.txt 10 ./gm/arguments/arg_id.hpp_iwyu.txt 10 ./gm/arguments/arg_history_size.hpp_iwyu.txt 10 ./gm/arguments/arg_fixed_param.hpp_iwyu.txt 10 ./gm/arguments/arg_fail.hpp_iwyu.txt 10 ./gm/arguments/arg_diagnostic_file.hpp_iwyu.txt 10 ./gm/arguments/arg_diag_e.hpp_iwyu.txt 10 ./gm/arguments/arg_dense_e.hpp_iwyu.txt 10 ./gm/arguments/arg_data_file.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_window.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_term_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_t0.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_kappa.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_init_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_gamma.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_engaged.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_delta.hpp_iwyu.txt 10 ./common/recorder/no_op.hpp_iwyu.txt 10 ./agrad/rev/internal/vvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/v_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/ddv_vari.hpp_iwyu.txt 10 ./agrad/rev/calculate_chain.hpp_iwyu.txt 9 ./math/matrix/Eigen.hpp_iwyu.txt 9 ./agrad/fwd/functions/fma.hpp_iwyu.txt 8 ./memory.hpp_iwyu.txt 8 ./gm.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_plus.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_not.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_plus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_not_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_multiply_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_minus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_divide_equal.hpp_iwyu.txt 8 ./agrad/rev/matrix/stan_print.hpp_iwyu.txt 8 ./agrad/rev/functions/if_else.hpp_iwyu.txt

5 ./math/error_handling/matrix/constraint_tolerance.hpp_iwyu.txt 2 ./version.hpp_iwyu.txt 2 ./mcmc/windowed_adaptation.hpp_iwyu.txt 2 ./mcmc/stepsize_adapter.hpp_iwyu.txt 2 ./mcmc/stepsize_adaptation.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_leapfrog.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_integrator.hpp_iwyu.txt 2 ./mcmc/hmc/hamiltonians/unit_e_point.hpp_iwyu.txt 2 ./mcmc/fixed_param_sampler.hpp_iwyu.txt 2 ./mcmc/base_adapter.hpp_iwyu.txt 2 ./mcmc/base_adaptation.hpp_iwyu.txt 2 ./math/matrix/size.hpp_iwyu.txt 2 ./math/matrix/promote_common.hpp_iwyu.txt 2 ./math/matrix/minus.hpp_iwyu.txt 2 ./math/matrix/array_builder.hpp_iwyu.txt 2 ./math/functions/value_of.hpp_iwyu.txt 2 ./math/functions/sum.hpp_iwyu.txt 2 ./math/functions/sub.hpp_iwyu.txt 2 ./math/functions/step.hpp_iwyu.txt 2 ./math/functions/square.hpp_iwyu.txt 2 ./math/functions/sign.hpp_iwyu.txt 2 ./math/functions/scaled_add.hpp_iwyu.txt 2 ./math/functions/Phi.hpp_iwyu.txt 2 ./math/functions/owens_t.hpp_iwyu.txt 2 ./math/functions/modified_bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/modified_bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/min.hpp_iwyu.txt 2 ./math/functions/max.hpp_iwyu.txt 2 ./math/functions/logical_or.hpp_iwyu.txt 2 ./math/functions/logical_neq.hpp_iwyu.txt 2 ./math/functions/logical_negation.hpp_iwyu.txt 2 ./math/functions/logical_lt.hpp_iwyu.txt 2 ./math/functions/logical_lte.hpp_iwyu.txt 2 ./math/functions/logical_gt.hpp_iwyu.txt 2 ./math/functions/logical_gte.hpp_iwyu.txt 2 ./math/functions/logical_eq.hpp_iwyu.txt 2 ./math/functions/logical_and.hpp_iwyu.txt 2 ./math/functions/log1m.hpp_iwyu.txt 2 ./math/functions/lmgamma.hpp_iwyu.txt 2 ./math/functions/lbeta.hpp_iwyu.txt 2 ./math/functions/is_uninitialized.hpp_iwyu.txt 2 ./math/functions/inv_square.hpp_iwyu.txt 2 ./math/functions/inv.hpp_iwyu.txt 2 ./math/functions/int_step.hpp_iwyu.txt 2 ./math/functions/if_else.hpp_iwyu.txt 2 ./math/functions/fma.hpp_iwyu.txt 2 ./math/functions/fdim.hpp_iwyu.txt 2 ./math/functions/dot_self.hpp_iwyu.txt 2 ./math/functions/dot.hpp_iwyu.txt 2 ./math/functions/dist.hpp_iwyu.txt 2 ./math/functions/bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/as_bool.hpp_iwyu.txt 2 ./math/functions/abs.hpp_iwyu.txt 2 ./io/util.hpp_iwyu.txt 2 ./io/json/json_handler.hpp_iwyu.txt 2 ./gm/error_codes.hpp_iwyu.txt 2 ./gm/compiler.hpp_iwyu.txt 2 ./common/write_stan.hpp_iwyu.txt 2 ./common/write_model.hpp_iwyu.txt 2 ./common/recorder/messages.hpp_iwyu.txt 2 ./common/recorder/csv.hpp_iwyu.txt 2 ./common/do_print.hpp_iwyu.txt 2 ./agrad/rev/error_handling.hpp_iwyu.txt 2 ./agrad.hpp_iwyu.txt 2 ./agrad/fwd/fvar.hpp_iwyu.txt

—

Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51705460.

[syclik]

Thanks. Got it.

Suggestions on actions? Should we just create a pull request with as many changes as we can make?

On Mon, Aug 11, 2014 at 12:53 PM, Daniel Lee bearlee@alum.mit.edu wrote:

Ben, github's issues swallowed the attachment. Can you either forward the attachment directly to me or to stan-dev?

On Sat, Aug 9, 2014 at 11:53 PM, bgoodri notifications@github.com wrote:

Sorry, I forgot to pull before running it. The attached is up to date with develop.

Ben

On Sat, Aug 9, 2014 at 11:06 PM, Ben Goodrich goodrich.ben@gmail.com wrote:

I have never tried to install it on a Mac. Attached is the output from my laptop. However, iwyu still gets confused by Eigen sometimes.

Ben

On Sat, Aug 9, 2014 at 10:39 PM, Daniel Lee notifications@github.com wrote:

Ben, I'm having a little trouble installing. Any suggestions? Or is there some way we can use the output from a working system?

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51704370.

22297 total 452 ./optimization/newton.hpp_iwyu.txt 406 ./mcmc/chains.hpp_iwyu.txt 361 ./agrad/fwd/matrix/to_fvar.hpp_iwyu.txt 265 ./prob/distributions/multivariate/continuous/lkj_corr.hpp_iwyu.txt 208 ./common/command.hpp_iwyu.txt 205 ./math/matrix/containers_conversion.hpp_iwyu.txt 200 ./agrad/rev/matrix/to_var.hpp_iwyu.txt 199 ./agrad/autodiff.hpp_iwyu.txt 193 ./command/print.hpp_iwyu.txt 180 ./math/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 165 ./io/dump.hpp_iwyu.txt 157 ./agrad/rev/matrix/softmax.hpp_iwyu.txt 157 ./agrad/rev/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 156 ./agrad/rev/matrix/tcrossprod.hpp_iwyu.txt 154 ./agrad/rev/matrix/log_softmax.hpp_iwyu.txt 153 ./math/matrix/tcrossprod.hpp_iwyu.txt 151 ./prob/distributions/multivariate/continuous/wishart.hpp_iwyu.txt 134 ./prob/distributions/multivariate/continuous/inv_wishart.hpp_iwyu.txt 133 ./prob/distributions/multivariate/continuous/multi_student_t.hpp_iwyu.txt 132 ./prob/welford_covar_estimator.hpp_iwyu.txt 125 ./gm/ast.hpp_iwyu.txt 123 ./gm/parser.hpp_iwyu.txt 122 ./prob/distributions/univariate/discrete/ordered_logistic.hpp_iwyu.txt 119 ./prob/distributions/multivariate/discrete/categorical.hpp_iwyu.txt 116 ./prob/distributions/multivariate/continuous/multi_normal_cholesky.hpp_iwyu.txt 115 ./math/matrix.hpp_iwyu.txt 114 ./agrad/rev/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 110 ./prob/distributions/multivariate/continuous/multi_normal.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/diag_e_nuts.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/dense_e_nuts.hpp_iwyu.txt 100 ./prob/distributions/multivariate/continuous/dirichlet.hpp_iwyu.txt 100 ./optimization/bfgs.hpp_iwyu.txt 100 ./mcmc/hmc/nuts/unit_e_nuts.hpp_iwyu.txt 98 ./io/mcmc_writer.hpp_iwyu.txt 98 ./agrad/rev/matrix/dot_product.hpp_iwyu.txt 95 ./mcmc/hmc/nuts/base_nuts.hpp_iwyu.txt 95 ./mcmc/hmc/hamiltonians/dense_e_metric.hpp_iwyu.txt 94 ./agrad/rev/matrix/crossprod.hpp_iwyu.txt 93 ./prob/transform.hpp_iwyu.txt 92 ./mcmc/hmc/hamiltonians/diag_e_metric.hpp_iwyu.txt 92 ./agrad/rev/matrix/multiply.hpp_iwyu.txt 90 ./model/util.hpp_iwyu.txt 88 ./mcmc/hmc/hamiltonians/unit_e_metric.hpp_iwyu.txt 87 ./prob/welford_var_estimator.hpp_iwyu.txt 87 ./math/matrix/crossprod.hpp_iwyu.txt 87 ./agrad/rev/functions.hpp_iwyu.txt 86 ./agrad/fwd/functions.hpp_iwyu.txt

85 ./gm/grammars/program_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/term_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/statement_grammar_def.hpp_iwyu.txt 76 ./gm/grammars/functions_grammar_def.hpp_iwyu.txt 75 ./math/functions.hpp_iwyu.txt 74 ./gm/grammars/var_decls_grammar_def.hpp_iwyu.txt 74 ./gm/grammars/bare_type_grammar_def.hpp_iwyu.txt 71 ./agrad/rev/functions/cbrt.hpp_iwyu.txt 65 ./gm/grammars/expression07_grammar_def.hpp_iwyu.txt 65 ./agrad/rev/functions/digamma.hpp_iwyu.txt 63 ./model/model_header.hpp_iwyu.txt 63 ./gm/grammars/expression_grammar_def.hpp_iwyu.txt 62 ./gm/grammars/statement_2_grammar_def.hpp_iwyu.txt 60 ./io/reader.hpp_iwyu.txt 60 ./agrad/rev/functions/ibeta.hpp_iwyu.txt 58 ./prob/distributions/multivariate/continuous/multi_normal_prec.hpp_iwyu.txt 58 ./prob/distributions/multivariate/continuous/gaussian_dlm_obs.hpp_iwyu.txt 57 ./prob/distributions/univariate/continuous/double_exponential.hpp_iwyu.txt 56 ./mcmc.hpp_iwyu.txt 55 ./agrad/rev/internal.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/inv_gamma.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/gamma.hpp_iwyu.txt 54 ./prob/distributions/multivariate/continuous/multi_gp.hpp_iwyu.txt 54 ./agrad/rev/functions/atanh.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/skew_normal.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/gumbel.hpp_iwyu.txt 53 ./prob/distributions/multivariate/continuous/matrix_normal.hpp_iwyu.txt 52 ./prob/distributions/univariate/discrete/neg_binomial.hpp_iwyu.txt 52 ./prob/distributions/univariate/continuous/student_t.hpp_iwyu.txt 52 ./common.hpp_iwyu.txt 52 ./agrad/rev/matrix.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/neg_binomial_2.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/binomial.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/exp_mod_normal.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/beta.hpp_iwyu.txt 51 ./prob/distributions/multivariate/continuous/lkj_cov.hpp_iwyu.txt 50 ./prob/distributions/univariate/continuous/inv_chi_square.hpp_iwyu.txt 50 ./prob/constants.hpp_iwyu.txt 50 ./agrad/rev/matrix/Eigen_NumTraits.hpp_iwyu.txt 50 ./agrad/rev/functions/trunc.hpp_iwyu.txt 50 ./agrad/rev/functions/round.hpp_iwyu.txt 49 ./prob/distributions/univariate/discrete/beta_binomial.hpp_iwyu.txt 49 ./prob/distributions/univariate/continuous/scaled_inv_chi_square.hpp_iwyu.txt 49 ./prob/distributions/multivariate/discrete/multinomial.hpp_iwyu.txt 48 ./prob/distributions/univariate/discrete/hypergeometric.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/von_mises.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/chi_square.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/cauchy.hpp_iwyu.txt 48 ./io/writer.hpp_iwyu.txt 47 ./prob/distributions/univariate/continuous/lognormal.hpp_iwyu.txt 47 ./io/stan_csv_reader.hpp_iwyu.txt 46 ./prob/traits.hpp_iwyu.txt 46 ./prob.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/normal.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/frechet.hpp_iwyu.txt 46 ./math/constants.hpp_iwyu.txt 45 ./prob/distributions/univariate/discrete/poisson.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/rayleigh.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/pareto.hpp_iwyu.txt 45 ./math/functions/digamma.hpp_iwyu.txt 45 ./agrad/rev/matrix/log_sum_exp.hpp_iwyu.txt 44 ./prob/distributions/univariate/discrete/bernoulli.hpp_iwyu.txt 44 ./prob/distributions/univariate/continuous/weibull.hpp_iwyu.txt 44 ./prob/distributions/multivariate/continuous/multi_gp_cholesky.hpp_iwyu.txt 44 ./prob/distributions/multivariate/continuous.hpp_iwyu.txt 44 ./math/matrix_error_handling.hpp_iwyu.txt 44 ./agrad/rev/functions/log_sum_exp.hpp_iwyu.txt 44 ./agrad/fwd/matrix.hpp_iwyu.txt 43 ./prob/distributions/univariate/continuous.hpp_iwyu.txt 43 ./agrad/rev/matrix/sd.hpp_iwyu.txt 42 ./io/json/json_data.hpp_iwyu.txt 42 ./io/json/json_data_handler.hpp_iwyu.txt 42 ./agrad/rev/functions/gamma_q.hpp_iwyu.txt 41 ./prob/distributions/univariate/continuous/exponential.hpp_iwyu.txt 41 ./common/warmup.hpp_iwyu.txt 41 ./common/sample.hpp_iwyu.txt 41 ./agrad/rev/matrix/log_determinant_spd.hpp_iwyu.txt 41 ./agrad/rev/functions/gamma_p.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_second_kind.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_first_kind.hpp_iwyu.txt 41 ./agrad/fwd/functions/trunc.hpp_iwyu.txt 41 ./agrad/fwd/functions/round.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/uniform.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/logistic.hpp_iwyu.txt 40 ./agrad/rev/matrix/variance.hpp_iwyu.txt 40 ./agrad/rev/matrix/mdivide_left_tri.hpp_iwyu.txt 39 ./common/run_markov_chain.hpp_iwyu.txt 39 ./agrad/rev/functions/rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_falling_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/falling_factorial.hpp_iwyu.txt 39 ./agrad/fwd/matrix/log_sum_exp.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_spd.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_ldlt.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left.hpp_iwyu.txt 37 ./prob/distributions/univariate/continuous/johnson.hpp_iwyu.txt 37 ./agrad/rev/functions/asinh.hpp_iwyu.txt 37 ./agrad/rev/functions/acosh.hpp_iwyu.txt 36 ./prob/distributions/multivariate.hpp_iwyu.txt 36 ./prob/autocovariance.hpp_iwyu.txt 36 ./meta/traits.hpp_iwyu.txt 36 ./math/error_handling.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right_tri_low.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right.hpp_iwyu.txt 35 ./prob/distributions.hpp_iwyu.txt 35 ./io.hpp_iwyu.txt 35 ./agrad/rev/functions/log_diff_exp.hpp_iwyu.txt 35 ./agrad/rev/functions/lmgamma.hpp_iwyu.txt 35 ./agrad/rev/functions/lgamma.hpp_iwyu.txt 35 ./agrad/fwd/matrix/mdivide_left_tri_low.hpp_iwyu.txt 35 ./agrad/fwd/matrix/inverse.hpp_iwyu.txt 34 ./math/error_handling/matrix/check_corr_matrix.hpp_iwyu.txt 34 ./agrad/rev/matrix/log_determinant.hpp_iwyu.txt 34 ./agrad/rev/matrix/determinant.hpp_iwyu.txt 34 ./agrad/rev/functions/modified_bessel_first_kind.hpp_iwyu.txt 34 ./agrad/fwd/prob/univariate/continuous/normal.hpp_iwyu.txt 33 ./prob/distributions/multivariate/discrete/categorical_logit.hpp_iwyu.txt 33 ./agrad/rev/operators.hpp_iwyu.txt 33 ./agrad/rev/matrix/trace_gen_quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/dot_self.hpp_iwyu.txt 33 ./agrad/rev/functions/fma.hpp_iwyu.txt 33 ./agrad/fwd/matrix/mdivide_left.hpp_iwyu.txt 32 ./prob/autocorrelation.hpp_iwyu.txt 32 ./io/csv_writer.hpp_iwyu.txt 32 ./agrad/rev/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 32 ./agrad/rev/matrix/squared_distance.hpp_iwyu.txt 32 ./agrad/rev/functions/tgamma.hpp_iwyu.txt 32 ./agrad/rev/functions/multiply_log.hpp_iwyu.txt 32 ./agrad/rev/functions/modified_bessel_second_kind.hpp_iwyu.txt 31 ./mcmc/var_adaptation.hpp_iwyu.txt 31 ./math/matrix/dot_product.hpp_iwyu.txt 31 ./gm/grammars/common_adaptors_def.hpp_iwyu.txt 31 ./agrad/rev/matrix/trace_quad_form.hpp_iwyu.txt 31 ./agrad/rev/matrix/LDLT_factor.hpp_iwyu.txt 31 ./agrad/rev/functions/owens_t.hpp_iwyu.txt 30 ./math/error_handling/dom_err_vec.hpp_iwyu.txt 29 ./prob/distributions/univariate/discrete.hpp_iwyu.txt 29 ./model/prob_grad.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_diag_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_dense_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_diag_e_nuts.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_dense_e_nuts.hpp_iwyu.txt 29 ./mcmc/covar_adaptation.hpp_iwyu.txt 29 ./io/json.hpp_iwyu.txt 29 ./agrad/rev/matrix/sum.hpp_iwyu.txt 29 ./agrad/rev/matrix/grad.hpp_iwyu.txt 29 ./agrad/fwd/matrix/multiply.hpp_iwyu.txt 29 ./agrad/fwd/matrix/dot_product.hpp_iwyu.txt 28 ./model.hpp_iwyu.txt 28 ./mcmc/hmc/hamiltonians/base_hamiltonian.hpp_iwyu.txt 28 ./math/matrix/qr_R.hpp_iwyu.txt 28 ./math/matrix/qr_Q.hpp_iwyu.txt 28 ./math/matrix/assign.hpp_iwyu.txt 28 ./agrad/rev/functions/pow.hpp_iwyu.txt 28 ./agrad/rev/functions/atan2.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_R.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_Q.hpp_iwyu.txt 28 ./agrad/fwd/matrix/log_softmax.hpp_iwyu.txt 28 ./agrad/fwd/matrix/divide.hpp_iwyu.txt 28 ./agrad/fwd/matrix/determinant.hpp_iwyu.txt 27 ./prob/internal_math.hpp_iwyu.txt 27 ./mcmc/hmc/static/adapt_unit_e_static_hmc.hpp_iwyu.txt 27 ./mcmc/hmc/nuts/adapt_unit_e_nuts.hpp_iwyu.txt 27 ./math/matrix/mdivide_right_tri.hpp_iwyu.txt 27 ./math/matrix/log_softmax.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_symmetric.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_simplex.hpp_iwyu.txt 27 ./agrad/rev/matrix/log_determinant_ldlt.hpp_iwyu.txt 27 ./agrad/rev/matrix/LDLT_alloc.hpp_iwyu.txt 27 ./agrad/fwd/matrix/typedefs.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_gen_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/rows_dot_self.hpp_iwyu.txt 27 ./agrad/fwd/matrix/columns_dot_self.hpp_iwyu.txt 26 ./mcmc/hmc/static/unit_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/diag_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/dense_e_static_hmc.hpp_iwyu.txt 26 ./math/matrix/segment.hpp_iwyu.txt 26 ./math/matrix/sd.hpp_iwyu.txt 26 ./math/matrix/quad_form.hpp_iwyu.txt 26 ./math/matrix/quad_form_diag.hpp_iwyu.txt 26 ./math/matrix/mdivide_right_ldlt.hpp_iwyu.txt 26 ./math/matrix/inverse_spd.hpp_iwyu.txt 26 ./math/matrix/distance.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_spsd_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cov_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cholesky_factor_corr.hpp_iwyu.txt 26 ./gm/grammars/functions_grammar.hpp_iwyu.txt 26 ./agrad/rev/matrix/sort.hpp_iwyu.txt 26 ./agrad/rev/functions/fmod.hpp_iwyu.txt 26 ./agrad/fwd/operators.hpp_iwyu.txt 26 ./agrad/fwd/functions/gamma_p.hpp_iwyu.txt 25 ./prob/distributions/univariate.hpp_iwyu.txt 25 ./prob/distributions/multivariate/discrete.hpp_iwyu.txt 25 ./math/matrix/variance.hpp_iwyu.txt 25 ./math/matrix/row.hpp_iwyu.txt 25 ./math/matrix/mdivide_right_tri_low.hpp_iwyu.txt 25 ./math/matrix/mdivide_left_tri_low.hpp_iwyu.txt 25 ./math/matrix/LDLT_factor.hpp_iwyu.txt 25 ./io/json/json_parser.hpp_iwyu.txt 25 ./gm/grammars/program_grammar.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_subtraction.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_division.hpp_iwyu.txt 25 ./agrad/fwd/matrix/softmax.hpp_iwyu.txt 25 ./agrad/fwd/matrix/rows_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/matrix/log_determinant.hpp_iwyu.txt 25 ./agrad/fwd/matrix/columns_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/functions/pow.hpp_iwyu.txt 25 ./agrad/fwd/functions/log_sum_exp.hpp_iwyu.txt 25 ./agrad/fwd/functions/gamma_q.hpp_iwyu.txt 24 ./mcmc/hmc/base_hmc.hpp_iwyu.txt 24 ./math/matrix/softmax.hpp_iwyu.txt 24 ./math/matrix/multiply.hpp_iwyu.txt 24 ./math/matrix/mdivide_right_spd.hpp_iwyu.txt 24 ./math/matrix/mdivide_right.hpp_iwyu.txt 24 ./math/matrix/mdivide_left_tri.hpp_iwyu.txt 24 ./math/matrix/eigenvectors_sym.hpp_iwyu.txt 24 ./math/matrix/eigenvalues_sym.hpp_iwyu.txt 24 ./math/matrix/cholesky_decompose.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_positive_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_lower_triangular.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_cholesky_factor.hpp_iwyu.txt

24 ./gm/grammars/term_grammar.hpp_iwyu.txt 24 ./gm/grammars/statement_grammar.hpp_iwyu.txt 24 ./gm/grammars/expression_grammar.hpp_iwyu.txt 24 ./agrad/rev/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 24 ./agrad/rev/functions/Phi.hpp_iwyu.txt 24 ./agrad/rev/functions/log1m_exp.hpp_iwyu.txt 24 ./agrad/rev/functions/hypot.hpp_iwyu.txt 24 ./agrad/rev/functions/erf.hpp_iwyu.txt 24 ./agrad/rev/functions/erfc.hpp_iwyu.txt 24 ./agrad/rev/functions/binary_log_loss.hpp_iwyu.txt 24 ./agrad/partials_vari.hpp_iwyu.txt 24 ./agrad/fwd/matrix/tcrossprod.hpp_iwyu.txt 24 ./agrad/fwd/matrix/sort.hpp_iwyu.txt 24 ./agrad/fwd/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 24 ./agrad/fwd/matrix/crossprod.hpp_iwyu.txt 24 ./agrad/fwd/functions/owens_t.hpp_iwyu.txt 23 ./math/rep_vector.hpp_iwyu.txt 23 ./math/rep_row_vector.hpp_iwyu.txt 23 ./math/rep_matrix.hpp_iwyu.txt 23 ./math/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 23 ./math/matrix/mean.hpp_iwyu.txt 23 ./math.hpp_iwyu.txt

23 ./gm/grammars/var_decls_grammar.hpp_iwyu.txt 23 ./gm/grammars/expression07_grammar.hpp_iwyu.txt 23 ./common/init_adapt.hpp_iwyu.txt 23 ./command/stanc_helper.hpp_iwyu.txt 23 ./agrad/rev/matrix/typedefs.hpp_iwyu.txt 23 ./agrad/rev/functions/inv_sqrt.hpp_iwyu.txt 23 ./agrad/rev/functions/expm1.hpp_iwyu.txt 23 ./agrad/rev/functions/exp2.hpp_iwyu.txt 23 ./agrad/fwd/matrix/dot_self.hpp_iwyu.txt 23 ./agrad/fwd/functions/log1m_exp.hpp_iwyu.txt 23 ./agrad/fwd/functions/erf.hpp_iwyu.txt 23 ./agrad/fwd/functions/erfc.hpp_iwyu.txt 23 ./agrad/fwd/functions/acosh.hpp_iwyu.txt 22 ./mcmc/hmc/hamiltonians/ps_point.hpp_iwyu.txt 22 ./math/matrix/trace_quad_form.hpp_iwyu.txt 22 ./math/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 22 ./math/matrix/trace_gen_quad_form.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_spd.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_ldlt.hpp_iwyu.txt 22 ./math/matrix/mdivide_left.hpp_iwyu.txt 22 ./math/matrix/append_row.hpp_iwyu.txt 22 ./math/matrix/append_col.hpp_iwyu.txt 22 ./math/functions/ibeta.hpp_iwyu.txt 22 ./math/error_handling/matrix/check_vector.hpp_iwyu.txt 22 ./math/error_handling/check_consistent_sizes.hpp_iwyu.txt 22 ./math/error_handling/check_bounded.hpp_iwyu.txt 22 ./gm/grammars/bare_type_grammar.hpp_iwyu.txt 22 ./gm/generator.hpp_iwyu.txt 22 ./agrad/rev/print_stack.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_multiplication.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_addition.hpp_iwyu.txt 22 ./agrad/rev/matrix/divide.hpp_iwyu.txt 22 ./agrad/rev/internal/matrix_vari.hpp_iwyu.txt 22 ./agrad/rev.hpp_iwyu.txt 22 ./agrad/rev/functions/sinh.hpp_iwyu.txt 22 ./agrad/rev/functions/log1p.hpp_iwyu.txt 22 ./agrad/rev/functions/inv_cloglog.hpp_iwyu.txt 22 ./agrad/rev/functions/fdim.hpp_iwyu.txt 22 ./agrad/rev/functions/cosh.hpp_iwyu.txt 22 ./agrad/rev/functions/atan.hpp_iwyu.txt 22 ./agrad/rev/functions/acos.hpp_iwyu.txt 22 ./agrad/fwd/functions/Phi.hpp_iwyu.txt 22 ./agrad/fwd/functions/log_diff_exp.hpp_iwyu.txt 22 ./agrad/fwd/functions/log2.hpp_iwyu.txt 22 ./agrad/fwd/functions/lmgamma.hpp_iwyu.txt 22 ./agrad/fwd/functions/hypot.hpp_iwyu.txt 22 ./agrad/fwd/functions/exp2.hpp_iwyu.txt 22 ./agrad/fwd/functions/binomial_coefficient_log.hpp_iwyu.txt 22 ./agrad/fwd/functions/asinh.hpp_iwyu.txt

21 ./optimization/lbfgs_update.hpp_iwyu.txt 21 ./mcmc/hmc/static/base_static_hmc.hpp_iwyu.txt 21 ./math/matrix/accumulator.hpp_iwyu.txt 21 ./math/error_handling/dom_err.hpp_iwyu.txt 21 ./math/error_handling/check_positive.hpp_iwyu.txt 21 ./math/error_handling/check_not_nan.hpp_iwyu.txt 21 ./math/error_handling/check_nonnegative.hpp_iwyu.txt 21 ./math/error_handling/check_less_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_less.hpp_iwyu.txt 21 ./math/error_handling/check_greater_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_greater.hpp_iwyu.txt 21 ./math/error_handling/check_finite.hpp_iwyu.txt 21 ./math/error_handling/check_equal.hpp_iwyu.txt 21 ./gm/grammars/statement_2_grammar.hpp_iwyu.txt 21 ./common/init_windowed_adapt.hpp_iwyu.txt 21 ./agrad/rev/var.hpp_iwyu.txt 21 ./agrad/rev/functions/log2.hpp_iwyu.txt 21 ./agrad/rev/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/rev/functions/log10.hpp_iwyu.txt 21 ./agrad/rev/functions/inv_square.hpp_iwyu.txt 21 ./agrad/rev/functions/inv.hpp_iwyu.txt 21 ./agrad/fwd/functions/sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/multiply_log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1m_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log10.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_cloglog.hpp_iwyu.txt 21 ./agrad/fwd/functions/expm1.hpp_iwyu.txt 21 ./agrad/fwd/functions/asin.hpp_iwyu.txt 21 ./agrad/fwd/functions/acos.hpp_iwyu.txt 20 ./math/matrix/squared_distance.hpp_iwyu.txt 20 ./math/matrix/rows_dot_product.hpp_iwyu.txt 20 ./math/matrix/columns_dot_product.hpp_iwyu.txt

20 ./math/functions/lgamma.hpp_iwyu.txt 20 ./math/functions/gamma_q.hpp_iwyu.txt 20 ./math/functions/gamma_p.hpp_iwyu.txt 20 ./gm/arguments/argument_parser.hpp_iwyu.txt 20 ./gm/arguments/arg_adapt.hpp_iwyu.txt 20 ./agrad/rev/vari.hpp_iwyu.txt 20 ./agrad/rev/matrix/initialize_variable.hpp_iwyu.txt 20 ./agrad/rev/functions/tan.hpp_iwyu.txt 20 ./agrad/rev/functions/tanh.hpp_iwyu.txt 20 ./agrad/rev/functions/sqrt.hpp_iwyu.txt 20 ./agrad/rev/functions/sin.hpp_iwyu.txt 20 ./agrad/rev/functions/Phi_approx.hpp_iwyu.txt 20 ./agrad/rev/functions/log.hpp_iwyu.txt 20 ./agrad/rev/functions/log1m.hpp_iwyu.txt 20 ./agrad/rev/functions/inv_logit.hpp_iwyu.txt 20 ./agrad/rev/functions/floor.hpp_iwyu.txt 20 ./agrad/rev/functions/fabs.hpp_iwyu.txt 20 ./agrad/rev/functions/exp.hpp_iwyu.txt 20 ./agrad/rev/functions/cos.hpp_iwyu.txt 20 ./agrad/rev/functions/ceil.hpp_iwyu.txt 20 ./agrad/rev/functions/asin.hpp_iwyu.txt 20 ./agrad/hessian.hpp_iwyu.txt 20 ./agrad/fwd/functions/tan.hpp_iwyu.txt 20 ./agrad/fwd/functions/tanh.hpp_iwyu.txt 20 ./agrad/fwd/functions/sin.hpp_iwyu.txt 20 ./agrad/fwd/functions/sinh.hpp_iwyu.txt 20 ./agrad/fwd/functions/exp.hpp_iwyu.txt 20 ./agrad/fwd/functions/cos.hpp_iwyu.txt 20 ./agrad/fwd/functions/cosh.hpp_iwyu.txt 19 ./math/matrix/dot_self.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_unit_vector.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_semidefinite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_multiplicable.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_matching_sizes.hpp_iwyu.txt 19 ./agrad/rev/var_stack.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_negative.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_increment.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_decrement.hpp_iwyu.txt 19 ./agrad/rev/matrix/value_of.hpp_iwyu.txt 19 ./agrad/rev/internal/precomp_v_vari.hpp_iwyu.txt 19 ./agrad/rev/internal/precomputed_gradients.hpp_iwyu.txt 19 ./agrad/rev/functions/square.hpp_iwyu.txt 19 ./agrad/rev/chainable.hpp_iwyu.txt 19 ./agrad/fwd/matrix/normalize.hpp_iwyu.txt 19 ./agrad/fwd.hpp_iwyu.txt 19 ./agrad/fwd/functions/tgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/logit.hpp_iwyu.txt 19 ./agrad/fwd/functions/lgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmin.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmax.hpp_iwyu.txt 19 ./agrad/fwd/functions/fdim.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan2.hpp_iwyu.txt

18 ./mcmc/hmc/hamiltonians/dense_e_point.hpp_iwyu.txt 18 ./math/matrix/tail.hpp_iwyu.txt 18 ./math/matrix/resize.hpp_iwyu.txt 18 ./math/matrix/log_sum_exp.hpp_iwyu.txt 18 ./math/matrix/head.hpp_iwyu.txt 18 ./math/matrix/get_base1_lhs.hpp_iwyu.txt 18 ./math/error_handling/matrix/check_nonzero_size.hpp_iwyu.txt 18 ./math/error_handling/check_consistent_size.hpp_iwyu.txt

18 ./gm/arguments/singleton_argument.hpp_iwyu.txt 18 ./gm/arguments/list_argument.hpp_iwyu.txt 18 ./gm/arguments/arg_sample.hpp_iwyu.txt 18 ./agrad/rev/matrix/stored_gradient_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vector_vari.hpp_iwyu.txt 18 ./agrad/rev/boost_fpclassify.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_not_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_equal.hpp_iwyu.txt 18 ./agrad/fwd/numeric_limits.hpp_iwyu.txt 18 ./agrad/fwd/functions/rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1p.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1m.hpp_iwyu.txt 18 ./agrad/fwd/functions/lbeta.hpp_iwyu.txt 18 ./agrad/fwd/functions/fmod.hpp_iwyu.txt 18 ./agrad/fwd/functions/floor.hpp_iwyu.txt 18 ./agrad/fwd/functions/falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/digamma.hpp_iwyu.txt 18 ./agrad/fwd/functions/ceil.hpp_iwyu.txt 18 ./agrad/fwd/functions/cbrt.hpp_iwyu.txt 18 ./agrad/fwd/functions/atanh.hpp_iwyu.txt 17 ./mcmc/hmc/integrators/expl_leapfrog.hpp_iwyu.txt 17 ./io/cmd_line.hpp_iwyu.txt 17 ./agrad/rev/numeric_limits.hpp_iwyu.txt 17 ./agrad/rev/functions/is_uninitialized.hpp_iwyu.txt 17 ./agrad/rev/functions/abs.hpp_iwyu.txt 17 ./agrad/fwd/functions/square.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv_square.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv.hpp_iwyu.txt 17 ./agrad/fwd/functions/fabs.hpp_iwyu.txt 17 ./agrad/fwd/functions/binary_log_loss.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/abs.hpp_iwyu.txt

16 ./memory/chunk_alloc.hpp_iwyu.txt 16 ./mcmc/hmc/hamiltonians/diag_e_point.hpp_iwyu.txt 16 ./math/matrix/typedefs.hpp_iwyu.txt 16 ./math/matrix/sub_row.hpp_iwyu.txt 16 ./math/matrix/sub_col.hpp_iwyu.txt 16 ./math/matrix/min.hpp_iwyu.txt 16 ./math/matrix/max.hpp_iwyu.txt 16 ./math/matrix/get_base1.hpp_iwyu.txt 16 ./math/matrix/block.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_row_index.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_column_index.hpp_iwyu.txt 16 ./gm/arguments/arg_hmc.hpp_iwyu.txt 16 ./agrad/rev/functions/value_of.hpp_iwyu.txt 16 ./agrad/rev/functions/step.hpp_iwyu.txt 16 ./agrad/rev/functions/fmin.hpp_iwyu.txt 16 ./agrad/rev/functions/fmax.hpp_iwyu.txt 16 ./agrad/rev/functions/as_bool.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_unary_minus.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_subtraction.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_multiplication.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_division.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_addition.hpp_iwyu.txt 15 ./meta.hpp_iwyu.txt

15 ./memory/stack_alloc.hpp_iwyu.txt 15 ./math/seq_view.hpp_iwyu.txt 15 ./math/matrix/stan_print.hpp_iwyu.txt 15 ./math/matrix/initialize.hpp_iwyu.txt 15 ./math/matrix/col.hpp_iwyu.txt 15 ./math/functions/log_sum_exp.hpp_iwyu.txt 15 ./math/error_handling/matrix/check_ldlt_factor.hpp_iwyu.txt 15 ./gm/arguments/arg_output.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize_algo.hpp_iwyu.txt 15 ./gm/arguments/arg_metric.hpp_iwyu.txt 15 ./gm/arguments/arg_method.hpp_iwyu.txt 15 ./common/do_bfgs_optimize.hpp_iwyu.txt 15 ./agrad/rev/jacobian.hpp_iwyu.txt 15 ./agrad/rev/error_handling/matrix.hpp_iwyu.txt

14 ./optimization/bfgs_linesearch.hpp_iwyu.txt 14 ./mcmc/sample.hpp_iwyu.txt 14 ./math/matrix/singular_values.hpp_iwyu.txt 14 ./math/matrix/rank.hpp_iwyu.txt 14 ./math/matrix/log_determinant_spd.hpp_iwyu.txt 14 ./math/functions/log2.hpp_iwyu.txt 14 ./math/functions/log1m_exp.hpp_iwyu.txt 14 ./math/functions/inverse_softmax.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_std_vector_index.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_square.hpp_iwyu.txt 14 ./gm/arguments/arg_test_gradient.hpp_iwyu.txt 14 ./gm/arguments/arg_sample_algo.hpp_iwyu.txt 14 ./gm/arguments/arg_engine.hpp_iwyu.txt 14 ./gm/arguments/arg_bfgs.hpp_iwyu.txt 14 ./common/recorder/filtered_values.hpp_iwyu.txt 14 ./agrad/agrad_thread_safe.hpp_iwyu.txt 13 ./math/matrix/sum.hpp_iwyu.txt 13 ./math/matrix/sort.hpp_iwyu.txt 13 ./math/matrix/promoter.hpp_iwyu.txt 13 ./math/matrix/prod.hpp_iwyu.txt 13 ./math/matrix/inverse.hpp_iwyu.txt 13 ./math/matrix/fill.hpp_iwyu.txt 13 ./math/matrix/cumulative_sum.hpp_iwyu.txt 13 ./math/functions/log_diff_exp.hpp_iwyu.txt 13 ./math/functions/binomial_coefficient_log.hpp_iwyu.txt 13 ./math/error_handling/matrix/check_matching_dims.hpp_iwyu.txt 13 ./io/var_context.hpp_iwyu.txt 13 ./gm/grammars/whitespace_grammar_def.hpp_iwyu.txt 13 ./gm/arguments/categorical_argument.hpp_iwyu.txt 13 ./gm/arguments/argument.hpp_iwyu.txt 13 ./gm/arguments/arg_tolerance.hpp_iwyu.txt 13 ./gm/arguments/arg_test.hpp_iwyu.txt 13 ./gm/arguments/arg_static.hpp_iwyu.txt 13 ./gm/arguments/arg_random.hpp_iwyu.txt 13 ./gm/arguments/arg_nuts.hpp_iwyu.txt 13 ./gm/arguments/arg_lbfgs.hpp_iwyu.txt 13 ./gm/arguments/arg_diagnose.hpp_iwyu.txt 13 ./gm/arguments/arg_data.hpp_iwyu.txt 13 ./common/recorder/values.hpp_iwyu.txt 13 ./common/recorder.hpp_iwyu.txt 13 ./common/print_progress.hpp_iwyu.txt 13 ./common/init_static_hmc.hpp_iwyu.txt 13 ./common/init_nuts.hpp_iwyu.txt 12 ./optimization/bfgs_update.hpp_iwyu.txt 12 ./mcmc/stepsize_var_adapter.hpp_iwyu.txt 12 ./mcmc/stepsize_covar_adapter.hpp_iwyu.txt 12 ./mcmc/base_mcmc.hpp_iwyu.txt 12 ./math/matrix/trace.hpp_iwyu.txt 12 ./math/matrix/subtract.hpp_iwyu.txt 12 ./math/matrix/rows.hpp_iwyu.txt 12 ./math/matrix/elt_multiply.hpp_iwyu.txt 12 ./math/matrix/elt_divide.hpp_iwyu.txt 12 ./math/matrix/divide.hpp_iwyu.txt 12 ./math/matrix/diag_pre_multiply.hpp_iwyu.txt 12 ./math/matrix/diag_post_multiply.hpp_iwyu.txt 12 ./math/matrix/diagonal.hpp_iwyu.txt 12 ./math/matrix/diag_matrix.hpp_iwyu.txt 12 ./math/matrix/common_type.hpp_iwyu.txt 12 ./math/matrix/cols.hpp_iwyu.txt 12 ./math/matrix/add.hpp_iwyu.txt 12 ./math/functions/trigamma.hpp_iwyu.txt 12 ./math/error_handling/matrix/check_size_match.hpp_iwyu.txt 12 ./gm/grammars/whitespace_grammar.hpp_iwyu.txt 12 ./gm/arguments/valued_argument.hpp_iwyu.txt 12 ./gm/arguments/unvalued_argument.hpp_iwyu.txt 12 ./common/recorder/sum_values.hpp_iwyu.txt 12 ./agrad/fwd/matrix/sum.hpp_iwyu.txt 11 ./math/rep_array.hpp_iwyu.txt

11 ./math/matrix/sort_indices.hpp_iwyu.txt 11 ./math/matrix/log_determinant.hpp_iwyu.txt 11 ./math/matrix/dims.hpp_iwyu.txt 11 ./math/matrix/determinant.hpp_iwyu.txt 11 ./math/functions/Phi_approx.hpp_iwyu.txt 11 ./math/functions/log1p.hpp_iwyu.txt 11 ./math/functions/log1p_exp.hpp_iwyu.txt 11 ./math/error_handling/matrix/validate_non_negative_index.hpp_iwyu.txt 11 ./math/error_handling/matrix/check_range.hpp_iwyu.txt 11 ./math/error_handling/check_positive_finite.hpp_iwyu.txt

11 ./gm/grammars/iterator_typedefs.hpp_iwyu.txt 11 ./gm/arguments/argument_probe.hpp_iwyu.txt 11 ./common/write_iteration.hpp_iwyu.txt 11 ./common/write_iteration_csv.hpp_iwyu.txt 11 ./common/write_error_msg.hpp_iwyu.txt 10 ./math/matrix/transpose.hpp_iwyu.txt 10 ./math/matrix/rows_dot_self.hpp_iwyu.txt 10 ./math/matrix/log.hpp_iwyu.txt 10 ./math/matrix/log_determinant_ldlt.hpp_iwyu.txt 10 ./math/matrix/exp.hpp_iwyu.txt 10 ./math/matrix/columns_dot_self.hpp_iwyu.txt 10 ./math/functions/rising_factorial.hpp_iwyu.txt 10 ./math/functions/multiply_log.hpp_iwyu.txt 10 ./math/functions/modulus.hpp_iwyu.txt

10 ./math/functions/log_rising_factorial.hpp_iwyu.txt 10 ./math/functions/logit.hpp_iwyu.txt 10 ./math/functions/log_inv_logit.hpp_iwyu.txt 10 ./math/functions/log_falling_factorial.hpp_iwyu.txt 10 ./math/functions/log1m_inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_sqrt.hpp_iwyu.txt 10 ./math/functions/inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_cloglog.hpp_iwyu.txt 10 ./math/functions/falling_factorial.hpp_iwyu.txt 10 ./math/functions/exp2.hpp_iwyu.txt 10 ./math/functions/divide.hpp_iwyu.txt

10 ./math/functions/binary_log_loss.hpp_iwyu.txt 10 ./io/json/json_error.hpp_iwyu.txt 10 ./gm/arguments/arg_unit_e.hpp_iwyu.txt 10 ./gm/arguments/arg_thin.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_err.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_eps.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize_jitter.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize.hpp_iwyu.txt 10 ./gm/arguments/arg_seed.hpp_iwyu.txt 10 ./gm/arguments/arg_save_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_save_iterations.hpp_iwyu.txt 10 ./gm/arguments/arg_rwm.hpp_iwyu.txt 10 ./gm/arguments/arg_refresh.hpp_iwyu.txt 10 ./gm/arguments/arg_output_file.hpp_iwyu.txt 10 ./gm/arguments/arg_num_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_num_samples.hpp_iwyu.txt 10 ./gm/arguments/arg_newton.hpp_iwyu.txt 10 ./gm/arguments/arg_max_depth.hpp_iwyu.txt 10 ./gm/arguments/arg_iter.hpp_iwyu.txt 10 ./gm/arguments/arg_int_time.hpp_iwyu.txt 10 ./gm/arguments/arg_init.hpp_iwyu.txt 10 ./gm/arguments/arg_init_alpha.hpp_iwyu.txt 10 ./gm/arguments/arg_id.hpp_iwyu.txt 10 ./gm/arguments/arg_history_size.hpp_iwyu.txt 10 ./gm/arguments/arg_fixed_param.hpp_iwyu.txt 10 ./gm/arguments/arg_fail.hpp_iwyu.txt 10 ./gm/arguments/arg_diagnostic_file.hpp_iwyu.txt 10 ./gm/arguments/arg_diag_e.hpp_iwyu.txt 10 ./gm/arguments/arg_dense_e.hpp_iwyu.txt 10 ./gm/arguments/arg_data_file.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_window.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_term_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_t0.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_kappa.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_init_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_gamma.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_engaged.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_delta.hpp_iwyu.txt 10 ./common/recorder/no_op.hpp_iwyu.txt 10 ./agrad/rev/internal/vvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/v_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/ddv_vari.hpp_iwyu.txt 10 ./agrad/rev/calculate_chain.hpp_iwyu.txt 9 ./math/matrix/Eigen.hpp_iwyu.txt 9 ./agrad/fwd/functions/fma.hpp_iwyu.txt 8 ./memory.hpp_iwyu.txt 8 ./gm.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_plus.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_not.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_plus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_not_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_multiply_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_minus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_divide_equal.hpp_iwyu.txt 8 ./agrad/rev/matrix/stan_print.hpp_iwyu.txt 8 ./agrad/rev/functions/if_else.hpp_iwyu.txt

5 ./math/error_handling/matrix/constraint_tolerance.hpp_iwyu.txt 2 ./version.hpp_iwyu.txt 2 ./mcmc/windowed_adaptation.hpp_iwyu.txt 2 ./mcmc/stepsize_adapter.hpp_iwyu.txt 2 ./mcmc/stepsize_adaptation.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_leapfrog.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_integrator.hpp_iwyu.txt 2 ./mcmc/hmc/hamiltonians/unit_e_point.hpp_iwyu.txt 2 ./mcmc/fixed_param_sampler.hpp_iwyu.txt 2 ./mcmc/base_adapter.hpp_iwyu.txt 2 ./mcmc/base_adaptation.hpp_iwyu.txt 2 ./math/matrix/size.hpp_iwyu.txt 2 ./math/matrix/promote_common.hpp_iwyu.txt 2 ./math/matrix/minus.hpp_iwyu.txt 2 ./math/matrix/array_builder.hpp_iwyu.txt 2 ./math/functions/value_of.hpp_iwyu.txt 2 ./math/functions/sum.hpp_iwyu.txt 2 ./math/functions/sub.hpp_iwyu.txt 2 ./math/functions/step.hpp_iwyu.txt 2 ./math/functions/square.hpp_iwyu.txt 2 ./math/functions/sign.hpp_iwyu.txt 2 ./math/functions/scaled_add.hpp_iwyu.txt 2 ./math/functions/Phi.hpp_iwyu.txt 2 ./math/functions/owens_t.hpp_iwyu.txt 2 ./math/functions/modified_bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/modified_bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/min.hpp_iwyu.txt 2 ./math/functions/max.hpp_iwyu.txt 2 ./math/functions/logical_or.hpp_iwyu.txt 2 ./math/functions/logical_neq.hpp_iwyu.txt 2 ./math/functions/logical_negation.hpp_iwyu.txt 2 ./math/functions/logical_lt.hpp_iwyu.txt 2 ./math/functions/logical_lte.hpp_iwyu.txt 2 ./math/functions/logical_gt.hpp_iwyu.txt 2 ./math/functions/logical_gte.hpp_iwyu.txt 2 ./math/functions/logical_eq.hpp_iwyu.txt 2 ./math/functions/logical_and.hpp_iwyu.txt 2 ./math/functions/log1m.hpp_iwyu.txt 2 ./math/functions/lmgamma.hpp_iwyu.txt 2 ./math/functions/lbeta.hpp_iwyu.txt 2 ./math/functions/is_uninitialized.hpp_iwyu.txt 2 ./math/functions/inv_square.hpp_iwyu.txt 2 ./math/functions/inv.hpp_iwyu.txt 2 ./math/functions/int_step.hpp_iwyu.txt 2 ./math/functions/if_else.hpp_iwyu.txt 2 ./math/functions/fma.hpp_iwyu.txt 2 ./math/functions/fdim.hpp_iwyu.txt 2 ./math/functions/dot_self.hpp_iwyu.txt 2 ./math/functions/dot.hpp_iwyu.txt 2 ./math/functions/dist.hpp_iwyu.txt 2 ./math/functions/bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/as_bool.hpp_iwyu.txt 2 ./math/functions/abs.hpp_iwyu.txt 2 ./io/util.hpp_iwyu.txt 2 ./io/json/json_handler.hpp_iwyu.txt 2 ./gm/error_codes.hpp_iwyu.txt 2 ./gm/compiler.hpp_iwyu.txt 2 ./common/write_stan.hpp_iwyu.txt 2 ./common/write_model.hpp_iwyu.txt 2 ./common/recorder/messages.hpp_iwyu.txt 2 ./common/recorder/csv.hpp_iwyu.txt 2 ./common/do_print.hpp_iwyu.txt 2 ./agrad/rev/error_handling.hpp_iwyu.txt 2 ./agrad.hpp_iwyu.txt 2 ./agrad/fwd/fvar.hpp_iwyu.txt

—

Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51705460.

[bgoodri]

There is an option to apply iwyu's recommendations automatically, instead of just writing the recommendations to a text file. I could push a branch with the recommendations implemented and then we could manually go through it, fix the build errors, and then potentially merge it.

On Mon, Aug 11, 2014 at 12:58 PM, Daniel Lee notifications@github.com wrote:

Thanks. Got it.

Suggestions on actions? Should we just create a pull request with as many changes as we can make?

On Mon, Aug 11, 2014 at 12:53 PM, Daniel Lee bearlee@alum.mit.edu wrote:

Ben, github's issues swallowed the attachment. Can you either forward the attachment directly to me or to stan-dev?

On Sat, Aug 9, 2014 at 11:53 PM, bgoodri notifications@github.com wrote:

Sorry, I forgot to pull before running it. The attached is up to date with develop.

Ben

On Sat, Aug 9, 2014 at 11:06 PM, Ben Goodrich goodrich.ben@gmail.com wrote:

I have never tried to install it on a Mac. Attached is the output from my laptop. However, iwyu still gets confused by Eigen sometimes.

Ben

On Sat, Aug 9, 2014 at 10:39 PM, Daniel Lee notifications@github.com

wrote:

Ben, I'm having a little trouble installing. Any suggestions? Or is there some way we can use the output from a working system?

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51704370.

22297 total 452 ./optimization/newton.hpp_iwyu.txt 406 ./mcmc/chains.hpp_iwyu.txt 361 ./agrad/fwd/matrix/to_fvar.hpp_iwyu.txt 265 ./prob/distributions/multivariate/continuous/lkj_corr.hpp_iwyu.txt 208 ./common/command.hpp_iwyu.txt 205 ./math/matrix/containers_conversion.hpp_iwyu.txt 200 ./agrad/rev/matrix/to_var.hpp_iwyu.txt 199 ./agrad/autodiff.hpp_iwyu.txt 193 ./command/print.hpp_iwyu.txt 180 ./math/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 165 ./io/dump.hpp_iwyu.txt 157 ./agrad/rev/matrix/softmax.hpp_iwyu.txt 157 ./agrad/rev/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 156 ./agrad/rev/matrix/tcrossprod.hpp_iwyu.txt 154 ./agrad/rev/matrix/log_softmax.hpp_iwyu.txt 153 ./math/matrix/tcrossprod.hpp_iwyu.txt 151 ./prob/distributions/multivariate/continuous/wishart.hpp_iwyu.txt 134 ./prob/distributions/multivariate/continuous/inv_wishart.hpp_iwyu.txt 133

./prob/distributions/multivariate/continuous/multi_student_t.hpp_iwyu.txt 132 ./prob/welford_covar_estimator.hpp_iwyu.txt 125 ./gm/ast.hpp_iwyu.txt 123 ./gm/parser.hpp_iwyu.txt 122 ./prob/distributions/univariate/discrete/ordered_logistic.hpp_iwyu.txt 119 ./prob/distributions/multivariate/discrete/categorical.hpp_iwyu.txt 116

./prob/distributions/multivariate/continuous/multi_normal_cholesky.hpp_iwyu.txt

115 ./math/matrix.hpp_iwyu.txt 114 ./agrad/rev/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 110 ./prob/distributions/multivariate/continuous/multi_normal.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/diag_e_nuts.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/dense_e_nuts.hpp_iwyu.txt 100 ./prob/distributions/multivariate/continuous/dirichlet.hpp_iwyu.txt 100 ./optimization/bfgs.hpp_iwyu.txt 100 ./mcmc/hmc/nuts/unit_e_nuts.hpp_iwyu.txt 98 ./io/mcmc_writer.hpp_iwyu.txt 98 ./agrad/rev/matrix/dot_product.hpp_iwyu.txt 95 ./mcmc/hmc/nuts/base_nuts.hpp_iwyu.txt 95 ./mcmc/hmc/hamiltonians/dense_e_metric.hpp_iwyu.txt 94 ./agrad/rev/matrix/crossprod.hpp_iwyu.txt 93 ./prob/transform.hpp_iwyu.txt 92 ./mcmc/hmc/hamiltonians/diag_e_metric.hpp_iwyu.txt 92 ./agrad/rev/matrix/multiply.hpp_iwyu.txt 90 ./model/util.hpp_iwyu.txt 88 ./mcmc/hmc/hamiltonians/unit_e_metric.hpp_iwyu.txt 87 ./prob/welford_var_estimator.hpp_iwyu.txt 87 ./math/matrix/crossprod.hpp_iwyu.txt 87 ./agrad/rev/functions.hpp_iwyu.txt 86 ./agrad/fwd/functions.hpp_iwyu.txt

85 ./gm/grammars/program_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/term_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/statement_grammar_def.hpp_iwyu.txt 76 ./gm/grammars/functions_grammar_def.hpp_iwyu.txt 75 ./math/functions.hpp_iwyu.txt 74 ./gm/grammars/var_decls_grammar_def.hpp_iwyu.txt 74 ./gm/grammars/bare_type_grammar_def.hpp_iwyu.txt 71 ./agrad/rev/functions/cbrt.hpp_iwyu.txt 65 ./gm/grammars/expression07_grammar_def.hpp_iwyu.txt 65 ./agrad/rev/functions/digamma.hpp_iwyu.txt 63 ./model/model_header.hpp_iwyu.txt 63 ./gm/grammars/expression_grammar_def.hpp_iwyu.txt 62 ./gm/grammars/statement_2_grammar_def.hpp_iwyu.txt 60 ./io/reader.hpp_iwyu.txt 60 ./agrad/rev/functions/ibeta.hpp_iwyu.txt 58

./prob/distributions/multivariate/continuous/multi_normal_prec.hpp_iwyu.txt 58

./prob/distributions/multivariate/continuous/gaussian_dlm_obs.hpp_iwyu.txt 57

./prob/distributions/univariate/continuous/double_exponential.hpp_iwyu.txt 56 ./mcmc.hpp_iwyu.txt 55 ./agrad/rev/internal.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/inv_gamma.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/gamma.hpp_iwyu.txt 54 ./prob/distributions/multivariate/continuous/multi_gp.hpp_iwyu.txt 54 ./agrad/rev/functions/atanh.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/skew_normal.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/gumbel.hpp_iwyu.txt 53 ./prob/distributions/multivariate/continuous/matrix_normal.hpp_iwyu.txt 52 ./prob/distributions/univariate/discrete/neg_binomial.hpp_iwyu.txt 52 ./prob/distributions/univariate/continuous/student_t.hpp_iwyu.txt 52 ./common.hpp_iwyu.txt 52 ./agrad/rev/matrix.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/neg_binomial_2.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/binomial.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/exp_mod_normal.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/beta.hpp_iwyu.txt 51 ./prob/distributions/multivariate/continuous/lkj_cov.hpp_iwyu.txt 50 ./prob/distributions/univariate/continuous/inv_chi_square.hpp_iwyu.txt 50 ./prob/constants.hpp_iwyu.txt 50 ./agrad/rev/matrix/Eigen_NumTraits.hpp_iwyu.txt 50 ./agrad/rev/functions/trunc.hpp_iwyu.txt 50 ./agrad/rev/functions/round.hpp_iwyu.txt 49 ./prob/distributions/univariate/discrete/beta_binomial.hpp_iwyu.txt 49

./prob/distributions/univariate/continuous/scaled_inv_chi_square.hpp_iwyu.txt

49 ./prob/distributions/multivariate/discrete/multinomial.hpp_iwyu.txt 48 ./prob/distributions/univariate/discrete/hypergeometric.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/von_mises.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/chi_square.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/cauchy.hpp_iwyu.txt 48 ./io/writer.hpp_iwyu.txt 47 ./prob/distributions/univariate/continuous/lognormal.hpp_iwyu.txt 47 ./io/stan_csv_reader.hpp_iwyu.txt 46 ./prob/traits.hpp_iwyu.txt 46 ./prob.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/normal.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/frechet.hpp_iwyu.txt 46 ./math/constants.hpp_iwyu.txt 45 ./prob/distributions/univariate/discrete/poisson.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/rayleigh.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/pareto.hpp_iwyu.txt 45 ./math/functions/digamma.hpp_iwyu.txt 45 ./agrad/rev/matrix/log_sum_exp.hpp_iwyu.txt 44 ./prob/distributions/univariate/discrete/bernoulli.hpp_iwyu.txt 44 ./prob/distributions/univariate/continuous/weibull.hpp_iwyu.txt 44

./prob/distributions/multivariate/continuous/multi_gp_cholesky.hpp_iwyu.txt 44 ./prob/distributions/multivariate/continuous.hpp_iwyu.txt 44 ./math/matrix_error_handling.hpp_iwyu.txt 44 ./agrad/rev/functions/log_sum_exp.hpp_iwyu.txt 44 ./agrad/fwd/matrix.hpp_iwyu.txt 43 ./prob/distributions/univariate/continuous.hpp_iwyu.txt 43 ./agrad/rev/matrix/sd.hpp_iwyu.txt 42 ./io/json/json_data.hpp_iwyu.txt 42 ./io/json/json_data_handler.hpp_iwyu.txt 42 ./agrad/rev/functions/gamma_q.hpp_iwyu.txt 41 ./prob/distributions/univariate/continuous/exponential.hpp_iwyu.txt 41 ./common/warmup.hpp_iwyu.txt 41 ./common/sample.hpp_iwyu.txt 41 ./agrad/rev/matrix/log_determinant_spd.hpp_iwyu.txt 41 ./agrad/rev/functions/gamma_p.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_second_kind.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_first_kind.hpp_iwyu.txt 41 ./agrad/fwd/functions/trunc.hpp_iwyu.txt 41 ./agrad/fwd/functions/round.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/uniform.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/logistic.hpp_iwyu.txt 40 ./agrad/rev/matrix/variance.hpp_iwyu.txt 40 ./agrad/rev/matrix/mdivide_left_tri.hpp_iwyu.txt 39 ./common/run_markov_chain.hpp_iwyu.txt 39 ./agrad/rev/functions/rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_falling_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/falling_factorial.hpp_iwyu.txt 39 ./agrad/fwd/matrix/log_sum_exp.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_spd.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_ldlt.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left.hpp_iwyu.txt 37 ./prob/distributions/univariate/continuous/johnson.hpp_iwyu.txt 37 ./agrad/rev/functions/asinh.hpp_iwyu.txt 37 ./agrad/rev/functions/acosh.hpp_iwyu.txt 36 ./prob/distributions/multivariate.hpp_iwyu.txt 36 ./prob/autocovariance.hpp_iwyu.txt 36 ./meta/traits.hpp_iwyu.txt 36 ./math/error_handling.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right_tri_low.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right.hpp_iwyu.txt 35 ./prob/distributions.hpp_iwyu.txt 35 ./io.hpp_iwyu.txt 35 ./agrad/rev/functions/log_diff_exp.hpp_iwyu.txt 35 ./agrad/rev/functions/lmgamma.hpp_iwyu.txt 35 ./agrad/rev/functions/lgamma.hpp_iwyu.txt 35 ./agrad/fwd/matrix/mdivide_left_tri_low.hpp_iwyu.txt 35 ./agrad/fwd/matrix/inverse.hpp_iwyu.txt 34 ./math/error_handling/matrix/check_corr_matrix.hpp_iwyu.txt 34 ./agrad/rev/matrix/log_determinant.hpp_iwyu.txt 34 ./agrad/rev/matrix/determinant.hpp_iwyu.txt 34 ./agrad/rev/functions/modified_bessel_first_kind.hpp_iwyu.txt 34 ./agrad/fwd/prob/univariate/continuous/normal.hpp_iwyu.txt 33

./prob/distributions/multivariate/discrete/categorical_logit.hpp_iwyu.txt 33 ./agrad/rev/operators.hpp_iwyu.txt 33 ./agrad/rev/matrix/trace_gen_quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/dot_self.hpp_iwyu.txt 33 ./agrad/rev/functions/fma.hpp_iwyu.txt 33 ./agrad/fwd/matrix/mdivide_left.hpp_iwyu.txt 32 ./prob/autocorrelation.hpp_iwyu.txt 32 ./io/csv_writer.hpp_iwyu.txt 32 ./agrad/rev/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 32 ./agrad/rev/matrix/squared_distance.hpp_iwyu.txt 32 ./agrad/rev/functions/tgamma.hpp_iwyu.txt 32 ./agrad/rev/functions/multiply_log.hpp_iwyu.txt 32 ./agrad/rev/functions/modified_bessel_second_kind.hpp_iwyu.txt 31 ./mcmc/var_adaptation.hpp_iwyu.txt 31 ./math/matrix/dot_product.hpp_iwyu.txt 31 ./gm/grammars/common_adaptors_def.hpp_iwyu.txt 31 ./agrad/rev/matrix/trace_quad_form.hpp_iwyu.txt 31 ./agrad/rev/matrix/LDLT_factor.hpp_iwyu.txt 31 ./agrad/rev/functions/owens_t.hpp_iwyu.txt 30 ./math/error_handling/dom_err_vec.hpp_iwyu.txt 29 ./prob/distributions/univariate/discrete.hpp_iwyu.txt 29 ./model/prob_grad.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_diag_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_dense_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_diag_e_nuts.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_dense_e_nuts.hpp_iwyu.txt 29 ./mcmc/covar_adaptation.hpp_iwyu.txt 29 ./io/json.hpp_iwyu.txt 29 ./agrad/rev/matrix/sum.hpp_iwyu.txt 29 ./agrad/rev/matrix/grad.hpp_iwyu.txt 29 ./agrad/fwd/matrix/multiply.hpp_iwyu.txt 29 ./agrad/fwd/matrix/dot_product.hpp_iwyu.txt 28 ./model.hpp_iwyu.txt 28 ./mcmc/hmc/hamiltonians/base_hamiltonian.hpp_iwyu.txt 28 ./math/matrix/qr_R.hpp_iwyu.txt 28 ./math/matrix/qr_Q.hpp_iwyu.txt 28 ./math/matrix/assign.hpp_iwyu.txt 28 ./agrad/rev/functions/pow.hpp_iwyu.txt 28 ./agrad/rev/functions/atan2.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_R.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_Q.hpp_iwyu.txt 28 ./agrad/fwd/matrix/log_softmax.hpp_iwyu.txt 28 ./agrad/fwd/matrix/divide.hpp_iwyu.txt 28 ./agrad/fwd/matrix/determinant.hpp_iwyu.txt 27 ./prob/internal_math.hpp_iwyu.txt 27 ./mcmc/hmc/static/adapt_unit_e_static_hmc.hpp_iwyu.txt 27 ./mcmc/hmc/nuts/adapt_unit_e_nuts.hpp_iwyu.txt 27 ./math/matrix/mdivide_right_tri.hpp_iwyu.txt 27 ./math/matrix/log_softmax.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_symmetric.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_simplex.hpp_iwyu.txt 27 ./agrad/rev/matrix/log_determinant_ldlt.hpp_iwyu.txt 27 ./agrad/rev/matrix/LDLT_alloc.hpp_iwyu.txt 27 ./agrad/fwd/matrix/typedefs.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_gen_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/rows_dot_self.hpp_iwyu.txt 27 ./agrad/fwd/matrix/columns_dot_self.hpp_iwyu.txt 26 ./mcmc/hmc/static/unit_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/diag_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/dense_e_static_hmc.hpp_iwyu.txt 26 ./math/matrix/segment.hpp_iwyu.txt 26 ./math/matrix/sd.hpp_iwyu.txt 26 ./math/matrix/quad_form.hpp_iwyu.txt 26 ./math/matrix/quad_form_diag.hpp_iwyu.txt 26 ./math/matrix/mdivide_right_ldlt.hpp_iwyu.txt 26 ./math/matrix/inverse_spd.hpp_iwyu.txt 26 ./math/matrix/distance.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_spsd_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cov_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cholesky_factor_corr.hpp_iwyu.txt 26 ./gm/grammars/functions_grammar.hpp_iwyu.txt 26 ./agrad/rev/matrix/sort.hpp_iwyu.txt 26 ./agrad/rev/functions/fmod.hpp_iwyu.txt 26 ./agrad/fwd/operators.hpp_iwyu.txt 26 ./agrad/fwd/functions/gamma_p.hpp_iwyu.txt 25 ./prob/distributions/univariate.hpp_iwyu.txt 25 ./prob/distributions/multivariate/discrete.hpp_iwyu.txt 25 ./math/matrix/variance.hpp_iwyu.txt 25 ./math/matrix/row.hpp_iwyu.txt 25 ./math/matrix/mdivide_right_tri_low.hpp_iwyu.txt 25 ./math/matrix/mdivide_left_tri_low.hpp_iwyu.txt 25 ./math/matrix/LDLT_factor.hpp_iwyu.txt 25 ./io/json/json_parser.hpp_iwyu.txt 25 ./gm/grammars/program_grammar.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_subtraction.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_division.hpp_iwyu.txt 25 ./agrad/fwd/matrix/softmax.hpp_iwyu.txt 25 ./agrad/fwd/matrix/rows_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/matrix/log_determinant.hpp_iwyu.txt 25 ./agrad/fwd/matrix/columns_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/functions/pow.hpp_iwyu.txt 25 ./agrad/fwd/functions/log_sum_exp.hpp_iwyu.txt 25 ./agrad/fwd/functions/gamma_q.hpp_iwyu.txt 24 ./mcmc/hmc/base_hmc.hpp_iwyu.txt 24 ./math/matrix/softmax.hpp_iwyu.txt 24 ./math/matrix/multiply.hpp_iwyu.txt 24 ./math/matrix/mdivide_right_spd.hpp_iwyu.txt 24 ./math/matrix/mdivide_right.hpp_iwyu.txt 24 ./math/matrix/mdivide_left_tri.hpp_iwyu.txt 24 ./math/matrix/eigenvectors_sym.hpp_iwyu.txt 24 ./math/matrix/eigenvalues_sym.hpp_iwyu.txt 24 ./math/matrix/cholesky_decompose.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_positive_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_lower_triangular.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_cholesky_factor.hpp_iwyu.txt

24 ./gm/grammars/term_grammar.hpp_iwyu.txt 24 ./gm/grammars/statement_grammar.hpp_iwyu.txt 24 ./gm/grammars/expression_grammar.hpp_iwyu.txt 24 ./agrad/rev/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 24 ./agrad/rev/functions/Phi.hpp_iwyu.txt 24 ./agrad/rev/functions/log1m_exp.hpp_iwyu.txt 24 ./agrad/rev/functions/hypot.hpp_iwyu.txt 24 ./agrad/rev/functions/erf.hpp_iwyu.txt 24 ./agrad/rev/functions/erfc.hpp_iwyu.txt 24 ./agrad/rev/functions/binary_log_loss.hpp_iwyu.txt 24 ./agrad/partials_vari.hpp_iwyu.txt 24 ./agrad/fwd/matrix/tcrossprod.hpp_iwyu.txt 24 ./agrad/fwd/matrix/sort.hpp_iwyu.txt 24 ./agrad/fwd/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 24 ./agrad/fwd/matrix/crossprod.hpp_iwyu.txt 24 ./agrad/fwd/functions/owens_t.hpp_iwyu.txt 23 ./math/rep_vector.hpp_iwyu.txt 23 ./math/rep_row_vector.hpp_iwyu.txt 23 ./math/rep_matrix.hpp_iwyu.txt 23 ./math/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 23 ./math/matrix/mean.hpp_iwyu.txt 23 ./math.hpp_iwyu.txt

23 ./gm/grammars/var_decls_grammar.hpp_iwyu.txt 23 ./gm/grammars/expression07_grammar.hpp_iwyu.txt 23 ./common/init_adapt.hpp_iwyu.txt 23 ./command/stanc_helper.hpp_iwyu.txt 23 ./agrad/rev/matrix/typedefs.hpp_iwyu.txt 23 ./agrad/rev/functions/inv_sqrt.hpp_iwyu.txt 23 ./agrad/rev/functions/expm1.hpp_iwyu.txt 23 ./agrad/rev/functions/exp2.hpp_iwyu.txt 23 ./agrad/fwd/matrix/dot_self.hpp_iwyu.txt 23 ./agrad/fwd/functions/log1m_exp.hpp_iwyu.txt 23 ./agrad/fwd/functions/erf.hpp_iwyu.txt 23 ./agrad/fwd/functions/erfc.hpp_iwyu.txt 23 ./agrad/fwd/functions/acosh.hpp_iwyu.txt 22 ./mcmc/hmc/hamiltonians/ps_point.hpp_iwyu.txt 22 ./math/matrix/trace_quad_form.hpp_iwyu.txt 22 ./math/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 22 ./math/matrix/trace_gen_quad_form.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_spd.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_ldlt.hpp_iwyu.txt 22 ./math/matrix/mdivide_left.hpp_iwyu.txt 22 ./math/matrix/append_row.hpp_iwyu.txt 22 ./math/matrix/append_col.hpp_iwyu.txt 22 ./math/functions/ibeta.hpp_iwyu.txt 22 ./math/error_handling/matrix/check_vector.hpp_iwyu.txt 22 ./math/error_handling/check_consistent_sizes.hpp_iwyu.txt 22 ./math/error_handling/check_bounded.hpp_iwyu.txt 22 ./gm/grammars/bare_type_grammar.hpp_iwyu.txt 22 ./gm/generator.hpp_iwyu.txt 22 ./agrad/rev/print_stack.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_multiplication.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_addition.hpp_iwyu.txt 22 ./agrad/rev/matrix/divide.hpp_iwyu.txt 22 ./agrad/rev/internal/matrix_vari.hpp_iwyu.txt 22 ./agrad/rev.hpp_iwyu.txt 22 ./agrad/rev/functions/sinh.hpp_iwyu.txt 22 ./agrad/rev/functions/log1p.hpp_iwyu.txt 22 ./agrad/rev/functions/inv_cloglog.hpp_iwyu.txt 22 ./agrad/rev/functions/fdim.hpp_iwyu.txt 22 ./agrad/rev/functions/cosh.hpp_iwyu.txt 22 ./agrad/rev/functions/atan.hpp_iwyu.txt 22 ./agrad/rev/functions/acos.hpp_iwyu.txt 22 ./agrad/fwd/functions/Phi.hpp_iwyu.txt 22 ./agrad/fwd/functions/log_diff_exp.hpp_iwyu.txt 22 ./agrad/fwd/functions/log2.hpp_iwyu.txt 22 ./agrad/fwd/functions/lmgamma.hpp_iwyu.txt 22 ./agrad/fwd/functions/hypot.hpp_iwyu.txt 22 ./agrad/fwd/functions/exp2.hpp_iwyu.txt 22 ./agrad/fwd/functions/binomial_coefficient_log.hpp_iwyu.txt 22 ./agrad/fwd/functions/asinh.hpp_iwyu.txt

21 ./optimization/lbfgs_update.hpp_iwyu.txt 21 ./mcmc/hmc/static/base_static_hmc.hpp_iwyu.txt 21 ./math/matrix/accumulator.hpp_iwyu.txt 21 ./math/error_handling/dom_err.hpp_iwyu.txt 21 ./math/error_handling/check_positive.hpp_iwyu.txt 21 ./math/error_handling/check_not_nan.hpp_iwyu.txt 21 ./math/error_handling/check_nonnegative.hpp_iwyu.txt 21 ./math/error_handling/check_less_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_less.hpp_iwyu.txt 21 ./math/error_handling/check_greater_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_greater.hpp_iwyu.txt 21 ./math/error_handling/check_finite.hpp_iwyu.txt 21 ./math/error_handling/check_equal.hpp_iwyu.txt 21 ./gm/grammars/statement_2_grammar.hpp_iwyu.txt 21 ./common/init_windowed_adapt.hpp_iwyu.txt 21 ./agrad/rev/var.hpp_iwyu.txt 21 ./agrad/rev/functions/log2.hpp_iwyu.txt 21 ./agrad/rev/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/rev/functions/log10.hpp_iwyu.txt 21 ./agrad/rev/functions/inv_square.hpp_iwyu.txt 21 ./agrad/rev/functions/inv.hpp_iwyu.txt 21 ./agrad/fwd/functions/sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/multiply_log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1m_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log10.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_cloglog.hpp_iwyu.txt 21 ./agrad/fwd/functions/expm1.hpp_iwyu.txt 21 ./agrad/fwd/functions/asin.hpp_iwyu.txt 21 ./agrad/fwd/functions/acos.hpp_iwyu.txt 20 ./math/matrix/squared_distance.hpp_iwyu.txt 20 ./math/matrix/rows_dot_product.hpp_iwyu.txt 20 ./math/matrix/columns_dot_product.hpp_iwyu.txt

20 ./math/functions/lgamma.hpp_iwyu.txt 20 ./math/functions/gamma_q.hpp_iwyu.txt 20 ./math/functions/gamma_p.hpp_iwyu.txt 20 ./gm/arguments/argument_parser.hpp_iwyu.txt 20 ./gm/arguments/arg_adapt.hpp_iwyu.txt 20 ./agrad/rev/vari.hpp_iwyu.txt 20 ./agrad/rev/matrix/initialize_variable.hpp_iwyu.txt 20 ./agrad/rev/functions/tan.hpp_iwyu.txt 20 ./agrad/rev/functions/tanh.hpp_iwyu.txt 20 ./agrad/rev/functions/sqrt.hpp_iwyu.txt 20 ./agrad/rev/functions/sin.hpp_iwyu.txt 20 ./agrad/rev/functions/Phi_approx.hpp_iwyu.txt 20 ./agrad/rev/functions/log.hpp_iwyu.txt 20 ./agrad/rev/functions/log1m.hpp_iwyu.txt 20 ./agrad/rev/functions/inv_logit.hpp_iwyu.txt 20 ./agrad/rev/functions/floor.hpp_iwyu.txt 20 ./agrad/rev/functions/fabs.hpp_iwyu.txt 20 ./agrad/rev/functions/exp.hpp_iwyu.txt 20 ./agrad/rev/functions/cos.hpp_iwyu.txt 20 ./agrad/rev/functions/ceil.hpp_iwyu.txt 20 ./agrad/rev/functions/asin.hpp_iwyu.txt 20 ./agrad/hessian.hpp_iwyu.txt 20 ./agrad/fwd/functions/tan.hpp_iwyu.txt 20 ./agrad/fwd/functions/tanh.hpp_iwyu.txt 20 ./agrad/fwd/functions/sin.hpp_iwyu.txt 20 ./agrad/fwd/functions/sinh.hpp_iwyu.txt 20 ./agrad/fwd/functions/exp.hpp_iwyu.txt 20 ./agrad/fwd/functions/cos.hpp_iwyu.txt 20 ./agrad/fwd/functions/cosh.hpp_iwyu.txt 19 ./math/matrix/dot_self.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_unit_vector.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_semidefinite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_multiplicable.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_matching_sizes.hpp_iwyu.txt 19 ./agrad/rev/var_stack.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_negative.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_increment.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_decrement.hpp_iwyu.txt 19 ./agrad/rev/matrix/value_of.hpp_iwyu.txt 19 ./agrad/rev/internal/precomp_v_vari.hpp_iwyu.txt 19 ./agrad/rev/internal/precomputed_gradients.hpp_iwyu.txt 19 ./agrad/rev/functions/square.hpp_iwyu.txt 19 ./agrad/rev/chainable.hpp_iwyu.txt 19 ./agrad/fwd/matrix/normalize.hpp_iwyu.txt 19 ./agrad/fwd.hpp_iwyu.txt 19 ./agrad/fwd/functions/tgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/logit.hpp_iwyu.txt 19 ./agrad/fwd/functions/lgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmin.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmax.hpp_iwyu.txt 19 ./agrad/fwd/functions/fdim.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan2.hpp_iwyu.txt

18 ./mcmc/hmc/hamiltonians/dense_e_point.hpp_iwyu.txt 18 ./math/matrix/tail.hpp_iwyu.txt 18 ./math/matrix/resize.hpp_iwyu.txt 18 ./math/matrix/log_sum_exp.hpp_iwyu.txt 18 ./math/matrix/head.hpp_iwyu.txt 18 ./math/matrix/get_base1_lhs.hpp_iwyu.txt 18 ./math/error_handling/matrix/check_nonzero_size.hpp_iwyu.txt 18 ./math/error_handling/check_consistent_size.hpp_iwyu.txt

18 ./gm/arguments/singleton_argument.hpp_iwyu.txt 18 ./gm/arguments/list_argument.hpp_iwyu.txt 18 ./gm/arguments/arg_sample.hpp_iwyu.txt 18 ./agrad/rev/matrix/stored_gradient_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vector_vari.hpp_iwyu.txt 18 ./agrad/rev/boost_fpclassify.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_not_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_equal.hpp_iwyu.txt 18 ./agrad/fwd/numeric_limits.hpp_iwyu.txt 18 ./agrad/fwd/functions/rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1p.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1m.hpp_iwyu.txt 18 ./agrad/fwd/functions/lbeta.hpp_iwyu.txt 18 ./agrad/fwd/functions/fmod.hpp_iwyu.txt 18 ./agrad/fwd/functions/floor.hpp_iwyu.txt 18 ./agrad/fwd/functions/falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/digamma.hpp_iwyu.txt 18 ./agrad/fwd/functions/ceil.hpp_iwyu.txt 18 ./agrad/fwd/functions/cbrt.hpp_iwyu.txt 18 ./agrad/fwd/functions/atanh.hpp_iwyu.txt 17 ./mcmc/hmc/integrators/expl_leapfrog.hpp_iwyu.txt 17 ./io/cmd_line.hpp_iwyu.txt 17 ./agrad/rev/numeric_limits.hpp_iwyu.txt 17 ./agrad/rev/functions/is_uninitialized.hpp_iwyu.txt 17 ./agrad/rev/functions/abs.hpp_iwyu.txt 17 ./agrad/fwd/functions/square.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv_square.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv.hpp_iwyu.txt 17 ./agrad/fwd/functions/fabs.hpp_iwyu.txt 17 ./agrad/fwd/functions/binary_log_loss.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/abs.hpp_iwyu.txt

16 ./memory/chunk_alloc.hpp_iwyu.txt 16 ./mcmc/hmc/hamiltonians/diag_e_point.hpp_iwyu.txt 16 ./math/matrix/typedefs.hpp_iwyu.txt 16 ./math/matrix/sub_row.hpp_iwyu.txt 16 ./math/matrix/sub_col.hpp_iwyu.txt 16 ./math/matrix/min.hpp_iwyu.txt 16 ./math/matrix/max.hpp_iwyu.txt 16 ./math/matrix/get_base1.hpp_iwyu.txt 16 ./math/matrix/block.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_row_index.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_column_index.hpp_iwyu.txt 16 ./gm/arguments/arg_hmc.hpp_iwyu.txt 16 ./agrad/rev/functions/value_of.hpp_iwyu.txt 16 ./agrad/rev/functions/step.hpp_iwyu.txt 16 ./agrad/rev/functions/fmin.hpp_iwyu.txt 16 ./agrad/rev/functions/fmax.hpp_iwyu.txt 16 ./agrad/rev/functions/as_bool.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_unary_minus.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_subtraction.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_multiplication.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_division.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_addition.hpp_iwyu.txt 15 ./meta.hpp_iwyu.txt

15 ./memory/stack_alloc.hpp_iwyu.txt 15 ./math/seq_view.hpp_iwyu.txt 15 ./math/matrix/stan_print.hpp_iwyu.txt 15 ./math/matrix/initialize.hpp_iwyu.txt 15 ./math/matrix/col.hpp_iwyu.txt 15 ./math/functions/log_sum_exp.hpp_iwyu.txt 15 ./math/error_handling/matrix/check_ldlt_factor.hpp_iwyu.txt 15 ./gm/arguments/arg_output.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize_algo.hpp_iwyu.txt 15 ./gm/arguments/arg_metric.hpp_iwyu.txt 15 ./gm/arguments/arg_method.hpp_iwyu.txt 15 ./common/do_bfgs_optimize.hpp_iwyu.txt 15 ./agrad/rev/jacobian.hpp_iwyu.txt 15 ./agrad/rev/error_handling/matrix.hpp_iwyu.txt

14 ./optimization/bfgs_linesearch.hpp_iwyu.txt 14 ./mcmc/sample.hpp_iwyu.txt 14 ./math/matrix/singular_values.hpp_iwyu.txt 14 ./math/matrix/rank.hpp_iwyu.txt 14 ./math/matrix/log_determinant_spd.hpp_iwyu.txt 14 ./math/functions/log2.hpp_iwyu.txt 14 ./math/functions/log1m_exp.hpp_iwyu.txt 14 ./math/functions/inverse_softmax.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_std_vector_index.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_square.hpp_iwyu.txt 14 ./gm/arguments/arg_test_gradient.hpp_iwyu.txt 14 ./gm/arguments/arg_sample_algo.hpp_iwyu.txt 14 ./gm/arguments/arg_engine.hpp_iwyu.txt 14 ./gm/arguments/arg_bfgs.hpp_iwyu.txt 14 ./common/recorder/filtered_values.hpp_iwyu.txt 14 ./agrad/agrad_thread_safe.hpp_iwyu.txt 13 ./math/matrix/sum.hpp_iwyu.txt 13 ./math/matrix/sort.hpp_iwyu.txt 13 ./math/matrix/promoter.hpp_iwyu.txt 13 ./math/matrix/prod.hpp_iwyu.txt 13 ./math/matrix/inverse.hpp_iwyu.txt 13 ./math/matrix/fill.hpp_iwyu.txt 13 ./math/matrix/cumulative_sum.hpp_iwyu.txt 13 ./math/functions/log_diff_exp.hpp_iwyu.txt 13 ./math/functions/binomial_coefficient_log.hpp_iwyu.txt 13 ./math/error_handling/matrix/check_matching_dims.hpp_iwyu.txt 13 ./io/var_context.hpp_iwyu.txt 13 ./gm/grammars/whitespace_grammar_def.hpp_iwyu.txt 13 ./gm/arguments/categorical_argument.hpp_iwyu.txt 13 ./gm/arguments/argument.hpp_iwyu.txt 13 ./gm/arguments/arg_tolerance.hpp_iwyu.txt 13 ./gm/arguments/arg_test.hpp_iwyu.txt 13 ./gm/arguments/arg_static.hpp_iwyu.txt 13 ./gm/arguments/arg_random.hpp_iwyu.txt 13 ./gm/arguments/arg_nuts.hpp_iwyu.txt 13 ./gm/arguments/arg_lbfgs.hpp_iwyu.txt 13 ./gm/arguments/arg_diagnose.hpp_iwyu.txt 13 ./gm/arguments/arg_data.hpp_iwyu.txt 13 ./common/recorder/values.hpp_iwyu.txt 13 ./common/recorder.hpp_iwyu.txt 13 ./common/print_progress.hpp_iwyu.txt 13 ./common/init_static_hmc.hpp_iwyu.txt 13 ./common/init_nuts.hpp_iwyu.txt 12 ./optimization/bfgs_update.hpp_iwyu.txt 12 ./mcmc/stepsize_var_adapter.hpp_iwyu.txt 12 ./mcmc/stepsize_covar_adapter.hpp_iwyu.txt 12 ./mcmc/base_mcmc.hpp_iwyu.txt 12 ./math/matrix/trace.hpp_iwyu.txt 12 ./math/matrix/subtract.hpp_iwyu.txt 12 ./math/matrix/rows.hpp_iwyu.txt 12 ./math/matrix/elt_multiply.hpp_iwyu.txt 12 ./math/matrix/elt_divide.hpp_iwyu.txt 12 ./math/matrix/divide.hpp_iwyu.txt 12 ./math/matrix/diag_pre_multiply.hpp_iwyu.txt 12 ./math/matrix/diag_post_multiply.hpp_iwyu.txt 12 ./math/matrix/diagonal.hpp_iwyu.txt 12 ./math/matrix/diag_matrix.hpp_iwyu.txt 12 ./math/matrix/common_type.hpp_iwyu.txt 12 ./math/matrix/cols.hpp_iwyu.txt 12 ./math/matrix/add.hpp_iwyu.txt 12 ./math/functions/trigamma.hpp_iwyu.txt 12 ./math/error_handling/matrix/check_size_match.hpp_iwyu.txt 12 ./gm/grammars/whitespace_grammar.hpp_iwyu.txt 12 ./gm/arguments/valued_argument.hpp_iwyu.txt 12 ./gm/arguments/unvalued_argument.hpp_iwyu.txt 12 ./common/recorder/sum_values.hpp_iwyu.txt 12 ./agrad/fwd/matrix/sum.hpp_iwyu.txt 11 ./math/rep_array.hpp_iwyu.txt

11 ./math/matrix/sort_indices.hpp_iwyu.txt 11 ./math/matrix/log_determinant.hpp_iwyu.txt 11 ./math/matrix/dims.hpp_iwyu.txt 11 ./math/matrix/determinant.hpp_iwyu.txt 11 ./math/functions/Phi_approx.hpp_iwyu.txt 11 ./math/functions/log1p.hpp_iwyu.txt 11 ./math/functions/log1p_exp.hpp_iwyu.txt 11 ./math/error_handling/matrix/validate_non_negative_index.hpp_iwyu.txt 11 ./math/error_handling/matrix/check_range.hpp_iwyu.txt 11 ./math/error_handling/check_positive_finite.hpp_iwyu.txt

11 ./gm/grammars/iterator_typedefs.hpp_iwyu.txt 11 ./gm/arguments/argument_probe.hpp_iwyu.txt 11 ./common/write_iteration.hpp_iwyu.txt 11 ./common/write_iteration_csv.hpp_iwyu.txt 11 ./common/write_error_msg.hpp_iwyu.txt 10 ./math/matrix/transpose.hpp_iwyu.txt 10 ./math/matrix/rows_dot_self.hpp_iwyu.txt 10 ./math/matrix/log.hpp_iwyu.txt 10 ./math/matrix/log_determinant_ldlt.hpp_iwyu.txt 10 ./math/matrix/exp.hpp_iwyu.txt 10 ./math/matrix/columns_dot_self.hpp_iwyu.txt 10 ./math/functions/rising_factorial.hpp_iwyu.txt 10 ./math/functions/multiply_log.hpp_iwyu.txt 10 ./math/functions/modulus.hpp_iwyu.txt

10 ./math/functions/log_rising_factorial.hpp_iwyu.txt 10 ./math/functions/logit.hpp_iwyu.txt 10 ./math/functions/log_inv_logit.hpp_iwyu.txt 10 ./math/functions/log_falling_factorial.hpp_iwyu.txt 10 ./math/functions/log1m_inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_sqrt.hpp_iwyu.txt 10 ./math/functions/inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_cloglog.hpp_iwyu.txt 10 ./math/functions/falling_factorial.hpp_iwyu.txt 10 ./math/functions/exp2.hpp_iwyu.txt 10 ./math/functions/divide.hpp_iwyu.txt

10 ./math/functions/binary_log_loss.hpp_iwyu.txt 10 ./io/json/json_error.hpp_iwyu.txt 10 ./gm/arguments/arg_unit_e.hpp_iwyu.txt 10 ./gm/arguments/arg_thin.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_err.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_eps.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize_jitter.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize.hpp_iwyu.txt 10 ./gm/arguments/arg_seed.hpp_iwyu.txt 10 ./gm/arguments/arg_save_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_save_iterations.hpp_iwyu.txt 10 ./gm/arguments/arg_rwm.hpp_iwyu.txt 10 ./gm/arguments/arg_refresh.hpp_iwyu.txt 10 ./gm/arguments/arg_output_file.hpp_iwyu.txt 10 ./gm/arguments/arg_num_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_num_samples.hpp_iwyu.txt 10 ./gm/arguments/arg_newton.hpp_iwyu.txt 10 ./gm/arguments/arg_max_depth.hpp_iwyu.txt 10 ./gm/arguments/arg_iter.hpp_iwyu.txt 10 ./gm/arguments/arg_int_time.hpp_iwyu.txt 10 ./gm/arguments/arg_init.hpp_iwyu.txt 10 ./gm/arguments/arg_init_alpha.hpp_iwyu.txt 10 ./gm/arguments/arg_id.hpp_iwyu.txt 10 ./gm/arguments/arg_history_size.hpp_iwyu.txt 10 ./gm/arguments/arg_fixed_param.hpp_iwyu.txt 10 ./gm/arguments/arg_fail.hpp_iwyu.txt 10 ./gm/arguments/arg_diagnostic_file.hpp_iwyu.txt 10 ./gm/arguments/arg_diag_e.hpp_iwyu.txt 10 ./gm/arguments/arg_dense_e.hpp_iwyu.txt 10 ./gm/arguments/arg_data_file.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_window.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_term_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_t0.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_kappa.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_init_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_gamma.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_engaged.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_delta.hpp_iwyu.txt 10 ./common/recorder/no_op.hpp_iwyu.txt 10 ./agrad/rev/internal/vvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/v_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/ddv_vari.hpp_iwyu.txt 10 ./agrad/rev/calculate_chain.hpp_iwyu.txt 9 ./math/matrix/Eigen.hpp_iwyu.txt 9 ./agrad/fwd/functions/fma.hpp_iwyu.txt 8 ./memory.hpp_iwyu.txt 8 ./gm.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_plus.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_not.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_plus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_not_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_multiply_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_minus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_divide_equal.hpp_iwyu.txt 8 ./agrad/rev/matrix/stan_print.hpp_iwyu.txt 8 ./agrad/rev/functions/if_else.hpp_iwyu.txt

5 ./math/error_handling/matrix/constraint_tolerance.hpp_iwyu.txt 2 ./version.hpp_iwyu.txt 2 ./mcmc/windowed_adaptation.hpp_iwyu.txt 2 ./mcmc/stepsize_adapter.hpp_iwyu.txt 2 ./mcmc/stepsize_adaptation.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_leapfrog.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_integrator.hpp_iwyu.txt 2 ./mcmc/hmc/hamiltonians/unit_e_point.hpp_iwyu.txt 2 ./mcmc/fixed_param_sampler.hpp_iwyu.txt 2 ./mcmc/base_adapter.hpp_iwyu.txt 2 ./mcmc/base_adaptation.hpp_iwyu.txt 2 ./math/matrix/size.hpp_iwyu.txt 2 ./math/matrix/promote_common.hpp_iwyu.txt 2 ./math/matrix/minus.hpp_iwyu.txt 2 ./math/matrix/array_builder.hpp_iwyu.txt 2 ./math/functions/value_of.hpp_iwyu.txt 2 ./math/functions/sum.hpp_iwyu.txt 2 ./math/functions/sub.hpp_iwyu.txt 2 ./math/functions/step.hpp_iwyu.txt 2 ./math/functions/square.hpp_iwyu.txt 2 ./math/functions/sign.hpp_iwyu.txt 2 ./math/functions/scaled_add.hpp_iwyu.txt 2 ./math/functions/Phi.hpp_iwyu.txt 2 ./math/functions/owens_t.hpp_iwyu.txt 2 ./math/functions/modified_bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/modified_bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/min.hpp_iwyu.txt 2 ./math/functions/max.hpp_iwyu.txt 2 ./math/functions/logical_or.hpp_iwyu.txt 2 ./math/functions/logical_neq.hpp_iwyu.txt 2 ./math/functions/logical_negation.hpp_iwyu.txt 2 ./math/functions/logical_lt.hpp_iwyu.txt 2 ./math/functions/logical_lte.hpp_iwyu.txt 2 ./math/functions/logical_gt.hpp_iwyu.txt 2 ./math/functions/logical_gte.hpp_iwyu.txt 2 ./math/functions/logical_eq.hpp_iwyu.txt 2 ./math/functions/logical_and.hpp_iwyu.txt 2 ./math/functions/log1m.hpp_iwyu.txt 2 ./math/functions/lmgamma.hpp_iwyu.txt 2 ./math/functions/lbeta.hpp_iwyu.txt 2 ./math/functions/is_uninitialized.hpp_iwyu.txt 2 ./math/functions/inv_square.hpp_iwyu.txt 2 ./math/functions/inv.hpp_iwyu.txt 2 ./math/functions/int_step.hpp_iwyu.txt 2 ./math/functions/if_else.hpp_iwyu.txt 2 ./math/functions/fma.hpp_iwyu.txt 2 ./math/functions/fdim.hpp_iwyu.txt 2 ./math/functions/dot_self.hpp_iwyu.txt 2 ./math/functions/dot.hpp_iwyu.txt 2 ./math/functions/dist.hpp_iwyu.txt 2 ./math/functions/bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/as_bool.hpp_iwyu.txt 2 ./math/functions/abs.hpp_iwyu.txt 2 ./io/util.hpp_iwyu.txt 2 ./io/json/json_handler.hpp_iwyu.txt 2 ./gm/error_codes.hpp_iwyu.txt 2 ./gm/compiler.hpp_iwyu.txt 2 ./common/write_stan.hpp_iwyu.txt 2 ./common/write_model.hpp_iwyu.txt 2 ./common/recorder/messages.hpp_iwyu.txt 2 ./common/recorder/csv.hpp_iwyu.txt 2 ./common/do_print.hpp_iwyu.txt 2 ./agrad/rev/error_handling.hpp_iwyu.txt 2 ./agrad.hpp_iwyu.txt 2 ./agrad/fwd/fvar.hpp_iwyu.txt

—

Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51705460.

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51808202.

[syclik]

That sounds great. If you think it'll be easier reviewing in subfolders, feel free to create a handful of pull requests. We can discuss them by hand.

On Mon, Aug 11, 2014 at 1:03 PM, bgoodri notifications@github.com wrote:

There is an option to apply iwyu's recommendations automatically, instead of just writing the recommendations to a text file. I could push a branch with the recommendations implemented and then we could manually go through it, fix the build errors, and then potentially merge it.

On Mon, Aug 11, 2014 at 12:58 PM, Daniel Lee notifications@github.com wrote:

Thanks. Got it.

Suggestions on actions? Should we just create a pull request with as many changes as we can make?

On Mon, Aug 11, 2014 at 12:53 PM, Daniel Lee bearlee@alum.mit.edu wrote:

Ben, github's issues swallowed the attachment. Can you either forward the attachment directly to me or to stan-dev?

On Sat, Aug 9, 2014 at 11:53 PM, bgoodri notifications@github.com wrote:

Sorry, I forgot to pull before running it. The attached is up to date with develop.

Ben

On Sat, Aug 9, 2014 at 11:06 PM, Ben Goodrich goodrich.ben@gmail.com

wrote:

I have never tried to install it on a Mac. Attached is the output from my laptop. However, iwyu still gets confused by Eigen sometimes.

Ben

On Sat, Aug 9, 2014 at 10:39 PM, Daniel Lee < notifications@github.com>

wrote:

Ben, I'm having a little trouble installing. Any suggestions? Or is there some way we can use the output from a working system?

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51704370.

22297 total 452 ./optimization/newton.hpp_iwyu.txt 406 ./mcmc/chains.hpp_iwyu.txt 361 ./agrad/fwd/matrix/to_fvar.hpp_iwyu.txt 265 ./prob/distributions/multivariate/continuous/lkj_corr.hpp_iwyu.txt 208 ./common/command.hpp_iwyu.txt 205 ./math/matrix/containers_conversion.hpp_iwyu.txt 200 ./agrad/rev/matrix/to_var.hpp_iwyu.txt 199 ./agrad/autodiff.hpp_iwyu.txt 193 ./command/print.hpp_iwyu.txt 180 ./math/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 165 ./io/dump.hpp_iwyu.txt 157 ./agrad/rev/matrix/softmax.hpp_iwyu.txt 157 ./agrad/rev/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 156 ./agrad/rev/matrix/tcrossprod.hpp_iwyu.txt 154 ./agrad/rev/matrix/log_softmax.hpp_iwyu.txt 153 ./math/matrix/tcrossprod.hpp_iwyu.txt 151 ./prob/distributions/multivariate/continuous/wishart.hpp_iwyu.txt 134 ./prob/distributions/multivariate/continuous/inv_wishart.hpp_iwyu.txt 133

./prob/distributions/multivariate/continuous/multi_student_t.hpp_iwyu.txt

132 ./prob/welford_covar_estimator.hpp_iwyu.txt 125 ./gm/ast.hpp_iwyu.txt 123 ./gm/parser.hpp_iwyu.txt 122 ./prob/distributions/univariate/discrete/ordered_logistic.hpp_iwyu.txt 119 ./prob/distributions/multivariate/discrete/categorical.hpp_iwyu.txt 116

./prob/distributions/multivariate/continuous/multi_normal_cholesky.hpp_iwyu.txt

115 ./math/matrix.hpp_iwyu.txt 114 ./agrad/rev/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 110 ./prob/distributions/multivariate/continuous/multi_normal.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/diag_e_nuts.hpp_iwyu.txt 104 ./mcmc/hmc/nuts/dense_e_nuts.hpp_iwyu.txt 100 ./prob/distributions/multivariate/continuous/dirichlet.hpp_iwyu.txt 100 ./optimization/bfgs.hpp_iwyu.txt 100 ./mcmc/hmc/nuts/unit_e_nuts.hpp_iwyu.txt 98 ./io/mcmc_writer.hpp_iwyu.txt 98 ./agrad/rev/matrix/dot_product.hpp_iwyu.txt 95 ./mcmc/hmc/nuts/base_nuts.hpp_iwyu.txt 95 ./mcmc/hmc/hamiltonians/dense_e_metric.hpp_iwyu.txt 94 ./agrad/rev/matrix/crossprod.hpp_iwyu.txt 93 ./prob/transform.hpp_iwyu.txt 92 ./mcmc/hmc/hamiltonians/diag_e_metric.hpp_iwyu.txt 92 ./agrad/rev/matrix/multiply.hpp_iwyu.txt 90 ./model/util.hpp_iwyu.txt 88 ./mcmc/hmc/hamiltonians/unit_e_metric.hpp_iwyu.txt 87 ./prob/welford_var_estimator.hpp_iwyu.txt 87 ./math/matrix/crossprod.hpp_iwyu.txt 87 ./agrad/rev/functions.hpp_iwyu.txt 86 ./agrad/fwd/functions.hpp_iwyu.txt

85 ./gm/grammars/program_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/term_grammar_def.hpp_iwyu.txt 84 ./gm/grammars/statement_grammar_def.hpp_iwyu.txt 76 ./gm/grammars/functions_grammar_def.hpp_iwyu.txt 75 ./math/functions.hpp_iwyu.txt 74 ./gm/grammars/var_decls_grammar_def.hpp_iwyu.txt 74 ./gm/grammars/bare_type_grammar_def.hpp_iwyu.txt 71 ./agrad/rev/functions/cbrt.hpp_iwyu.txt 65 ./gm/grammars/expression07_grammar_def.hpp_iwyu.txt 65 ./agrad/rev/functions/digamma.hpp_iwyu.txt 63 ./model/model_header.hpp_iwyu.txt 63 ./gm/grammars/expression_grammar_def.hpp_iwyu.txt 62 ./gm/grammars/statement_2_grammar_def.hpp_iwyu.txt 60 ./io/reader.hpp_iwyu.txt 60 ./agrad/rev/functions/ibeta.hpp_iwyu.txt 58

./prob/distributions/multivariate/continuous/multi_normal_prec.hpp_iwyu.txt

58

./prob/distributions/multivariate/continuous/gaussian_dlm_obs.hpp_iwyu.txt

57

./prob/distributions/univariate/continuous/double_exponential.hpp_iwyu.txt

56 ./mcmc.hpp_iwyu.txt 55 ./agrad/rev/internal.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/inv_gamma.hpp_iwyu.txt 54 ./prob/distributions/univariate/continuous/gamma.hpp_iwyu.txt 54 ./prob/distributions/multivariate/continuous/multi_gp.hpp_iwyu.txt 54 ./agrad/rev/functions/atanh.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/skew_normal.hpp_iwyu.txt 53 ./prob/distributions/univariate/continuous/gumbel.hpp_iwyu.txt 53 ./prob/distributions/multivariate/continuous/matrix_normal.hpp_iwyu.txt 52 ./prob/distributions/univariate/discrete/neg_binomial.hpp_iwyu.txt 52 ./prob/distributions/univariate/continuous/student_t.hpp_iwyu.txt 52 ./common.hpp_iwyu.txt 52 ./agrad/rev/matrix.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/neg_binomial_2.hpp_iwyu.txt 51 ./prob/distributions/univariate/discrete/binomial.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/exp_mod_normal.hpp_iwyu.txt 51 ./prob/distributions/univariate/continuous/beta.hpp_iwyu.txt 51 ./prob/distributions/multivariate/continuous/lkj_cov.hpp_iwyu.txt 50 ./prob/distributions/univariate/continuous/inv_chi_square.hpp_iwyu.txt 50 ./prob/constants.hpp_iwyu.txt 50 ./agrad/rev/matrix/Eigen_NumTraits.hpp_iwyu.txt 50 ./agrad/rev/functions/trunc.hpp_iwyu.txt 50 ./agrad/rev/functions/round.hpp_iwyu.txt 49 ./prob/distributions/univariate/discrete/beta_binomial.hpp_iwyu.txt 49

./prob/distributions/univariate/continuous/scaled_inv_chi_square.hpp_iwyu.txt

49 ./prob/distributions/multivariate/discrete/multinomial.hpp_iwyu.txt 48 ./prob/distributions/univariate/discrete/hypergeometric.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/von_mises.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/chi_square.hpp_iwyu.txt 48 ./prob/distributions/univariate/continuous/cauchy.hpp_iwyu.txt 48 ./io/writer.hpp_iwyu.txt 47 ./prob/distributions/univariate/continuous/lognormal.hpp_iwyu.txt 47 ./io/stan_csv_reader.hpp_iwyu.txt 46 ./prob/traits.hpp_iwyu.txt 46 ./prob.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/normal.hpp_iwyu.txt 46 ./prob/distributions/univariate/continuous/frechet.hpp_iwyu.txt 46 ./math/constants.hpp_iwyu.txt 45 ./prob/distributions/univariate/discrete/poisson.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/rayleigh.hpp_iwyu.txt 45 ./prob/distributions/univariate/continuous/pareto.hpp_iwyu.txt 45 ./math/functions/digamma.hpp_iwyu.txt 45 ./agrad/rev/matrix/log_sum_exp.hpp_iwyu.txt 44 ./prob/distributions/univariate/discrete/bernoulli.hpp_iwyu.txt 44 ./prob/distributions/univariate/continuous/weibull.hpp_iwyu.txt 44

./prob/distributions/multivariate/continuous/multi_gp_cholesky.hpp_iwyu.txt

44 ./prob/distributions/multivariate/continuous.hpp_iwyu.txt 44 ./math/matrix_error_handling.hpp_iwyu.txt 44 ./agrad/rev/functions/log_sum_exp.hpp_iwyu.txt 44 ./agrad/fwd/matrix.hpp_iwyu.txt 43 ./prob/distributions/univariate/continuous.hpp_iwyu.txt 43 ./agrad/rev/matrix/sd.hpp_iwyu.txt 42 ./io/json/json_data.hpp_iwyu.txt 42 ./io/json/json_data_handler.hpp_iwyu.txt 42 ./agrad/rev/functions/gamma_q.hpp_iwyu.txt 41 ./prob/distributions/univariate/continuous/exponential.hpp_iwyu.txt 41 ./common/warmup.hpp_iwyu.txt 41 ./common/sample.hpp_iwyu.txt 41 ./agrad/rev/matrix/log_determinant_spd.hpp_iwyu.txt 41 ./agrad/rev/functions/gamma_p.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_second_kind.hpp_iwyu.txt 41 ./agrad/rev/functions/bessel_first_kind.hpp_iwyu.txt 41 ./agrad/fwd/functions/trunc.hpp_iwyu.txt 41 ./agrad/fwd/functions/round.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/uniform.hpp_iwyu.txt 40 ./prob/distributions/univariate/continuous/logistic.hpp_iwyu.txt 40 ./agrad/rev/matrix/variance.hpp_iwyu.txt 40 ./agrad/rev/matrix/mdivide_left_tri.hpp_iwyu.txt 39 ./common/run_markov_chain.hpp_iwyu.txt 39 ./agrad/rev/functions/rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_rising_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/log_falling_factorial.hpp_iwyu.txt 39 ./agrad/rev/functions/falling_factorial.hpp_iwyu.txt 39 ./agrad/fwd/matrix/log_sum_exp.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_spd.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left_ldlt.hpp_iwyu.txt 38 ./agrad/rev/matrix/mdivide_left.hpp_iwyu.txt 37 ./prob/distributions/univariate/continuous/johnson.hpp_iwyu.txt 37 ./agrad/rev/functions/asinh.hpp_iwyu.txt 37 ./agrad/rev/functions/acosh.hpp_iwyu.txt 36 ./prob/distributions/multivariate.hpp_iwyu.txt 36 ./prob/autocovariance.hpp_iwyu.txt 36 ./meta/traits.hpp_iwyu.txt 36 ./math/error_handling.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right_tri_low.hpp_iwyu.txt 36 ./agrad/fwd/matrix/mdivide_right.hpp_iwyu.txt 35 ./prob/distributions.hpp_iwyu.txt 35 ./io.hpp_iwyu.txt 35 ./agrad/rev/functions/log_diff_exp.hpp_iwyu.txt 35 ./agrad/rev/functions/lmgamma.hpp_iwyu.txt 35 ./agrad/rev/functions/lgamma.hpp_iwyu.txt 35 ./agrad/fwd/matrix/mdivide_left_tri_low.hpp_iwyu.txt 35 ./agrad/fwd/matrix/inverse.hpp_iwyu.txt 34 ./math/error_handling/matrix/check_corr_matrix.hpp_iwyu.txt 34 ./agrad/rev/matrix/log_determinant.hpp_iwyu.txt 34 ./agrad/rev/matrix/determinant.hpp_iwyu.txt 34 ./agrad/rev/functions/modified_bessel_first_kind.hpp_iwyu.txt 34 ./agrad/fwd/prob/univariate/continuous/normal.hpp_iwyu.txt 33

./prob/distributions/multivariate/discrete/categorical_logit.hpp_iwyu.txt

33 ./agrad/rev/operators.hpp_iwyu.txt 33 ./agrad/rev/matrix/trace_gen_quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/quad_form.hpp_iwyu.txt 33 ./agrad/rev/matrix/dot_self.hpp_iwyu.txt 33 ./agrad/rev/functions/fma.hpp_iwyu.txt 33 ./agrad/fwd/matrix/mdivide_left.hpp_iwyu.txt 32 ./prob/autocorrelation.hpp_iwyu.txt 32 ./io/csv_writer.hpp_iwyu.txt 32 ./agrad/rev/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 32 ./agrad/rev/matrix/squared_distance.hpp_iwyu.txt 32 ./agrad/rev/functions/tgamma.hpp_iwyu.txt 32 ./agrad/rev/functions/multiply_log.hpp_iwyu.txt 32 ./agrad/rev/functions/modified_bessel_second_kind.hpp_iwyu.txt 31 ./mcmc/var_adaptation.hpp_iwyu.txt 31 ./math/matrix/dot_product.hpp_iwyu.txt 31 ./gm/grammars/common_adaptors_def.hpp_iwyu.txt 31 ./agrad/rev/matrix/trace_quad_form.hpp_iwyu.txt 31 ./agrad/rev/matrix/LDLT_factor.hpp_iwyu.txt 31 ./agrad/rev/functions/owens_t.hpp_iwyu.txt 30 ./math/error_handling/dom_err_vec.hpp_iwyu.txt 29 ./prob/distributions/univariate/discrete.hpp_iwyu.txt 29 ./model/prob_grad.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_diag_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/static/adapt_dense_e_static_hmc.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_diag_e_nuts.hpp_iwyu.txt 29 ./mcmc/hmc/nuts/adapt_dense_e_nuts.hpp_iwyu.txt 29 ./mcmc/covar_adaptation.hpp_iwyu.txt 29 ./io/json.hpp_iwyu.txt 29 ./agrad/rev/matrix/sum.hpp_iwyu.txt 29 ./agrad/rev/matrix/grad.hpp_iwyu.txt 29 ./agrad/fwd/matrix/multiply.hpp_iwyu.txt 29 ./agrad/fwd/matrix/dot_product.hpp_iwyu.txt 28 ./model.hpp_iwyu.txt 28 ./mcmc/hmc/hamiltonians/base_hamiltonian.hpp_iwyu.txt 28 ./math/matrix/qr_R.hpp_iwyu.txt 28 ./math/matrix/qr_Q.hpp_iwyu.txt 28 ./math/matrix/assign.hpp_iwyu.txt 28 ./agrad/rev/functions/pow.hpp_iwyu.txt 28 ./agrad/rev/functions/atan2.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_R.hpp_iwyu.txt 28 ./agrad/fwd/matrix/qr_Q.hpp_iwyu.txt 28 ./agrad/fwd/matrix/log_softmax.hpp_iwyu.txt 28 ./agrad/fwd/matrix/divide.hpp_iwyu.txt 28 ./agrad/fwd/matrix/determinant.hpp_iwyu.txt 27 ./prob/internal_math.hpp_iwyu.txt 27 ./mcmc/hmc/static/adapt_unit_e_static_hmc.hpp_iwyu.txt 27 ./mcmc/hmc/nuts/adapt_unit_e_nuts.hpp_iwyu.txt 27 ./math/matrix/mdivide_right_tri.hpp_iwyu.txt 27 ./math/matrix/log_softmax.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_symmetric.hpp_iwyu.txt 27 ./math/error_handling/matrix/check_simplex.hpp_iwyu.txt 27 ./agrad/rev/matrix/log_determinant_ldlt.hpp_iwyu.txt 27 ./agrad/rev/matrix/LDLT_alloc.hpp_iwyu.txt 27 ./agrad/fwd/matrix/typedefs.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/trace_gen_quad_form.hpp_iwyu.txt 27 ./agrad/fwd/matrix/rows_dot_self.hpp_iwyu.txt 27 ./agrad/fwd/matrix/columns_dot_self.hpp_iwyu.txt 26 ./mcmc/hmc/static/unit_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/diag_e_static_hmc.hpp_iwyu.txt 26 ./mcmc/hmc/static/dense_e_static_hmc.hpp_iwyu.txt 26 ./math/matrix/segment.hpp_iwyu.txt 26 ./math/matrix/sd.hpp_iwyu.txt 26 ./math/matrix/quad_form.hpp_iwyu.txt 26 ./math/matrix/quad_form_diag.hpp_iwyu.txt 26 ./math/matrix/mdivide_right_ldlt.hpp_iwyu.txt 26 ./math/matrix/inverse_spd.hpp_iwyu.txt 26 ./math/matrix/distance.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_spsd_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cov_matrix.hpp_iwyu.txt 26 ./math/error_handling/matrix/check_cholesky_factor_corr.hpp_iwyu.txt 26 ./gm/grammars/functions_grammar.hpp_iwyu.txt 26 ./agrad/rev/matrix/sort.hpp_iwyu.txt 26 ./agrad/rev/functions/fmod.hpp_iwyu.txt 26 ./agrad/fwd/operators.hpp_iwyu.txt 26 ./agrad/fwd/functions/gamma_p.hpp_iwyu.txt 25 ./prob/distributions/univariate.hpp_iwyu.txt 25 ./prob/distributions/multivariate/discrete.hpp_iwyu.txt 25 ./math/matrix/variance.hpp_iwyu.txt 25 ./math/matrix/row.hpp_iwyu.txt 25 ./math/matrix/mdivide_right_tri_low.hpp_iwyu.txt 25 ./math/matrix/mdivide_left_tri_low.hpp_iwyu.txt 25 ./math/matrix/LDLT_factor.hpp_iwyu.txt 25 ./io/json/json_parser.hpp_iwyu.txt 25 ./gm/grammars/program_grammar.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_subtraction.hpp_iwyu.txt 25 ./agrad/rev/operators/operator_division.hpp_iwyu.txt 25 ./agrad/fwd/matrix/softmax.hpp_iwyu.txt 25 ./agrad/fwd/matrix/rows_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/matrix/log_determinant.hpp_iwyu.txt 25 ./agrad/fwd/matrix/columns_dot_product.hpp_iwyu.txt 25 ./agrad/fwd/functions/pow.hpp_iwyu.txt 25 ./agrad/fwd/functions/log_sum_exp.hpp_iwyu.txt 25 ./agrad/fwd/functions/gamma_q.hpp_iwyu.txt 24 ./mcmc/hmc/base_hmc.hpp_iwyu.txt 24 ./math/matrix/softmax.hpp_iwyu.txt 24 ./math/matrix/multiply.hpp_iwyu.txt 24 ./math/matrix/mdivide_right_spd.hpp_iwyu.txt 24 ./math/matrix/mdivide_right.hpp_iwyu.txt 24 ./math/matrix/mdivide_left_tri.hpp_iwyu.txt 24 ./math/matrix/eigenvectors_sym.hpp_iwyu.txt 24 ./math/matrix/eigenvalues_sym.hpp_iwyu.txt 24 ./math/matrix/cholesky_decompose.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_positive_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_ordered.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_lower_triangular.hpp_iwyu.txt 24 ./math/error_handling/matrix/check_cholesky_factor.hpp_iwyu.txt

24 ./gm/grammars/term_grammar.hpp_iwyu.txt 24 ./gm/grammars/statement_grammar.hpp_iwyu.txt 24 ./gm/grammars/expression_grammar.hpp_iwyu.txt 24 ./agrad/rev/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 24 ./agrad/rev/functions/Phi.hpp_iwyu.txt 24 ./agrad/rev/functions/log1m_exp.hpp_iwyu.txt 24 ./agrad/rev/functions/hypot.hpp_iwyu.txt 24 ./agrad/rev/functions/erf.hpp_iwyu.txt 24 ./agrad/rev/functions/erfc.hpp_iwyu.txt 24 ./agrad/rev/functions/binary_log_loss.hpp_iwyu.txt 24 ./agrad/partials_vari.hpp_iwyu.txt 24 ./agrad/fwd/matrix/tcrossprod.hpp_iwyu.txt 24 ./agrad/fwd/matrix/sort.hpp_iwyu.txt 24 ./agrad/fwd/matrix/multiply_lower_tri_self_transpose.hpp_iwyu.txt 24 ./agrad/fwd/matrix/crossprod.hpp_iwyu.txt 24 ./agrad/fwd/functions/owens_t.hpp_iwyu.txt 23 ./math/rep_vector.hpp_iwyu.txt 23 ./math/rep_row_vector.hpp_iwyu.txt 23 ./math/rep_matrix.hpp_iwyu.txt 23 ./math/matrix/trace_gen_inv_quad_form_ldlt.hpp_iwyu.txt 23 ./math/matrix/mean.hpp_iwyu.txt 23 ./math.hpp_iwyu.txt

23 ./gm/grammars/var_decls_grammar.hpp_iwyu.txt 23 ./gm/grammars/expression07_grammar.hpp_iwyu.txt 23 ./common/init_adapt.hpp_iwyu.txt 23 ./command/stanc_helper.hpp_iwyu.txt 23 ./agrad/rev/matrix/typedefs.hpp_iwyu.txt 23 ./agrad/rev/functions/inv_sqrt.hpp_iwyu.txt 23 ./agrad/rev/functions/expm1.hpp_iwyu.txt 23 ./agrad/rev/functions/exp2.hpp_iwyu.txt 23 ./agrad/fwd/matrix/dot_self.hpp_iwyu.txt 23 ./agrad/fwd/functions/log1m_exp.hpp_iwyu.txt 23 ./agrad/fwd/functions/erf.hpp_iwyu.txt 23 ./agrad/fwd/functions/erfc.hpp_iwyu.txt 23 ./agrad/fwd/functions/acosh.hpp_iwyu.txt 22 ./mcmc/hmc/hamiltonians/ps_point.hpp_iwyu.txt 22 ./math/matrix/trace_quad_form.hpp_iwyu.txt 22 ./math/matrix/trace_inv_quad_form_ldlt.hpp_iwyu.txt 22 ./math/matrix/trace_gen_quad_form.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_spd.hpp_iwyu.txt 22 ./math/matrix/mdivide_left_ldlt.hpp_iwyu.txt 22 ./math/matrix/mdivide_left.hpp_iwyu.txt 22 ./math/matrix/append_row.hpp_iwyu.txt 22 ./math/matrix/append_col.hpp_iwyu.txt 22 ./math/functions/ibeta.hpp_iwyu.txt 22 ./math/error_handling/matrix/check_vector.hpp_iwyu.txt 22 ./math/error_handling/check_consistent_sizes.hpp_iwyu.txt 22 ./math/error_handling/check_bounded.hpp_iwyu.txt 22 ./gm/grammars/bare_type_grammar.hpp_iwyu.txt 22 ./gm/generator.hpp_iwyu.txt 22 ./agrad/rev/print_stack.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_multiplication.hpp_iwyu.txt 22 ./agrad/rev/operators/operator_addition.hpp_iwyu.txt 22 ./agrad/rev/matrix/divide.hpp_iwyu.txt 22 ./agrad/rev/internal/matrix_vari.hpp_iwyu.txt 22 ./agrad/rev.hpp_iwyu.txt 22 ./agrad/rev/functions/sinh.hpp_iwyu.txt 22 ./agrad/rev/functions/log1p.hpp_iwyu.txt 22 ./agrad/rev/functions/inv_cloglog.hpp_iwyu.txt 22 ./agrad/rev/functions/fdim.hpp_iwyu.txt 22 ./agrad/rev/functions/cosh.hpp_iwyu.txt 22 ./agrad/rev/functions/atan.hpp_iwyu.txt 22 ./agrad/rev/functions/acos.hpp_iwyu.txt 22 ./agrad/fwd/functions/Phi.hpp_iwyu.txt 22 ./agrad/fwd/functions/log_diff_exp.hpp_iwyu.txt 22 ./agrad/fwd/functions/log2.hpp_iwyu.txt 22 ./agrad/fwd/functions/lmgamma.hpp_iwyu.txt 22 ./agrad/fwd/functions/hypot.hpp_iwyu.txt 22 ./agrad/fwd/functions/exp2.hpp_iwyu.txt 22 ./agrad/fwd/functions/binomial_coefficient_log.hpp_iwyu.txt 22 ./agrad/fwd/functions/asinh.hpp_iwyu.txt

21 ./optimization/lbfgs_update.hpp_iwyu.txt 21 ./mcmc/hmc/static/base_static_hmc.hpp_iwyu.txt 21 ./math/matrix/accumulator.hpp_iwyu.txt 21 ./math/error_handling/dom_err.hpp_iwyu.txt 21 ./math/error_handling/check_positive.hpp_iwyu.txt 21 ./math/error_handling/check_not_nan.hpp_iwyu.txt 21 ./math/error_handling/check_nonnegative.hpp_iwyu.txt 21 ./math/error_handling/check_less_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_less.hpp_iwyu.txt 21 ./math/error_handling/check_greater_or_equal.hpp_iwyu.txt 21 ./math/error_handling/check_greater.hpp_iwyu.txt 21 ./math/error_handling/check_finite.hpp_iwyu.txt 21 ./math/error_handling/check_equal.hpp_iwyu.txt 21 ./gm/grammars/statement_2_grammar.hpp_iwyu.txt 21 ./common/init_windowed_adapt.hpp_iwyu.txt 21 ./agrad/rev/var.hpp_iwyu.txt 21 ./agrad/rev/functions/log2.hpp_iwyu.txt 21 ./agrad/rev/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/rev/functions/log10.hpp_iwyu.txt 21 ./agrad/rev/functions/inv_square.hpp_iwyu.txt 21 ./agrad/rev/functions/inv.hpp_iwyu.txt 21 ./agrad/fwd/functions/sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/multiply_log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1p_exp.hpp_iwyu.txt 21 ./agrad/fwd/functions/log1m_inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/log10.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_sqrt.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_logit.hpp_iwyu.txt 21 ./agrad/fwd/functions/inv_cloglog.hpp_iwyu.txt 21 ./agrad/fwd/functions/expm1.hpp_iwyu.txt 21 ./agrad/fwd/functions/asin.hpp_iwyu.txt 21 ./agrad/fwd/functions/acos.hpp_iwyu.txt 20 ./math/matrix/squared_distance.hpp_iwyu.txt 20 ./math/matrix/rows_dot_product.hpp_iwyu.txt 20 ./math/matrix/columns_dot_product.hpp_iwyu.txt

20 ./math/functions/lgamma.hpp_iwyu.txt 20 ./math/functions/gamma_q.hpp_iwyu.txt 20 ./math/functions/gamma_p.hpp_iwyu.txt 20 ./gm/arguments/argument_parser.hpp_iwyu.txt 20 ./gm/arguments/arg_adapt.hpp_iwyu.txt 20 ./agrad/rev/vari.hpp_iwyu.txt 20 ./agrad/rev/matrix/initialize_variable.hpp_iwyu.txt 20 ./agrad/rev/functions/tan.hpp_iwyu.txt 20 ./agrad/rev/functions/tanh.hpp_iwyu.txt 20 ./agrad/rev/functions/sqrt.hpp_iwyu.txt 20 ./agrad/rev/functions/sin.hpp_iwyu.txt 20 ./agrad/rev/functions/Phi_approx.hpp_iwyu.txt 20 ./agrad/rev/functions/log.hpp_iwyu.txt 20 ./agrad/rev/functions/log1m.hpp_iwyu.txt 20 ./agrad/rev/functions/inv_logit.hpp_iwyu.txt 20 ./agrad/rev/functions/floor.hpp_iwyu.txt 20 ./agrad/rev/functions/fabs.hpp_iwyu.txt 20 ./agrad/rev/functions/exp.hpp_iwyu.txt 20 ./agrad/rev/functions/cos.hpp_iwyu.txt 20 ./agrad/rev/functions/ceil.hpp_iwyu.txt 20 ./agrad/rev/functions/asin.hpp_iwyu.txt 20 ./agrad/hessian.hpp_iwyu.txt 20 ./agrad/fwd/functions/tan.hpp_iwyu.txt 20 ./agrad/fwd/functions/tanh.hpp_iwyu.txt 20 ./agrad/fwd/functions/sin.hpp_iwyu.txt 20 ./agrad/fwd/functions/sinh.hpp_iwyu.txt 20 ./agrad/fwd/functions/exp.hpp_iwyu.txt 20 ./agrad/fwd/functions/cos.hpp_iwyu.txt 20 ./agrad/fwd/functions/cosh.hpp_iwyu.txt 19 ./math/matrix/dot_self.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_unit_vector.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_semidefinite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_pos_definite.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_multiplicable.hpp_iwyu.txt 19 ./math/error_handling/matrix/check_matching_sizes.hpp_iwyu.txt 19 ./agrad/rev/var_stack.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_negative.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_increment.hpp_iwyu.txt 19 ./agrad/rev/operators/operator_unary_decrement.hpp_iwyu.txt 19 ./agrad/rev/matrix/value_of.hpp_iwyu.txt 19 ./agrad/rev/internal/precomp_v_vari.hpp_iwyu.txt 19 ./agrad/rev/internal/precomputed_gradients.hpp_iwyu.txt 19 ./agrad/rev/functions/square.hpp_iwyu.txt 19 ./agrad/rev/chainable.hpp_iwyu.txt 19 ./agrad/fwd/matrix/normalize.hpp_iwyu.txt 19 ./agrad/fwd.hpp_iwyu.txt 19 ./agrad/fwd/functions/tgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/logit.hpp_iwyu.txt 19 ./agrad/fwd/functions/lgamma.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmin.hpp_iwyu.txt 19 ./agrad/fwd/functions/fmax.hpp_iwyu.txt 19 ./agrad/fwd/functions/fdim.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan.hpp_iwyu.txt 19 ./agrad/fwd/functions/atan2.hpp_iwyu.txt

18 ./mcmc/hmc/hamiltonians/dense_e_point.hpp_iwyu.txt 18 ./math/matrix/tail.hpp_iwyu.txt 18 ./math/matrix/resize.hpp_iwyu.txt 18 ./math/matrix/log_sum_exp.hpp_iwyu.txt 18 ./math/matrix/head.hpp_iwyu.txt 18 ./math/matrix/get_base1_lhs.hpp_iwyu.txt 18 ./math/error_handling/matrix/check_nonzero_size.hpp_iwyu.txt 18 ./math/error_handling/check_consistent_size.hpp_iwyu.txt

18 ./gm/arguments/singleton_argument.hpp_iwyu.txt 18 ./gm/arguments/list_argument.hpp_iwyu.txt 18 ./gm/arguments/arg_sample.hpp_iwyu.txt 18 ./agrad/rev/matrix/stored_gradient_vari.hpp_iwyu.txt 18 ./agrad/rev/internal/vector_vari.hpp_iwyu.txt 18 ./agrad/rev/boost_fpclassify.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_not_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_less_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than_or_equal.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_greater_than.hpp_iwyu.txt 18 ./agrad/fwd/operators/operator_equal.hpp_iwyu.txt 18 ./agrad/fwd/numeric_limits.hpp_iwyu.txt 18 ./agrad/fwd/functions/rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_rising_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log_falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1p.hpp_iwyu.txt 18 ./agrad/fwd/functions/log1m.hpp_iwyu.txt 18 ./agrad/fwd/functions/lbeta.hpp_iwyu.txt 18 ./agrad/fwd/functions/fmod.hpp_iwyu.txt 18 ./agrad/fwd/functions/floor.hpp_iwyu.txt 18 ./agrad/fwd/functions/falling_factorial.hpp_iwyu.txt 18 ./agrad/fwd/functions/digamma.hpp_iwyu.txt 18 ./agrad/fwd/functions/ceil.hpp_iwyu.txt 18 ./agrad/fwd/functions/cbrt.hpp_iwyu.txt 18 ./agrad/fwd/functions/atanh.hpp_iwyu.txt 17 ./mcmc/hmc/integrators/expl_leapfrog.hpp_iwyu.txt 17 ./io/cmd_line.hpp_iwyu.txt 17 ./agrad/rev/numeric_limits.hpp_iwyu.txt 17 ./agrad/rev/functions/is_uninitialized.hpp_iwyu.txt 17 ./agrad/rev/functions/abs.hpp_iwyu.txt 17 ./agrad/fwd/functions/square.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/modified_bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv_square.hpp_iwyu.txt 17 ./agrad/fwd/functions/inv.hpp_iwyu.txt 17 ./agrad/fwd/functions/fabs.hpp_iwyu.txt 17 ./agrad/fwd/functions/binary_log_loss.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_second_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/bessel_first_kind.hpp_iwyu.txt 17 ./agrad/fwd/functions/abs.hpp_iwyu.txt

16 ./memory/chunk_alloc.hpp_iwyu.txt 16 ./mcmc/hmc/hamiltonians/diag_e_point.hpp_iwyu.txt 16 ./math/matrix/typedefs.hpp_iwyu.txt 16 ./math/matrix/sub_row.hpp_iwyu.txt 16 ./math/matrix/sub_col.hpp_iwyu.txt 16 ./math/matrix/min.hpp_iwyu.txt 16 ./math/matrix/max.hpp_iwyu.txt 16 ./math/matrix/get_base1.hpp_iwyu.txt 16 ./math/matrix/block.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_row_index.hpp_iwyu.txt 16 ./math/error_handling/matrix/check_column_index.hpp_iwyu.txt 16 ./gm/arguments/arg_hmc.hpp_iwyu.txt 16 ./agrad/rev/functions/value_of.hpp_iwyu.txt 16 ./agrad/rev/functions/step.hpp_iwyu.txt 16 ./agrad/rev/functions/fmin.hpp_iwyu.txt 16 ./agrad/rev/functions/fmax.hpp_iwyu.txt 16 ./agrad/rev/functions/as_bool.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_unary_minus.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_subtraction.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_multiplication.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_division.hpp_iwyu.txt 16 ./agrad/fwd/operators/operator_addition.hpp_iwyu.txt 15 ./meta.hpp_iwyu.txt

15 ./memory/stack_alloc.hpp_iwyu.txt 15 ./math/seq_view.hpp_iwyu.txt 15 ./math/matrix/stan_print.hpp_iwyu.txt 15 ./math/matrix/initialize.hpp_iwyu.txt 15 ./math/matrix/col.hpp_iwyu.txt 15 ./math/functions/log_sum_exp.hpp_iwyu.txt 15 ./math/error_handling/matrix/check_ldlt_factor.hpp_iwyu.txt 15 ./gm/arguments/arg_output.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize.hpp_iwyu.txt 15 ./gm/arguments/arg_optimize_algo.hpp_iwyu.txt 15 ./gm/arguments/arg_metric.hpp_iwyu.txt 15 ./gm/arguments/arg_method.hpp_iwyu.txt 15 ./common/do_bfgs_optimize.hpp_iwyu.txt 15 ./agrad/rev/jacobian.hpp_iwyu.txt 15 ./agrad/rev/error_handling/matrix.hpp_iwyu.txt

14 ./optimization/bfgs_linesearch.hpp_iwyu.txt 14 ./mcmc/sample.hpp_iwyu.txt 14 ./math/matrix/singular_values.hpp_iwyu.txt 14 ./math/matrix/rank.hpp_iwyu.txt 14 ./math/matrix/log_determinant_spd.hpp_iwyu.txt 14 ./math/functions/log2.hpp_iwyu.txt 14 ./math/functions/log1m_exp.hpp_iwyu.txt 14 ./math/functions/inverse_softmax.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_std_vector_index.hpp_iwyu.txt 14 ./math/error_handling/matrix/check_square.hpp_iwyu.txt 14 ./gm/arguments/arg_test_gradient.hpp_iwyu.txt 14 ./gm/arguments/arg_sample_algo.hpp_iwyu.txt 14 ./gm/arguments/arg_engine.hpp_iwyu.txt 14 ./gm/arguments/arg_bfgs.hpp_iwyu.txt 14 ./common/recorder/filtered_values.hpp_iwyu.txt 14 ./agrad/agrad_thread_safe.hpp_iwyu.txt 13 ./math/matrix/sum.hpp_iwyu.txt 13 ./math/matrix/sort.hpp_iwyu.txt 13 ./math/matrix/promoter.hpp_iwyu.txt 13 ./math/matrix/prod.hpp_iwyu.txt 13 ./math/matrix/inverse.hpp_iwyu.txt 13 ./math/matrix/fill.hpp_iwyu.txt 13 ./math/matrix/cumulative_sum.hpp_iwyu.txt 13 ./math/functions/log_diff_exp.hpp_iwyu.txt 13 ./math/functions/binomial_coefficient_log.hpp_iwyu.txt 13 ./math/error_handling/matrix/check_matching_dims.hpp_iwyu.txt 13 ./io/var_context.hpp_iwyu.txt 13 ./gm/grammars/whitespace_grammar_def.hpp_iwyu.txt 13 ./gm/arguments/categorical_argument.hpp_iwyu.txt 13 ./gm/arguments/argument.hpp_iwyu.txt 13 ./gm/arguments/arg_tolerance.hpp_iwyu.txt 13 ./gm/arguments/arg_test.hpp_iwyu.txt 13 ./gm/arguments/arg_static.hpp_iwyu.txt 13 ./gm/arguments/arg_random.hpp_iwyu.txt 13 ./gm/arguments/arg_nuts.hpp_iwyu.txt 13 ./gm/arguments/arg_lbfgs.hpp_iwyu.txt 13 ./gm/arguments/arg_diagnose.hpp_iwyu.txt 13 ./gm/arguments/arg_data.hpp_iwyu.txt 13 ./common/recorder/values.hpp_iwyu.txt 13 ./common/recorder.hpp_iwyu.txt 13 ./common/print_progress.hpp_iwyu.txt 13 ./common/init_static_hmc.hpp_iwyu.txt 13 ./common/init_nuts.hpp_iwyu.txt 12 ./optimization/bfgs_update.hpp_iwyu.txt 12 ./mcmc/stepsize_var_adapter.hpp_iwyu.txt 12 ./mcmc/stepsize_covar_adapter.hpp_iwyu.txt 12 ./mcmc/base_mcmc.hpp_iwyu.txt 12 ./math/matrix/trace.hpp_iwyu.txt 12 ./math/matrix/subtract.hpp_iwyu.txt 12 ./math/matrix/rows.hpp_iwyu.txt 12 ./math/matrix/elt_multiply.hpp_iwyu.txt 12 ./math/matrix/elt_divide.hpp_iwyu.txt 12 ./math/matrix/divide.hpp_iwyu.txt 12 ./math/matrix/diag_pre_multiply.hpp_iwyu.txt 12 ./math/matrix/diag_post_multiply.hpp_iwyu.txt 12 ./math/matrix/diagonal.hpp_iwyu.txt 12 ./math/matrix/diag_matrix.hpp_iwyu.txt 12 ./math/matrix/common_type.hpp_iwyu.txt 12 ./math/matrix/cols.hpp_iwyu.txt 12 ./math/matrix/add.hpp_iwyu.txt 12 ./math/functions/trigamma.hpp_iwyu.txt 12 ./math/error_handling/matrix/check_size_match.hpp_iwyu.txt 12 ./gm/grammars/whitespace_grammar.hpp_iwyu.txt 12 ./gm/arguments/valued_argument.hpp_iwyu.txt 12 ./gm/arguments/unvalued_argument.hpp_iwyu.txt 12 ./common/recorder/sum_values.hpp_iwyu.txt 12 ./agrad/fwd/matrix/sum.hpp_iwyu.txt 11 ./math/rep_array.hpp_iwyu.txt

11 ./math/matrix/sort_indices.hpp_iwyu.txt 11 ./math/matrix/log_determinant.hpp_iwyu.txt 11 ./math/matrix/dims.hpp_iwyu.txt 11 ./math/matrix/determinant.hpp_iwyu.txt 11 ./math/functions/Phi_approx.hpp_iwyu.txt 11 ./math/functions/log1p.hpp_iwyu.txt 11 ./math/functions/log1p_exp.hpp_iwyu.txt 11 ./math/error_handling/matrix/validate_non_negative_index.hpp_iwyu.txt 11 ./math/error_handling/matrix/check_range.hpp_iwyu.txt 11 ./math/error_handling/check_positive_finite.hpp_iwyu.txt

11 ./gm/grammars/iterator_typedefs.hpp_iwyu.txt 11 ./gm/arguments/argument_probe.hpp_iwyu.txt 11 ./common/write_iteration.hpp_iwyu.txt 11 ./common/write_iteration_csv.hpp_iwyu.txt 11 ./common/write_error_msg.hpp_iwyu.txt 10 ./math/matrix/transpose.hpp_iwyu.txt 10 ./math/matrix/rows_dot_self.hpp_iwyu.txt 10 ./math/matrix/log.hpp_iwyu.txt 10 ./math/matrix/log_determinant_ldlt.hpp_iwyu.txt 10 ./math/matrix/exp.hpp_iwyu.txt 10 ./math/matrix/columns_dot_self.hpp_iwyu.txt 10 ./math/functions/rising_factorial.hpp_iwyu.txt 10 ./math/functions/multiply_log.hpp_iwyu.txt 10 ./math/functions/modulus.hpp_iwyu.txt

10 ./math/functions/log_rising_factorial.hpp_iwyu.txt 10 ./math/functions/logit.hpp_iwyu.txt 10 ./math/functions/log_inv_logit.hpp_iwyu.txt 10 ./math/functions/log_falling_factorial.hpp_iwyu.txt 10 ./math/functions/log1m_inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_sqrt.hpp_iwyu.txt 10 ./math/functions/inv_logit.hpp_iwyu.txt 10 ./math/functions/inv_cloglog.hpp_iwyu.txt 10 ./math/functions/falling_factorial.hpp_iwyu.txt 10 ./math/functions/exp2.hpp_iwyu.txt 10 ./math/functions/divide.hpp_iwyu.txt

10 ./math/functions/binary_log_loss.hpp_iwyu.txt 10 ./io/json/json_error.hpp_iwyu.txt 10 ./gm/arguments/arg_unit_e.hpp_iwyu.txt 10 ./gm/arguments/arg_thin.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_err.hpp_iwyu.txt 10 ./gm/arguments/arg_test_grad_eps.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize_jitter.hpp_iwyu.txt 10 ./gm/arguments/arg_stepsize.hpp_iwyu.txt 10 ./gm/arguments/arg_seed.hpp_iwyu.txt 10 ./gm/arguments/arg_save_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_save_iterations.hpp_iwyu.txt 10 ./gm/arguments/arg_rwm.hpp_iwyu.txt 10 ./gm/arguments/arg_refresh.hpp_iwyu.txt 10 ./gm/arguments/arg_output_file.hpp_iwyu.txt 10 ./gm/arguments/arg_num_warmup.hpp_iwyu.txt 10 ./gm/arguments/arg_num_samples.hpp_iwyu.txt 10 ./gm/arguments/arg_newton.hpp_iwyu.txt 10 ./gm/arguments/arg_max_depth.hpp_iwyu.txt 10 ./gm/arguments/arg_iter.hpp_iwyu.txt 10 ./gm/arguments/arg_int_time.hpp_iwyu.txt 10 ./gm/arguments/arg_init.hpp_iwyu.txt 10 ./gm/arguments/arg_init_alpha.hpp_iwyu.txt 10 ./gm/arguments/arg_id.hpp_iwyu.txt 10 ./gm/arguments/arg_history_size.hpp_iwyu.txt 10 ./gm/arguments/arg_fixed_param.hpp_iwyu.txt 10 ./gm/arguments/arg_fail.hpp_iwyu.txt 10 ./gm/arguments/arg_diagnostic_file.hpp_iwyu.txt 10 ./gm/arguments/arg_diag_e.hpp_iwyu.txt 10 ./gm/arguments/arg_dense_e.hpp_iwyu.txt 10 ./gm/arguments/arg_data_file.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_window.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_term_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_t0.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_kappa.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_init_buffer.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_gamma.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_engaged.hpp_iwyu.txt 10 ./gm/arguments/arg_adapt_delta.hpp_iwyu.txt 10 ./common/recorder/no_op.hpp_iwyu.txt 10 ./agrad/rev/internal/vvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/v_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/vdd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dv_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/dvd_vari.hpp_iwyu.txt 10 ./agrad/rev/internal/ddv_vari.hpp_iwyu.txt 10 ./agrad/rev/calculate_chain.hpp_iwyu.txt 9 ./math/matrix/Eigen.hpp_iwyu.txt 9 ./agrad/fwd/functions/fma.hpp_iwyu.txt 8 ./memory.hpp_iwyu.txt 8 ./gm.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_plus.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_unary_not.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_plus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_not_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_multiply_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_minus_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_less_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than_or_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_greater_than.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_equal.hpp_iwyu.txt 8 ./agrad/rev/operators/operator_divide_equal.hpp_iwyu.txt 8 ./agrad/rev/matrix/stan_print.hpp_iwyu.txt 8 ./agrad/rev/functions/if_else.hpp_iwyu.txt

5 ./math/error_handling/matrix/constraint_tolerance.hpp_iwyu.txt 2 ./version.hpp_iwyu.txt 2 ./mcmc/windowed_adaptation.hpp_iwyu.txt 2 ./mcmc/stepsize_adapter.hpp_iwyu.txt 2 ./mcmc/stepsize_adaptation.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_leapfrog.hpp_iwyu.txt 2 ./mcmc/hmc/integrators/base_integrator.hpp_iwyu.txt 2 ./mcmc/hmc/hamiltonians/unit_e_point.hpp_iwyu.txt 2 ./mcmc/fixed_param_sampler.hpp_iwyu.txt 2 ./mcmc/base_adapter.hpp_iwyu.txt 2 ./mcmc/base_adaptation.hpp_iwyu.txt 2 ./math/matrix/size.hpp_iwyu.txt 2 ./math/matrix/promote_common.hpp_iwyu.txt 2 ./math/matrix/minus.hpp_iwyu.txt 2 ./math/matrix/array_builder.hpp_iwyu.txt 2 ./math/functions/value_of.hpp_iwyu.txt 2 ./math/functions/sum.hpp_iwyu.txt 2 ./math/functions/sub.hpp_iwyu.txt 2 ./math/functions/step.hpp_iwyu.txt 2 ./math/functions/square.hpp_iwyu.txt 2 ./math/functions/sign.hpp_iwyu.txt 2 ./math/functions/scaled_add.hpp_iwyu.txt 2 ./math/functions/Phi.hpp_iwyu.txt 2 ./math/functions/owens_t.hpp_iwyu.txt 2 ./math/functions/modified_bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/modified_bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/min.hpp_iwyu.txt 2 ./math/functions/max.hpp_iwyu.txt 2 ./math/functions/logical_or.hpp_iwyu.txt 2 ./math/functions/logical_neq.hpp_iwyu.txt 2 ./math/functions/logical_negation.hpp_iwyu.txt 2 ./math/functions/logical_lt.hpp_iwyu.txt 2 ./math/functions/logical_lte.hpp_iwyu.txt 2 ./math/functions/logical_gt.hpp_iwyu.txt 2 ./math/functions/logical_gte.hpp_iwyu.txt 2 ./math/functions/logical_eq.hpp_iwyu.txt 2 ./math/functions/logical_and.hpp_iwyu.txt 2 ./math/functions/log1m.hpp_iwyu.txt 2 ./math/functions/lmgamma.hpp_iwyu.txt 2 ./math/functions/lbeta.hpp_iwyu.txt 2 ./math/functions/is_uninitialized.hpp_iwyu.txt 2 ./math/functions/inv_square.hpp_iwyu.txt 2 ./math/functions/inv.hpp_iwyu.txt 2 ./math/functions/int_step.hpp_iwyu.txt 2 ./math/functions/if_else.hpp_iwyu.txt 2 ./math/functions/fma.hpp_iwyu.txt 2 ./math/functions/fdim.hpp_iwyu.txt 2 ./math/functions/dot_self.hpp_iwyu.txt 2 ./math/functions/dot.hpp_iwyu.txt 2 ./math/functions/dist.hpp_iwyu.txt 2 ./math/functions/bessel_second_kind.hpp_iwyu.txt 2 ./math/functions/bessel_first_kind.hpp_iwyu.txt 2 ./math/functions/as_bool.hpp_iwyu.txt 2 ./math/functions/abs.hpp_iwyu.txt 2 ./io/util.hpp_iwyu.txt 2 ./io/json/json_handler.hpp_iwyu.txt 2 ./gm/error_codes.hpp_iwyu.txt 2 ./gm/compiler.hpp_iwyu.txt 2 ./common/write_stan.hpp_iwyu.txt 2 ./common/write_model.hpp_iwyu.txt 2 ./common/recorder/messages.hpp_iwyu.txt 2 ./common/recorder/csv.hpp_iwyu.txt 2 ./common/do_print.hpp_iwyu.txt 2 ./agrad/rev/error_handling.hpp_iwyu.txt 2 ./agrad.hpp_iwyu.txt 2 ./agrad/fwd/fvar.hpp_iwyu.txt

—

Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51705460.

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51808202.

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51808909.

[syclik]

(sorry -- my language skills aren't working so well today)

We can review each change by hand if they're a small enough number and discuss on the pull request.

[bgoodri]

Done: https://github.com/stan-dev/stan/tree/iwyu

On Mon, Aug 11, 2014 at 1:07 PM, Daniel Lee notifications@github.com wrote:

(sorry -- my language skills aren't working so well today)

We can review each change by hand if they're a small enough number and discuss on the pull request.

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51809331.

[syclik]

I'm starting to spot-check some of the changes. Questions:

• why does it prefer a certain include order? (src/stan/agrad/agrad_thread_safe.hpp)
• why does it switch between including within quotes and including with angle brackets? (src/stan/agrad/autodiff.hpp)
• what's going on with src/stan/agrad/fwd/functions/lgamma.hpp? What's with the include of the booth's math_fwd.hpp?

If we're going to create pull requests, can we break them into smaller chunks of files? I think I'm happy with most of the changes; it's just hard to review everything since so many files are changing.

On Wed, Aug 13, 2014 at 11:45 AM, bgoodri notifications@github.com wrote:

Done: https://github.com/stan-dev/stan/tree/iwyu

On Mon, Aug 11, 2014 at 1:07 PM, Daniel Lee notifications@github.com wrote:

(sorry -- my language skills aren't working so well today)

We can review each change by hand if they're a small enough number and discuss on the pull request.

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-51809331.

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/stan/issues/225#issuecomment-52067064.

[bgoodri]

On Thu, Aug 14, 2014 at 1:06 AM, Daniel Lee notifications@github.com wrote:

I'm starting to spot-check some of the changes. Questions:

• why does it prefer a certain include order? (src/stan/agrad/agrad_thread_safe.hpp)

Don't know. Reordering is possibly wrong for some of the parser stuff.

• why does it switch between including within quotes and including with angle brackets? (src/stan/agrad/autodiff.hpp)

I think that is part of the Google style.

• what's going on with src/stan/agrad/fwd/functions/lgamma.hpp? What's with the include of the booth's math_fwd.hpp?

That is where lgamma is declared.

If we're going to create pull requests, can we break them into smaller chunks of files? I think I'm happy with most of the changes; it's just hard to review everything since so many files are changing.

It's probably a long way from a pull request. And it is primarily a question of getting things to build, since the functionality doesn't change. But I am not seeing a non-arbitrary way to break it into chunks. Maybe just one chunk for each of the folders under src/stan/ ?

[syclik]

Thanks for the replies. That all made sense.

On Thu, Aug 14, 2014 at 1:26 AM, bgoodri notifications@github.com wrote:

On Thu, Aug 14, 2014 at 1:06 AM, Daniel Lee notifications@github.com wrote:

If we're going to create pull requests, can we break them into smaller chunks of files? I think I'm happy with most of the changes; it's just hard to review everything since so many files are changing.

It's probably a long way from a pull request. And it is primarily a question of getting things to build, since the functionality doesn't change. But I am not seeing a non-arbitrary way to break it into chunks. Maybe just one chunk for each of the folders under src/stan/ ?

Looking at it, didn't seem too far off. We could verify that builds before we commit.

Yes, chunks would be arbitrary, but hopefully limiting it to a reasonable number of files per pull request will make it easier to review.

[bob-carpenter]

Consolidated into #811