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Andrew Johnson
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Merge branch 'develop' into feature/vec_gen_design
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‎doxygen/contributor_help_pages/distribution_tests.md

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The types of arguments that are valid are: `Int`, `Double`, `Ints`, and `Doubles`. The first two indicate that the argument is not vectorized and only takes single, scalar values. The last two plural versions indicate that the argument types are vectorized.
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3. The next lines are includes. Most of the files will have:
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```
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\#include <stan/math/prim/scal.hpp>
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\#include <stan/math/prim.hpp>
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\#include <stdexcept>
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```

‎runChecks.py

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},
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]
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errors.extend(grep_patterns("rev", "stan/math/rev", rev_checks))
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# Check for files inside stan/math/*/scal that contain stan/math/*/arr or stan/math/*/mat
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scal_checks = [
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{
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"pattern": "<stan/math/.*/arr/",
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"message": "File includes an array header file.",
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},
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{"pattern": "<vector>", "message": "File includes an std::vector header."},
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{"pattern": "std::vector", "message": "File uses std::vector."},
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{
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"pattern": "<stan/math/.*/mat/",
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"message": "File includes a matrix header file.",
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},
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{"pattern": "<Eigen", "message": "File includes an Eigen header."},
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{"pattern": "Eigen::", "message": "File uses Eigen."},
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]
194-
errors.extend(grep_patterns("scal", "stan/math/*/scal", scal_checks))
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# Check for files inside stan/math/*/arr that contain stan/math/*/mat or Eigen
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arr_checks = [
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{
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"pattern": "<stan/math/.*/mat/",
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"message": "File includes an matrix header file.",
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},
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{"pattern": "<Eigen", "message": "File includes an Eigen header."},
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{"pattern": "Eigen::", "message": "File uses Eigen."},
204-
]
205-
errors.extend(grep_patterns("arr", "stan/math/*/arr", arr_checks))
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# Check to make sure we use C++14 constructs in stan/math
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cpp14_checks = [
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{
@@ -257,16 +229,6 @@ def main():
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]
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errors.extend(grep_patterns("C++14", "stan/math", cpp14_checks))
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# Check for includes of stan/math/*/meta/*.hpp inside stan/math, excluding meta.hpp files and the /meta subfolder
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meta_checks = [
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{
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"pattern": "<stan/math/.*/meta/.*hpp",
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"message": "File includes */meta/*.hpp header file. Should include meta.hpp",
265-
}
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]
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meta_exclude = ["stan/math/*/meta", "stan/math/*/meta.hpp"]
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errors.extend(grep_patterns("meta", "stan/math", meta_checks, meta_exclude))
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# Check that we do not use non-reentrant safe functions from std
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thread_safe_checks = [
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{

‎runTests.py

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tests_help_msg = "The path(s) to the test case(s) to run.\n"
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tests_help_msg += "Example: 'test/unit', 'test/prob', and/or\n"
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tests_help_msg += " 'test/unit/math/prim/scal/fun/abs_test.cpp'"
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tests_help_msg += " 'test/unit/math/prim/fun/abs_test.cpp'"
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parser.add_argument("tests", nargs="+", type=str,
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help=tests_help_msg)
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f_help_msg = "Only tests with file names matching these will be executed.\n"

‎stan/math/fwd.hpp

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#ifndef STAN_MATH_FWD_HPP
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#define STAN_MATH_FWD_HPP
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#include <stan/math/prim/mat/fun/Eigen.hpp>
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#include <stan/math/prim/fun/Eigen.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/vectorize.hpp>
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#include <stan/math/prim/arr.hpp>
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#include <stan/math/prim/mat.hpp>
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#include <stan/math/prim/scal.hpp>
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#include <stan/math/prim.hpp>
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#include <stan/math/fwd/fun.hpp>
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#include <stan/math/fwd/functor.hpp>

‎stan/math/fwd/core/fvar.hpp

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#define STAN_MATH_FWD_CORE_FVAR_HPP
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#include <stan/math/prim/meta.hpp>
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#include <stan/math/prim/scal/fun/is_nan.hpp>
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#include <stan/math/prim/fun/is_nan.hpp>
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#include <ostream>
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#include <type_traits>
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‎stan/math/fwd/fun/Eigen_NumTraits.hpp

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#include <stan/math/fwd/core.hpp>
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#include <stan/math/fwd/core/std_numeric_limits.hpp>
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#include <stan/math/prim/mat/fun/Eigen.hpp>
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#include <stan/math/prim/fun/Eigen.hpp>
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#include <limits>
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namespace Eigen {

‎stan/math/fwd/fun/Phi.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/constants.hpp>
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#include <stan/math/prim/scal/fun/Phi.hpp>
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#include <stan/math/prim/fun/constants.hpp>
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#include <stan/math/prim/fun/Phi.hpp>
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#include <cmath>
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namespace stan {

‎stan/math/fwd/fun/Phi_approx.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/inv_logit.hpp>
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#include <stan/math/prim/fun/inv_logit.hpp>
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#include <cmath>
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namespace stan {

‎stan/math/fwd/fun/abs.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/constants.hpp>
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#include <stan/math/prim/scal/fun/abs.hpp>
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#include <stan/math/prim/scal/fun/value_of.hpp>
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#include <stan/math/prim/fun/constants.hpp>
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#include <stan/math/prim/fun/abs.hpp>
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#include <stan/math/prim/fun/value_of.hpp>
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namespace stan {
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namespace math {

‎stan/math/fwd/fun/acos.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/square.hpp>
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#include <cmath>
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namespace stan {

‎stan/math/fwd/fun/acosh.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/acosh.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/acosh.hpp>
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#include <stan/math/prim/fun/square.hpp>
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#include <cmath>
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namespace stan {

‎stan/math/fwd/fun/asin.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/square.hpp>
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#include <cmath>
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namespace stan {

‎stan/math/fwd/fun/asinh.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/asinh.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/asinh.hpp>
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#include <stan/math/prim/fun/square.hpp>
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#include <cmath>
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‎stan/math/fwd/fun/atan.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/square.hpp>
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#include <cmath>
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namespace stan {

‎stan/math/fwd/fun/atan2.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/square.hpp>
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namespace stan {

‎stan/math/fwd/fun/atanh.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/atanh.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/atanh.hpp>
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#include <stan/math/prim/fun/square.hpp>
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namespace stan {
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namespace math {

‎stan/math/fwd/fun/bessel_first_kind.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/bessel_first_kind.hpp>
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#include <stan/math/prim/fun/bessel_first_kind.hpp>
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namespace stan {
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‎stan/math/fwd/fun/bessel_second_kind.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/bessel_second_kind.hpp>
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#include <stan/math/prim/fun/bessel_second_kind.hpp>
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‎stan/math/fwd/fun/beta.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/beta.hpp>
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#include <stan/math/prim/scal/fun/digamma.hpp>
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#include <stan/math/prim/fun/beta.hpp>
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#include <stan/math/prim/fun/digamma.hpp>
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‎stan/math/fwd/fun/binary_log_loss.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/binary_log_loss.hpp>
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#include <stan/math/prim/fun/binary_log_loss.hpp>
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‎stan/math/fwd/fun/cbrt.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/cbrt.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/cbrt.hpp>
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#include <stan/math/prim/fun/square.hpp>
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‎stan/math/fwd/fun/columns_dot_product.hpp

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#define STAN_MATH_FWD_FUN_COLUMNS_DOT_PRODUCT_HPP
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#include <stan/math/prim/err.hpp>
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#include <stan/math/prim/mat/fun/Eigen.hpp>
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#include <stan/math/prim/fun/Eigen.hpp>
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#include <stan/math/fwd/fun/typedefs.hpp>
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#include <stan/math/fwd/core.hpp>
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‎stan/math/fwd/fun/columns_dot_self.hpp

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#ifndef STAN_MATH_FWD_FUN_COLUMNS_DOT_SELF_HPP
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#define STAN_MATH_FWD_FUN_COLUMNS_DOT_SELF_HPP
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#include <stan/math/prim/mat/fun/Eigen.hpp>
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#include <stan/math/prim/fun/Eigen.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/fwd/fun/dot_self.hpp>
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‎stan/math/fwd/fun/crossprod.hpp

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#ifndef STAN_MATH_FWD_FUN_CROSSPROD_HPP
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#include <stan/math/prim/mat/fun/Eigen.hpp>
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#include <stan/math/prim/fun/Eigen.hpp>
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#include <stan/math/prim/fun/transpose.hpp>
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#include <stan/math/fwd/fun/multiply.hpp>
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#include <stan/math/prim/mat/fun/transpose.hpp>
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‎stan/math/fwd/fun/determinant.hpp

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#define STAN_MATH_FWD_FUN_DETERMINANT_HPP
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#include <stan/math/prim/err.hpp>
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#include <stan/math/prim/mat/fun/Eigen.hpp>
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#include <stan/math/prim/fun/Eigen.hpp>
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#include <stan/math/fwd/core.hpp>
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‎stan/math/fwd/fun/digamma.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/digamma.hpp>
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#include <stan/math/prim/scal/fun/trigamma.hpp>
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#include <stan/math/prim/fun/digamma.hpp>
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#include <stan/math/prim/fun/trigamma.hpp>
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‎stan/math/fwd/fun/divide.hpp

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#ifndef STAN_MATH_FWD_FUN_DIVIDE_HPP
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#define STAN_MATH_FWD_FUN_DIVIDE_HPP
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#include <stan/math/prim/mat/fun/Eigen.hpp>
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#include <stan/math/prim/fun/Eigen.hpp>
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‎stan/math/fwd/fun/dot_product.hpp

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#define STAN_MATH_FWD_FUN_DOT_PRODUCT_HPP
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#include <stan/math/prim/err.hpp>
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#include <stan/math/prim/fun/Eigen.hpp>
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#include <stan/math/fwd/fun/typedefs.hpp>
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#include <vector>
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‎stan/math/fwd/fun/dot_self.hpp

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#define STAN_MATH_FWD_FUN_DOT_SELF_HPP
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#include <stan/math/prim/err.hpp>
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#include <stan/math/prim/mat/fun/Eigen.hpp>
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#include <stan/math/prim/fun/Eigen.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/fwd/fun/dot_product.hpp>
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‎stan/math/fwd/fun/erf.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/prim/scal/fun/constants.hpp>
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#include <stan/math/prim/scal/fun/erf.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/constants.hpp>
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#include <stan/math/prim/fun/erf.hpp>
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#include <stan/math/prim/fun/square.hpp>
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‎stan/math/fwd/fun/erfc.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/constants.hpp>
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#include <stan/math/prim/scal/fun/erfc.hpp>
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#include <stan/math/prim/scal/fun/square.hpp>
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#include <stan/math/prim/fun/constants.hpp>
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#include <stan/math/prim/fun/erfc.hpp>
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#include <stan/math/prim/fun/square.hpp>
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‎stan/math/fwd/fun/exp2.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/exp2.hpp>
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#include <stan/math/prim/fun/exp2.hpp>
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#include <stan/math/prim/fun/constants.hpp>
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‎stan/math/fwd/fun/expm1.hpp

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#ifndef STAN_MATH_FWD_FUN_EXPM1_HPP
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#include <stan/math/prim/fun/expm1.hpp>
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#include <stan/math/prim/scal/fun/expm1.hpp>
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‎stan/math/fwd/fun/fabs.hpp

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#include <stan/math/fwd/meta.hpp>
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#include <stan/math/fwd/core.hpp>
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#include <stan/math/prim/scal/fun/constants.hpp>
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#include <stan/math/prim/scal/fun/is_nan.hpp>
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#include <stan/math/prim/scal/fun/value_of.hpp>
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#include <stan/math/prim/fun/constants.hpp>
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#include <stan/math/prim/fun/is_nan.hpp>
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#include <stan/math/prim/fun/value_of.hpp>
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namespace stan {

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