Mercurial > hg > sv-dependency-builds
diff any/include/boost/math/distributions/negative_binomial.hpp @ 160:cff480c41f97
Add some cross-platform Boost headers
author | Chris Cannam <cannam@all-day-breakfast.com> |
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date | Sat, 16 Feb 2019 16:31:25 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/any/include/boost/math/distributions/negative_binomial.hpp Sat Feb 16 16:31:25 2019 +0000 @@ -0,0 +1,607 @@ +// boost\math\special_functions\negative_binomial.hpp + +// Copyright Paul A. Bristow 2007. +// Copyright John Maddock 2007. + +// Use, modification and distribution are subject to the +// Boost Software License, Version 1.0. +// (See accompanying file LICENSE_1_0.txt +// or copy at http://www.boost.org/LICENSE_1_0.txt) + +// http://en.wikipedia.org/wiki/negative_binomial_distribution +// http://mathworld.wolfram.com/NegativeBinomialDistribution.html +// http://documents.wolfram.com/teachersedition/Teacher/Statistics/DiscreteDistributions.html + +// The negative binomial distribution NegativeBinomialDistribution[n, p] +// is the distribution of the number (k) of failures that occur in a sequence of trials before +// r successes have occurred, where the probability of success in each trial is p. + +// In a sequence of Bernoulli trials or events +// (independent, yes or no, succeed or fail) with success_fraction probability p, +// negative_binomial is the probability that k or fewer failures +// preceed the r th trial's success. +// random variable k is the number of failures (NOT the probability). + +// Negative_binomial distribution is a discrete probability distribution. +// But note that the negative binomial distribution +// (like others including the binomial, Poisson & Bernoulli) +// is strictly defined as a discrete function: only integral values of k are envisaged. +// However because of the method of calculation using a continuous gamma function, +// it is convenient to treat it as if a continous function, +// and permit non-integral values of k. + +// However, by default the policy is to use discrete_quantile_policy. + +// To enforce the strict mathematical model, users should use conversion +// on k outside this function to ensure that k is integral. + +// MATHCAD cumulative negative binomial pnbinom(k, n, p) + +// Implementation note: much greater speed, and perhaps greater accuracy, +// might be achieved for extreme values by using a normal approximation. +// This is NOT been tested or implemented. + +#ifndef BOOST_MATH_SPECIAL_NEGATIVE_BINOMIAL_HPP +#define BOOST_MATH_SPECIAL_NEGATIVE_BINOMIAL_HPP + +#include <boost/math/distributions/fwd.hpp> +#include <boost/math/special_functions/beta.hpp> // for ibeta(a, b, x) == Ix(a, b). +#include <boost/math/distributions/complement.hpp> // complement. +#include <boost/math/distributions/detail/common_error_handling.hpp> // error checks domain_error & logic_error. +#include <boost/math/special_functions/fpclassify.hpp> // isnan. +#include <boost/math/tools/roots.hpp> // for root finding. +#include <boost/math/distributions/detail/inv_discrete_quantile.hpp> + +#include <boost/type_traits/is_floating_point.hpp> +#include <boost/type_traits/is_integral.hpp> +#include <boost/type_traits/is_same.hpp> +#include <boost/mpl/if.hpp> + +#include <limits> // using std::numeric_limits; +#include <utility> + +#if defined (BOOST_MSVC) +# pragma warning(push) +// This believed not now necessary, so commented out. +//# pragma warning(disable: 4702) // unreachable code. +// in domain_error_imp in error_handling. +#endif + +namespace boost +{ + namespace math + { + namespace negative_binomial_detail + { + // Common error checking routines for negative binomial distribution functions: + template <class RealType, class Policy> + inline bool check_successes(const char* function, const RealType& r, RealType* result, const Policy& pol) + { + if( !(boost::math::isfinite)(r) || (r <= 0) ) + { + *result = policies::raise_domain_error<RealType>( + function, + "Number of successes argument is %1%, but must be > 0 !", r, pol); + return false; + } + return true; + } + template <class RealType, class Policy> + inline bool check_success_fraction(const char* function, const RealType& p, RealType* result, const Policy& pol) + { + if( !(boost::math::isfinite)(p) || (p < 0) || (p > 1) ) + { + *result = policies::raise_domain_error<RealType>( + function, + "Success fraction argument is %1%, but must be >= 0 and <= 1 !", p, pol); + return false; + } + return true; + } + template <class RealType, class Policy> + inline bool check_dist(const char* function, const RealType& r, const RealType& p, RealType* result, const Policy& pol) + { + return check_success_fraction(function, p, result, pol) + && check_successes(function, r, result, pol); + } + template <class RealType, class Policy> + inline bool check_dist_and_k(const char* function, const RealType& r, const RealType& p, RealType k, RealType* result, const Policy& pol) + { + if(check_dist(function, r, p, result, pol) == false) + { + return false; + } + if( !(boost::math::isfinite)(k) || (k < 0) ) + { // Check k failures. + *result = policies::raise_domain_error<RealType>( + function, + "Number of failures argument is %1%, but must be >= 0 !", k, pol); + return false; + } + return true; + } // Check_dist_and_k + + template <class RealType, class Policy> + inline bool check_dist_and_prob(const char* function, const RealType& r, RealType p, RealType prob, RealType* result, const Policy& pol) + { + if((check_dist(function, r, p, result, pol) && detail::check_probability(function, prob, result, pol)) == false) + { + return false; + } + return true; + } // check_dist_and_prob + } // namespace negative_binomial_detail + + template <class RealType = double, class Policy = policies::policy<> > + class negative_binomial_distribution + { + public: + typedef RealType value_type; + typedef Policy policy_type; + + negative_binomial_distribution(RealType r, RealType p) : m_r(r), m_p(p) + { // Constructor. + RealType result; + negative_binomial_detail::check_dist( + "negative_binomial_distribution<%1%>::negative_binomial_distribution", + m_r, // Check successes r > 0. + m_p, // Check success_fraction 0 <= p <= 1. + &result, Policy()); + } // negative_binomial_distribution constructor. + + // Private data getter class member functions. + RealType success_fraction() const + { // Probability of success as fraction in range 0 to 1. + return m_p; + } + RealType successes() const + { // Total number of successes r. + return m_r; + } + + static RealType find_lower_bound_on_p( + RealType trials, + RealType successes, + RealType alpha) // alpha 0.05 equivalent to 95% for one-sided test. + { + static const char* function = "boost::math::negative_binomial<%1%>::find_lower_bound_on_p"; + RealType result = 0; // of error checks. + RealType failures = trials - successes; + if(false == detail::check_probability(function, alpha, &result, Policy()) + && negative_binomial_detail::check_dist_and_k( + function, successes, RealType(0), failures, &result, Policy())) + { + return result; + } + // Use complement ibeta_inv function for lower bound. + // This is adapted from the corresponding binomial formula + // here: http://www.itl.nist.gov/div898/handbook/prc/section2/prc241.htm + // This is a Clopper-Pearson interval, and may be overly conservative, + // see also "A Simple Improved Inferential Method for Some + // Discrete Distributions" Yong CAI and K. KRISHNAMOORTHY + // http://www.ucs.louisiana.edu/~kxk4695/Discrete_new.pdf + // + return ibeta_inv(successes, failures + 1, alpha, static_cast<RealType*>(0), Policy()); + } // find_lower_bound_on_p + + static RealType find_upper_bound_on_p( + RealType trials, + RealType successes, + RealType alpha) // alpha 0.05 equivalent to 95% for one-sided test. + { + static const char* function = "boost::math::negative_binomial<%1%>::find_upper_bound_on_p"; + RealType result = 0; // of error checks. + RealType failures = trials - successes; + if(false == negative_binomial_detail::check_dist_and_k( + function, successes, RealType(0), failures, &result, Policy()) + && detail::check_probability(function, alpha, &result, Policy())) + { + return result; + } + if(failures == 0) + return 1; + // Use complement ibetac_inv function for upper bound. + // Note adjusted failures value: *not* failures+1 as usual. + // This is adapted from the corresponding binomial formula + // here: http://www.itl.nist.gov/div898/handbook/prc/section2/prc241.htm + // This is a Clopper-Pearson interval, and may be overly conservative, + // see also "A Simple Improved Inferential Method for Some + // Discrete Distributions" Yong CAI and K. KRISHNAMOORTHY + // http://www.ucs.louisiana.edu/~kxk4695/Discrete_new.pdf + // + return ibetac_inv(successes, failures, alpha, static_cast<RealType*>(0), Policy()); + } // find_upper_bound_on_p + + // Estimate number of trials : + // "How many trials do I need to be P% sure of seeing k or fewer failures?" + + static RealType find_minimum_number_of_trials( + RealType k, // number of failures (k >= 0). + RealType p, // success fraction 0 <= p <= 1. + RealType alpha) // risk level threshold 0 <= alpha <= 1. + { + static const char* function = "boost::math::negative_binomial<%1%>::find_minimum_number_of_trials"; + // Error checks: + RealType result = 0; + if(false == negative_binomial_detail::check_dist_and_k( + function, RealType(1), p, k, &result, Policy()) + && detail::check_probability(function, alpha, &result, Policy())) + { return result; } + + result = ibeta_inva(k + 1, p, alpha, Policy()); // returns n - k + return result + k; + } // RealType find_number_of_failures + + static RealType find_maximum_number_of_trials( + RealType k, // number of failures (k >= 0). + RealType p, // success fraction 0 <= p <= 1. + RealType alpha) // risk level threshold 0 <= alpha <= 1. + { + static const char* function = "boost::math::negative_binomial<%1%>::find_maximum_number_of_trials"; + // Error checks: + RealType result = 0; + if(false == negative_binomial_detail::check_dist_and_k( + function, RealType(1), p, k, &result, Policy()) + && detail::check_probability(function, alpha, &result, Policy())) + { return result; } + + result = ibetac_inva(k + 1, p, alpha, Policy()); // returns n - k + return result + k; + } // RealType find_number_of_trials complemented + + private: + RealType m_r; // successes. + RealType m_p; // success_fraction + }; // template <class RealType, class Policy> class negative_binomial_distribution + + typedef negative_binomial_distribution<double> negative_binomial; // Reserved name of type double. + + template <class RealType, class Policy> + inline const std::pair<RealType, RealType> range(const negative_binomial_distribution<RealType, Policy>& /* dist */) + { // Range of permissible values for random variable k. + using boost::math::tools::max_value; + return std::pair<RealType, RealType>(static_cast<RealType>(0), max_value<RealType>()); // max_integer? + } + + template <class RealType, class Policy> + inline const std::pair<RealType, RealType> support(const negative_binomial_distribution<RealType, Policy>& /* dist */) + { // Range of supported values for random variable k. + // This is range where cdf rises from 0 to 1, and outside it, the pdf is zero. + using boost::math::tools::max_value; + return std::pair<RealType, RealType>(static_cast<RealType>(0), max_value<RealType>()); // max_integer? + } + + template <class RealType, class Policy> + inline RealType mean(const negative_binomial_distribution<RealType, Policy>& dist) + { // Mean of Negative Binomial distribution = r(1-p)/p. + return dist.successes() * (1 - dist.success_fraction() ) / dist.success_fraction(); + } // mean + + //template <class RealType, class Policy> + //inline RealType median(const negative_binomial_distribution<RealType, Policy>& dist) + //{ // Median of negative_binomial_distribution is not defined. + // return policies::raise_domain_error<RealType>(BOOST_CURRENT_FUNCTION, "Median is not implemented, result is %1%!", std::numeric_limits<RealType>::quiet_NaN()); + //} // median + // Now implemented via quantile(half) in derived accessors. + + template <class RealType, class Policy> + inline RealType mode(const negative_binomial_distribution<RealType, Policy>& dist) + { // Mode of Negative Binomial distribution = floor[(r-1) * (1 - p)/p] + BOOST_MATH_STD_USING // ADL of std functions. + return floor((dist.successes() -1) * (1 - dist.success_fraction()) / dist.success_fraction()); + } // mode + + template <class RealType, class Policy> + inline RealType skewness(const negative_binomial_distribution<RealType, Policy>& dist) + { // skewness of Negative Binomial distribution = 2-p / (sqrt(r(1-p)) + BOOST_MATH_STD_USING // ADL of std functions. + RealType p = dist.success_fraction(); + RealType r = dist.successes(); + + return (2 - p) / + sqrt(r * (1 - p)); + } // skewness + + template <class RealType, class Policy> + inline RealType kurtosis(const negative_binomial_distribution<RealType, Policy>& dist) + { // kurtosis of Negative Binomial distribution + // http://en.wikipedia.org/wiki/Negative_binomial is kurtosis_excess so add 3 + RealType p = dist.success_fraction(); + RealType r = dist.successes(); + return 3 + (6 / r) + ((p * p) / (r * (1 - p))); + } // kurtosis + + template <class RealType, class Policy> + inline RealType kurtosis_excess(const negative_binomial_distribution<RealType, Policy>& dist) + { // kurtosis excess of Negative Binomial distribution + // http://mathworld.wolfram.com/Kurtosis.html table of kurtosis_excess + RealType p = dist.success_fraction(); + RealType r = dist.successes(); + return (6 - p * (6-p)) / (r * (1-p)); + } // kurtosis_excess + + template <class RealType, class Policy> + inline RealType variance(const negative_binomial_distribution<RealType, Policy>& dist) + { // Variance of Binomial distribution = r (1-p) / p^2. + return dist.successes() * (1 - dist.success_fraction()) + / (dist.success_fraction() * dist.success_fraction()); + } // variance + + // RealType standard_deviation(const negative_binomial_distribution<RealType, Policy>& dist) + // standard_deviation provided by derived accessors. + // RealType hazard(const negative_binomial_distribution<RealType, Policy>& dist) + // hazard of Negative Binomial distribution provided by derived accessors. + // RealType chf(const negative_binomial_distribution<RealType, Policy>& dist) + // chf of Negative Binomial distribution provided by derived accessors. + + template <class RealType, class Policy> + inline RealType pdf(const negative_binomial_distribution<RealType, Policy>& dist, const RealType& k) + { // Probability Density/Mass Function. + BOOST_FPU_EXCEPTION_GUARD + + static const char* function = "boost::math::pdf(const negative_binomial_distribution<%1%>&, %1%)"; + + RealType r = dist.successes(); + RealType p = dist.success_fraction(); + RealType result = 0; + if(false == negative_binomial_detail::check_dist_and_k( + function, + r, + dist.success_fraction(), + k, + &result, Policy())) + { + return result; + } + + result = (p/(r + k)) * ibeta_derivative(r, static_cast<RealType>(k+1), p, Policy()); + // Equivalent to: + // return exp(lgamma(r + k) - lgamma(r) - lgamma(k+1)) * pow(p, r) * pow((1-p), k); + return result; + } // negative_binomial_pdf + + template <class RealType, class Policy> + inline RealType cdf(const negative_binomial_distribution<RealType, Policy>& dist, const RealType& k) + { // Cumulative Distribution Function of Negative Binomial. + static const char* function = "boost::math::cdf(const negative_binomial_distribution<%1%>&, %1%)"; + using boost::math::ibeta; // Regularized incomplete beta function. + // k argument may be integral, signed, or unsigned, or floating point. + // If necessary, it has already been promoted from an integral type. + RealType p = dist.success_fraction(); + RealType r = dist.successes(); + // Error check: + RealType result = 0; + if(false == negative_binomial_detail::check_dist_and_k( + function, + r, + dist.success_fraction(), + k, + &result, Policy())) + { + return result; + } + + RealType probability = ibeta(r, static_cast<RealType>(k+1), p, Policy()); + // Ip(r, k+1) = ibeta(r, k+1, p) + return probability; + } // cdf Cumulative Distribution Function Negative Binomial. + + template <class RealType, class Policy> + inline RealType cdf(const complemented2_type<negative_binomial_distribution<RealType, Policy>, RealType>& c) + { // Complemented Cumulative Distribution Function Negative Binomial. + + static const char* function = "boost::math::cdf(const negative_binomial_distribution<%1%>&, %1%)"; + using boost::math::ibetac; // Regularized incomplete beta function complement. + // k argument may be integral, signed, or unsigned, or floating point. + // If necessary, it has already been promoted from an integral type. + RealType const& k = c.param; + negative_binomial_distribution<RealType, Policy> const& dist = c.dist; + RealType p = dist.success_fraction(); + RealType r = dist.successes(); + // Error check: + RealType result = 0; + if(false == negative_binomial_detail::check_dist_and_k( + function, + r, + p, + k, + &result, Policy())) + { + return result; + } + // Calculate cdf negative binomial using the incomplete beta function. + // Use of ibeta here prevents cancellation errors in calculating + // 1-p if p is very small, perhaps smaller than machine epsilon. + // Ip(k+1, r) = ibetac(r, k+1, p) + // constrain_probability here? + RealType probability = ibetac(r, static_cast<RealType>(k+1), p, Policy()); + // Numerical errors might cause probability to be slightly outside the range < 0 or > 1. + // This might cause trouble downstream, so warn, possibly throw exception, but constrain to the limits. + return probability; + } // cdf Cumulative Distribution Function Negative Binomial. + + template <class RealType, class Policy> + inline RealType quantile(const negative_binomial_distribution<RealType, Policy>& dist, const RealType& P) + { // Quantile, percentile/100 or Percent Point Negative Binomial function. + // Return the number of expected failures k for a given probability p. + + // Inverse cumulative Distribution Function or Quantile (percentile / 100) of negative_binomial Probability. + // MAthCAD pnbinom return smallest k such that negative_binomial(k, n, p) >= probability. + // k argument may be integral, signed, or unsigned, or floating point. + // BUT Cephes/CodeCogs says: finds argument p (0 to 1) such that cdf(k, n, p) = y + static const char* function = "boost::math::quantile(const negative_binomial_distribution<%1%>&, %1%)"; + BOOST_MATH_STD_USING // ADL of std functions. + + RealType p = dist.success_fraction(); + RealType r = dist.successes(); + // Check dist and P. + RealType result = 0; + if(false == negative_binomial_detail::check_dist_and_prob + (function, r, p, P, &result, Policy())) + { + return result; + } + + // Special cases. + if (P == 1) + { // Would need +infinity failures for total confidence. + result = policies::raise_overflow_error<RealType>( + function, + "Probability argument is 1, which implies infinite failures !", Policy()); + return result; + // usually means return +std::numeric_limits<RealType>::infinity(); + // unless #define BOOST_MATH_THROW_ON_OVERFLOW_ERROR + } + if (P == 0) + { // No failures are expected if P = 0. + return 0; // Total trials will be just dist.successes. + } + if (P <= pow(dist.success_fraction(), dist.successes())) + { // p <= pdf(dist, 0) == cdf(dist, 0) + return 0; + } + if(p == 0) + { // Would need +infinity failures for total confidence. + result = policies::raise_overflow_error<RealType>( + function, + "Success fraction is 0, which implies infinite failures !", Policy()); + return result; + // usually means return +std::numeric_limits<RealType>::infinity(); + // unless #define BOOST_MATH_THROW_ON_OVERFLOW_ERROR + } + /* + // Calculate quantile of negative_binomial using the inverse incomplete beta function. + using boost::math::ibeta_invb; + return ibeta_invb(r, p, P, Policy()) - 1; // + */ + RealType guess = 0; + RealType factor = 5; + if(r * r * r * P * p > 0.005) + guess = detail::inverse_negative_binomial_cornish_fisher(r, p, RealType(1-p), P, RealType(1-P), Policy()); + + if(guess < 10) + { + // + // Cornish-Fisher Negative binomial approximation not accurate in this area: + // + guess = (std::min)(RealType(r * 2), RealType(10)); + } + else + factor = (1-P < sqrt(tools::epsilon<RealType>())) ? 2 : (guess < 20 ? 1.2f : 1.1f); + BOOST_MATH_INSTRUMENT_CODE("guess = " << guess); + // + // Max iterations permitted: + // + boost::uintmax_t max_iter = policies::get_max_root_iterations<Policy>(); + typedef typename Policy::discrete_quantile_type discrete_type; + return detail::inverse_discrete_quantile( + dist, + P, + false, + guess, + factor, + RealType(1), + discrete_type(), + max_iter); + } // RealType quantile(const negative_binomial_distribution dist, p) + + template <class RealType, class Policy> + inline RealType quantile(const complemented2_type<negative_binomial_distribution<RealType, Policy>, RealType>& c) + { // Quantile or Percent Point Binomial function. + // Return the number of expected failures k for a given + // complement of the probability Q = 1 - P. + static const char* function = "boost::math::quantile(const negative_binomial_distribution<%1%>&, %1%)"; + BOOST_MATH_STD_USING + + // Error checks: + RealType Q = c.param; + const negative_binomial_distribution<RealType, Policy>& dist = c.dist; + RealType p = dist.success_fraction(); + RealType r = dist.successes(); + RealType result = 0; + if(false == negative_binomial_detail::check_dist_and_prob( + function, + r, + p, + Q, + &result, Policy())) + { + return result; + } + + // Special cases: + // + if(Q == 1) + { // There may actually be no answer to this question, + // since the probability of zero failures may be non-zero, + return 0; // but zero is the best we can do: + } + if(Q == 0) + { // Probability 1 - Q == 1 so infinite failures to achieve certainty. + // Would need +infinity failures for total confidence. + result = policies::raise_overflow_error<RealType>( + function, + "Probability argument complement is 0, which implies infinite failures !", Policy()); + return result; + // usually means return +std::numeric_limits<RealType>::infinity(); + // unless #define BOOST_MATH_THROW_ON_OVERFLOW_ERROR + } + if (-Q <= boost::math::powm1(dist.success_fraction(), dist.successes(), Policy())) + { // q <= cdf(complement(dist, 0)) == pdf(dist, 0) + return 0; // + } + if(p == 0) + { // Success fraction is 0 so infinite failures to achieve certainty. + // Would need +infinity failures for total confidence. + result = policies::raise_overflow_error<RealType>( + function, + "Success fraction is 0, which implies infinite failures !", Policy()); + return result; + // usually means return +std::numeric_limits<RealType>::infinity(); + // unless #define BOOST_MATH_THROW_ON_OVERFLOW_ERROR + } + //return ibetac_invb(r, p, Q, Policy()) -1; + RealType guess = 0; + RealType factor = 5; + if(r * r * r * (1-Q) * p > 0.005) + guess = detail::inverse_negative_binomial_cornish_fisher(r, p, RealType(1-p), RealType(1-Q), Q, Policy()); + + if(guess < 10) + { + // + // Cornish-Fisher Negative binomial approximation not accurate in this area: + // + guess = (std::min)(RealType(r * 2), RealType(10)); + } + else + factor = (Q < sqrt(tools::epsilon<RealType>())) ? 2 : (guess < 20 ? 1.2f : 1.1f); + BOOST_MATH_INSTRUMENT_CODE("guess = " << guess); + // + // Max iterations permitted: + // + boost::uintmax_t max_iter = policies::get_max_root_iterations<Policy>(); + typedef typename Policy::discrete_quantile_type discrete_type; + return detail::inverse_discrete_quantile( + dist, + Q, + true, + guess, + factor, + RealType(1), + discrete_type(), + max_iter); + } // quantile complement + + } // namespace math +} // namespace boost + +// This include must be at the end, *after* the accessors +// for this distribution have been defined, in order to +// keep compilers that support two-phase lookup happy. +#include <boost/math/distributions/detail/derived_accessors.hpp> + +#if defined (BOOST_MSVC) +# pragma warning(pop) +#endif + +#endif // BOOST_MATH_SPECIAL_NEGATIVE_BINOMIAL_HPP