From: John Darrington Date: Sun, 20 Jul 2008 12:16:05 +0000 (+0800) Subject: Deleted lib/gsl-extras and updated gsl dependence to 1.8 X-Git-Tag: v0.7.0~14 X-Git-Url: https://pintos-os.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=97da90c80bee9a04fa19eeaf577a7c61d7ad1110;p=pspp-builds.git Deleted lib/gsl-extras and updated gsl dependence to 1.8 --- diff --git a/lib/gsl-extras/.gitignore b/lib/gsl-extras/.gitignore deleted file mode 100644 index 282522db..00000000 --- a/lib/gsl-extras/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -Makefile -Makefile.in diff --git a/lib/gsl-extras/ChangeLog b/lib/gsl-extras/ChangeLog deleted file mode 100644 index 6e462c61..00000000 --- a/lib/gsl-extras/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -Thu Apr 14 10:48:17 2005 Ben Pfaff - - * betadistinv.c: Apply patch from Jason Stover - to obtain better initial approximation - and tidy up a bit. - ----------------------------------------------------------------------- -Local Variables: -mode: change-log -version-control: never -End: diff --git a/lib/gsl-extras/README b/lib/gsl-extras/README deleted file mode 100644 index 275bab1a..00000000 --- a/lib/gsl-extras/README +++ /dev/null @@ -1,3 +0,0 @@ -The files in this directory are not part of GNU PSPP, but they are -used with GNU PSPP. In the future, they will likely become part of -the GNU Scientific Library. diff --git a/lib/gsl-extras/automake.mk b/lib/gsl-extras/automake.mk deleted file mode 100644 index 7d1ed62b..00000000 --- a/lib/gsl-extras/automake.mk +++ /dev/null @@ -1,9 +0,0 @@ -## Process this file with automake to produce Makefile.in -*- makefile -*- - -noinst_LIBRARIES += lib/gsl-extras/libgsl-extras.a - -lib_gsl_extras_libgsl_extras_a_SOURCES = \ - lib/gsl-extras/betadistinv.c lib/gsl-extras/binomial.c lib/gsl-extras/geometric.c \ - lib/gsl-extras/hypergeometric.c lib/gsl-extras/negbinom.c lib/gsl-extras/poisson.c lib/gsl-extras/gsl-extras.h - -EXTRA_DIST += lib/gsl-extras/README diff --git a/lib/gsl-extras/betadistinv.c b/lib/gsl-extras/betadistinv.c deleted file mode 100644 index b6192bfd..00000000 --- a/lib/gsl-extras/betadistinv.c +++ /dev/null @@ -1,686 +0,0 @@ -/* cdf/betadistinv.c - * - * Copyright (C) 2004 Free Software Foundation, Inc. - * - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 2 of the License, or (at - * your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - */ - -/* - * Invert the Beta distribution. - * - * References: - * - * Roger W. Abernathy and Robert P. Smith. "Applying Series Expansion - * to the Inverse Beta Distribution to Find Percentiles of the F-Distribution," - * ACM Transactions on Mathematical Software, volume 19, number 4, December 1993, - * pages 474-480. - * - * G.W. Hill and A.W. Davis. "Generalized asymptotic expansions of a - * Cornish-Fisher type," Annals of Mathematical Statistics, volume 39, number 8, - * August 1968, pages 1264-1273. - */ - -#include -#include -#include -#include -#include -#include -#include "gsl-extras.h" - -#define BETAINV_INIT_ERR .001 -#define BETADISTINV_N_TERMS 3 -#define BETADISTINV_MAXITER 20 - -static double -s_bisect (double x, double y) -{ - double result = GSL_MIN(x,y) + fabs(x - y) / 2.0; - return result; -} -static double -new_guess_P ( double old_guess, double x, double y, - double prob, double a, double b) -{ - double result; - double p_hat; - double end_point; - - p_hat = gsl_cdf_beta_P(old_guess, a, b); - if (p_hat < prob) - { - end_point = GSL_MAX(x,y); - } - else if ( p_hat > prob ) - { - end_point = GSL_MIN(x,y); - } - else - { - end_point = old_guess; - } - result = s_bisect(old_guess, end_point); - - return result; -} - -static double -new_guess_Q ( double old_guess, double x, double y, - double prob, double a, double b) -{ - double result; - double q_hat; - double end_point; - - q_hat = gsl_cdf_beta_Q(old_guess, a, b); - if (q_hat >= prob) - { - end_point = GSL_MAX(x,y); - } - else if ( q_hat < prob ) - { - end_point = GSL_MIN(x,y); - } - else - { - end_point = old_guess; - } - result = s_bisect(old_guess, end_point); - - return result; -} - -/* - * The get_corn_fish_* functions below return the first - * three terms of the Cornish-Fisher expansion - * without recursion. The recursive functions - * make the code more legible when higher order coefficients - * are used, but terms beyond the cubic do not - * improve accuracy. - */ - /* - * Linear coefficient for the - * Cornish-Fisher expansion. - */ -static double -get_corn_fish_lin (const double x, const double a, const double b) -{ - double result; - - result = gsl_ran_beta_pdf (x, a, b); - if(result > 0) - { - result = 1.0 / result; - } - else - { - result = GSL_DBL_MAX; - } - - return result; -} - /* - * Quadratic coefficient for the - * Cornish-Fisher expansion. - */ -static double -get_corn_fish_quad (const double x, const double a, const double b) -{ - double result; - double gam_ab; - double gam_a; - double gam_b; - double num; - double den; - - gam_ab = gsl_sf_lngamma(a + b); - gam_a = gsl_sf_lngamma (a); - gam_b = gsl_sf_lngamma (b); - num = exp(2 * (gam_a + gam_b - gam_ab)) * (1 - a + x * (b + a - 2)); - den = 2.0 * pow ( x, 2*a - 1 ) * pow ( 1 - x, 2 * b - 1 ); - if ( fabs(den) > 0.0) - { - result = num / den; - } - else - { - result = 0.0; - } - - return result; -} -/* - * The cubic term for the Cornish-Fisher expansion. - * Theoretically, use of this term should give a better approximation, - * but in practice inclusion of the cubic term worsens the - * iterative procedure in gsl_cdf_beta_Pinv and gsl_cdf_beta_Qinv - * for extreme values of p, a or b. - */ -#if 0 -static double -get_corn_fish_cube (const double x, const double a, const double b) -{ - double result; - double am1 = a - 1.0; - double am2 = a - 2.0; - double apbm2 = a+b-2.0; - double apbm3 = a+b-3.0; - double apbm4 = a+b-4.0; - double ab1ab2 = am1 * am2; - double tmp; - double num; - double den; - - num = (am1 - x * apbm2) * (am1 - x * apbm2); - tmp = ab1ab2 - x * (apbm2 * ( ab1ab2 * apbm4 + 1) + x * apbm2 * apbm3); - num += tmp; - tmp = gsl_ran_beta_pdf(x,a,b); - den = 2.0 * x * x * (1 - x) * (1 - x) * pow(tmp,3.0); - if ( fabs(den) > 0.0) - { - result = num / den; - } - else - { - result = 0.0; - } - - return result; -} -#endif -/* - * The Cornish-Fisher coefficients can be defined recursivley, - * starting with the nth derivative of s_psi = -f'(x)/f(x), - * where f is the beta density. - * - * The section below was commented out since - * the recursive generation of the coeficients did - * not improve the accuracy of the directly coded - * the first three coefficients. - */ -#if 0 -static double -s_d_psi (double x, double a, double b, int n) -{ - double result; - double np1 = (double) n + 1; - double asgn; - double bsgn; - double bm1 = b - 1.0; - double am1 = a - 1.0; - double mx = 1.0 - x; - - asgn = (n % 2) ? 1.0:-1.0; - bsgn = (n % 2) ? -1.0:1.0; - result = gsl_sf_gamma(np1) * ((bsgn * bm1 / (pow(mx, np1))) - + (asgn * am1 / (pow(x,np1)))); - return result; -} -/* - * nth derivative of a coefficient with respect - * to x. - */ -static double -get_d_coeff ( double x, double a, - double b, double n, double k) -{ - double result; - double d_psi; - double k_fac; - double i_fac; - double kmi_fac; - double i; - - if (n == 2) - { - result = s_d_psi(x, a, b, k); - } - else - { - result = 0.0; - for (i = 0.0; i < (k+1); i++) - { - k_fac = gsl_sf_lngamma(k+1.0); - i_fac = gsl_sf_lngamma(i+1.0); - kmi_fac = gsl_sf_lngamma(k-i+1.0); - - result += exp(k_fac - i_fac - kmi_fac) - * get_d_coeff( x, a, b, 2.0, i) - * get_d_coeff( x, a, b, (n - 1.0), (k - i)); - } - result += get_d_coeff ( x, a, b, (n-1.0), (k+1.0)); - } - - return result; -} -/* - * Cornish-Fisher coefficient. - */ -static double -get_corn_fish (double c, double x, - double a, double b, double n) -{ - double result; - double dc; - double c_prev; - - if(n == 1.0) - { - result = 1; - } - else if (n==2.0) - { - result = s_d_psi(x, a, b, 0); - } - else - { - dc = get_d_coeff(x, a, b, (n-1.0), 1.0); - c_prev = get_corn_fish(c, x, a, b, (n-1.0)); - result = (n-1) * s_d_psi(x,a,b,0) * c_prev + dc; - } - return result; -} -#endif - -double -gslextras_cdf_beta_Pinv ( const double p, const double a, const double b) -{ - double result; - double state; - double beta_result; - double lower = 0.0; - double upper = 1.0; - double c1; - double c2; -#if 0 - double c3; -#endif - double frac1; - double frac2; - double frac3; - double frac4; - double p0; - double p1; - double p2; - double tmp; - double err; - double abserr; - double relerr; - double min_err; - int n_iter = 0; - - if ( p < 0.0 ) - { - GSLEXTRAS_CDF_ERROR("p < 0", GSL_EDOM); - } - if ( p > 1.0 ) - { - GSLEXTRAS_CDF_ERROR("p > 1",GSL_EDOM); - } - if ( a < 0.0 ) - { - GSLEXTRAS_CDF_ERROR ("a < 0", GSL_EDOM ); - } - if ( b < 0.0 ) - { - GSLEXTRAS_CDF_ERROR ( "b < 0", GSL_EDOM ); - } - if ( p == 0.0 ) - { - return 0.0; - } - if ( p == 1.0 ) - { - return 1.0; - } - - if (p > (1.0 - GSL_DBL_EPSILON)) - { - /* - * When p is close to 1.0, the bisection - * works better with gsl_cdf_Q. - */ - state = gslextras_cdf_beta_Qinv ( p, a, b); - result = 1.0 - state; - return result; - } - if (p < GSL_DBL_EPSILON ) - { - /* - * Start at a small value and rise until - * we are above the correct result. This - * avoids overflow. When p is very close to - * 0, an initial state value of a/(a+b) will - * cause the interpolating polynomial - * to overflow. - */ - upper = GSL_DBL_MIN; - beta_result = gsl_cdf_beta_P (upper, a, b); - while (beta_result < p) - { - lower = upper; - upper *= 4.0; - beta_result = gsl_cdf_beta_P (upper, a, b); - } - state = (lower + upper) / 2.0; - } - else - { - /* - * First guess is the expected value. - */ - lower = 0.0; - upper = 1.0; - state = a/(a+b); - beta_result = gsl_cdf_beta_P (state, a, b); - } - err = beta_result - p; - abserr = fabs(err); - relerr = abserr / p; - while ( relerr > BETAINV_INIT_ERR) - { - tmp = new_guess_P ( state, lower, upper, - p, a, b); - lower = ( tmp < state ) ? lower:state; - upper = ( tmp < state ) ? state:upper; - state = tmp; - beta_result = gsl_cdf_beta_P (state, a, b); - err = p - beta_result; - abserr = fabs(err); - relerr = abserr / p; - } - - result = state; - min_err = relerr; - /* - * Use a second order Lagrange interpolating - * polynomial to get closer before switching to - * the iterative method. - */ - p0 = gsl_cdf_beta_P (lower, a, b); - p1 = gsl_cdf_beta_P (state, a, b); - p2 = gsl_cdf_beta_P (upper, a, b); - if( p0 < p1 && p1 < p2) - { - frac1 = (p - p2) / (p0 - p1); - frac2 = (p - p1) / (p0 - p2); - frac3 = (p - p0) / (p1 - p2); - frac4 = (p - p0) * (p - p1) / ((p2 - p0) * (p2 - p1)); - state = frac1 * (frac2 * lower - frac3 * state) - + frac4 * upper; - - beta_result = gsl_cdf_beta_P( state, a, b); - err = p - beta_result; - abserr = fabs(err); - relerr = abserr / p; - if (relerr < min_err) - { - result = state; - min_err = relerr; - } - else - { - /* - * Lagrange polynomial failed to reduce the error. - * This will happen with a very skewed beta density. - * Undo previous steps. - */ - state = result; - beta_result = gsl_cdf_beta_P(state,a,b); - err = p - beta_result; - abserr = fabs(err); - relerr = abserr / p; - } - } - - n_iter = 0; - - /* - * Newton-type iteration using the terms from the - * Cornish-Fisher expansion. If only the first term - * of the expansion is used, this is Newton's method. - */ - while ( relerr > GSL_DBL_EPSILON && n_iter < BETADISTINV_MAXITER) - { - n_iter++; - c1 = get_corn_fish_lin (state, a, b); - c2 = get_corn_fish_quad (state, a, b); - /* - * The cubic term does not help, and can can - * harm the approximation for extreme values of - * p, a, or b. - */ -#if 0 - c3 = get_corn_fish_cube (state, a, b); - state += err * (c1 + (err / 2.0 ) * (c2 + c3 * err / 3.0)); -#endif - state += err * (c1 + (c2 * err / 2.0 )); - /* - * The section below which is commented out uses - * a recursive function to get the coefficients. - * The recursion makes coding higher-order terms - * easier, but did not improve the result beyond - * the use of three terms. Since explicitly coding - * those three terms in the get_corn_fish_* functions - * was not difficult, the recursion was abandoned. - */ -#if 0 - coeff = 1.0; - for(i = 1.0; i < BETADISTINV_N_TERMS; i += 1.0) - { - i_fac *= i; - coeff = get_corn_fish (coeff, prior_state, a, b, i); - state += coeff * pow(err, i) / - (i_fac * pow (gsl_ran_beta_pdf(prior_state,a,b), i)); - } -#endif - beta_result = gsl_cdf_beta_P ( state, a, b ); - err = p - beta_result; - abserr = fabs(err); - relerr = abserr / p; - if (relerr < min_err) - { - result = state; - min_err = relerr; - } - } - - return result; -} - -double -gslextras_cdf_beta_Qinv (double q, double a, double b) -{ - double result; - double state; - double beta_result; - double lower = 0.0; - double upper = 1.0; - double c1; - double c2; -#if 0 - double c3; -#endif - double p0; - double p1; - double p2; - double frac1; - double frac2; - double frac3; - double frac4; - double tmp; - double err; - double abserr; - double relerr; - double min_err; - int n_iter = 0; - - if ( q < 0.0 ) - { - GSLEXTRAS_CDF_ERROR("q < 0", GSL_EDOM); - } - if ( q > 1.0 ) - { - GSLEXTRAS_CDF_ERROR("q > 1",GSL_EDOM); - } - if ( a < 0.0 ) - { - GSLEXTRAS_CDF_ERROR ("a < 0", GSL_EDOM ); - } - if ( b < 0.0 ) - { - GSLEXTRAS_CDF_ERROR ( "b < 0", GSL_EDOM ); - } - if ( q == 0.0 ) - { - return 1.0; - } - if ( q == 1.0 ) - { - return 0.0; - } - - if ( q < GSL_DBL_EPSILON ) - { - /* - * When q is close to 0, the bisection - * and interpolation done in the rest of - * this routine will not give the correct - * value within double precision, so - * gsl_cdf_beta_Qinv is called instead. - */ - state = gslextras_cdf_beta_Pinv ( q, a, b); - result = 1.0 - state; - return result; - } - if ( q > 1.0 - GSL_DBL_EPSILON ) - { - /* - * Make the initial guess close to 0.0. - */ - upper = GSL_DBL_MIN; - beta_result = gsl_cdf_beta_Q ( upper, a, b); - while (beta_result > q ) - { - lower = upper; - upper *= 4.0; - beta_result = gsl_cdf_beta_Q ( upper, a, b); - } - state = (upper + lower) / 2.0; - } - else - { - /* Bisection to get an initial approximation. - * First guess is the expected value. - */ - state = a/(a+b); - lower = 0.0; - upper = 1.0; - } - beta_result = gsl_cdf_beta_Q (state, a, b); - err = beta_result - q; - abserr = fabs(err); - relerr = abserr / q; - while ( relerr > BETAINV_INIT_ERR) - { - n_iter++; - tmp = new_guess_Q ( state, lower, upper, - q, a, b); - lower = ( tmp < state ) ? lower:state; - upper = ( tmp < state ) ? state:upper; - state = tmp; - beta_result = gsl_cdf_beta_Q (state, a, b); - err = q - beta_result; - abserr = fabs(err); - relerr = abserr / q; - } - result = state; - min_err = relerr; - - /* - * Use a second order Lagrange interpolating - * polynomial to get closer before switching to - * the iterative method. - */ - p0 = gsl_cdf_beta_Q (lower, a, b); - p1 = gsl_cdf_beta_Q (state, a, b); - p2 = gsl_cdf_beta_Q (upper, a, b); - if(p0 > p1 && p1 > p2) - { - frac1 = (q - p2) / (p0 - p1); - frac2 = (q - p1) / (p0 - p2); - frac3 = (q - p0) / (p1 - p2); - frac4 = (q - p0) * (q - p1) / ((p2 - p0) * (p2 - p1)); - state = frac1 * (frac2 * lower - frac3 * state) - + frac4 * upper; - beta_result = gsl_cdf_beta_Q( state, a, b); - err = beta_result - q; - abserr = fabs(err); - relerr = abserr / q; - if (relerr < min_err) - { - result = state; - min_err = relerr; - } - else - { - /* - * Lagrange polynomial failed to reduce the error. - * This will happen with a very skewed beta density. - * Undo previous steps. - */ - state = result; - beta_result = gsl_cdf_beta_P(state,a,b); - err = q - beta_result; - abserr = fabs(err); - relerr = abserr / q; - } - } - - /* - * Iteration using the terms from the - * Cornish-Fisher expansion. If only the first term - * of the expansion is used, this is Newton's method. - */ - - n_iter = 0; - while ( relerr > GSL_DBL_EPSILON && n_iter < BETADISTINV_MAXITER) - { - n_iter++; - c1 = get_corn_fish_lin (state, a, b); - c2 = get_corn_fish_quad (state, a, b); - /* - * The cubic term does not help, and can harm - * the approximation for extreme values of p, a and b. - */ -#if 0 - c3 = get_corn_fish_cube (state, a, b); - state += err * (c1 + (err / 2.0 ) * (c2 + c3 * err / 3.0)); -#endif - state += err * (c1 + (c2 * err / 2.0 )); - beta_result = gsl_cdf_beta_Q ( state, a, b ); - err = beta_result - q; - abserr = fabs(err); - relerr = abserr / q; - if (relerr < min_err) - { - result = state; - min_err = relerr; - } - } - - return result; -} diff --git a/lib/gsl-extras/binomial.c b/lib/gsl-extras/binomial.c deleted file mode 100644 index 847247d4..00000000 --- a/lib/gsl-extras/binomial.c +++ /dev/null @@ -1,98 +0,0 @@ -/* cdf/binomial.c - * - * Copyright (C) 2004 Free Software Foundation, Inc. - * - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 2 of the License, or (at - * your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - */ - -/* - * Computes the cumulative distribution function for a binomial - * random variable. For a binomial random variable X with n trials - * and success probability p, - * - * Pr( X <= k ) = Pr( Y >= p ) - * - * where Y is a beta random variable with parameters k+1 and n-k. - * - * Reference: - * - * W. Feller, "An Introduction to Probability and Its - * Applications," volume 1. Wiley, 1968. Exercise 45, page 173, - * chapter 6. - */ -#include -#include -#include -#include -#include "gsl-extras.h" - -double -gslextras_cdf_binomial_P(const long k, const long n, const double p) -{ - double P; - double a; - double b; - - if(p > 1.0 || p < 0.0) - { - GSLEXTRAS_CDF_ERROR("p < 0 or p > 1",GSL_EDOM); - } - if ( k >= n ) - { - P = 1.0; - } - else if (k < 0) - { - P = 0.0; - } - else - { - a = (double) k+1; - b = (double) n - k; - P = gsl_cdf_beta_Q( p, a, b); - } - - return P; -} -double -gslextras_cdf_binomial_Q(const long k, const long n, const double q) -{ - double P; - double a; - double b; - - if(q > 1.0 || q < 0.0) - { - GSLEXTRAS_CDF_ERROR("p < 0 or p > 1",GSL_EDOM); - } - if( k >= n ) - { - P = 0.0; - } - else if ( k < 0 ) - { - P = 1.0; - } - else - { - a = (double) k+1; - b = (double) n - k; - P = gsl_cdf_beta_P(q, a, b); - } - - return P; -} - diff --git a/lib/gsl-extras/geometric.c b/lib/gsl-extras/geometric.c deleted file mode 100644 index de0f0006..00000000 --- a/lib/gsl-extras/geometric.c +++ /dev/null @@ -1,105 +0,0 @@ -/* cdf/geometric.c - * - * Copyright (C) 2004 Free Software Foundation, Inc. - * - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 2 of the License, or (at - * your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - */ - -/* - * Pr(X <= n) for a negative binomial random variable X, i.e., - * the probability of n or fewer failuers before success k. - */ - -#include -#include -#include -#include -#include -#include "gsl-extras.h" - -/* - * Pr (X <= n), i.e., the probability of n or fewer - * failures until the first success. - */ -double -gslextras_cdf_geometric_P (const long n, const double p) -{ - double P; - double a; - int i; - int m; - double sign = 1.0; - double term; - double q; - - if(p > 1.0 || p < 0.0) - { - GSLEXTRAS_CDF_ERROR("p < 0 or p > 1",GSL_EDOM); - } - if ( n < 0 ) - { - return 0.0; - } - q = 1.0 - p; - a = (double) n+1; - if( p < GSL_DBL_EPSILON ) - { - /* - * 1.0 - pow(q,a) will overflow, so use - * a Taylor series. - */ - i = 2; - m = n+1; - term = exp(log(a) + log(p)); - P = term; - while ( term > GSL_DBL_MIN && i < m) - { - term = exp (sign * gsl_sf_lnchoose(m,i) + i * log(p)); - P += term; - i++; - sign = -sign; - } - } - else - { - P = 1.0 - pow ( q, a); - } - return P; -} -double -gslextras_cdf_geometric_Q ( const long n, const double p) -{ - double P; - double q; - double a; - - if(p > 1.0 || p < 0.0) - { - GSLEXTRAS_CDF_ERROR("p < 0 or p > 1",GSL_EDOM); - } - if ( n < 0 ) - { - P = 1.0; - } - else - { - a = (double) n+1; - q = 1.0 - p; - P = pow(q, a); - } - - return P; -} diff --git a/lib/gsl-extras/gsl-extras.h b/lib/gsl-extras/gsl-extras.h deleted file mode 100644 index 48bf105a..00000000 --- a/lib/gsl-extras/gsl-extras.h +++ /dev/null @@ -1,33 +0,0 @@ -#ifndef GSL_EXTRAS_H -#define GSL_EXTRAS_H - -/* GSLEXTRAS_CDF_ERROR: call the error handler, and return a NAN. */ -#define GSLEXTRAS_CDF_ERROR(reason, gsl_errno) \ - do { \ - gsl_error (reason, __FILE__, __LINE__, gsl_errno) ; \ - return GSL_NAN ; \ - } while (0) - -double gslextras_cdf_beta_Pinv (const double p, const double a, - const double b); -double gslextras_cdf_beta_Qinv (double q, double a, double b); -double gslextras_cdf_binomial_P(const long k, const long n, const double p); -double gslextras_cdf_binomial_Q(const long k, const long n, const double q); -double gslextras_cdf_geometric_P (const long n, const double p); -double gslextras_cdf_geometric_Q ( const long n, const double p); -double gslextras_cdf_hypergeometric_P (const unsigned int k, - const unsigned int n0, - const unsigned int n1, - const unsigned int t); -double gslextras_cdf_hypergeometric_Q (const unsigned int k, - const unsigned int n0, - const unsigned int n1, - const unsigned int t); -double gslextras_cdf_negative_binomial_P(const long n, - const long k, const double p); -double gslextras_cdf_negative_binomial_Q(const long n, const long k, - const double p); -double gslextras_cdf_poisson_P (const long k, const double lambda); -double gslextras_cdf_poisson_Q (const long k, const double lambda); - -#endif /* gsl-extras.h */ diff --git a/lib/gsl-extras/hypergeometric.c b/lib/gsl-extras/hypergeometric.c deleted file mode 100644 index 67b757b2..00000000 --- a/lib/gsl-extras/hypergeometric.c +++ /dev/null @@ -1,195 +0,0 @@ -/* cdf/hypergeometric.c - * - * Copyright (C) 2004 Free Software Foundation, Inc. - * - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 2 of the License, or (at - * your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - */ - -/* - * Computes the cumulative distribution function for a hypergeometric - * random variable. A hypergeometric random variable X is the number - * of elements of type 0 in a sample of size t, drawn from a population - * of size n1 + n0, in which n1 are of type 1 and n0 are of type 0. - * - * This algorithm computes Pr( X <= k ) by summing the terms from - * the mass function, Pr( X = k ). - * - * References: - * - * T. Wu. An accurate computation of the hypergeometric distribution - * function. ACM Transactions on Mathematical Software. Volume 19, number 1, - * March 1993. - * This algorithm is not used, since it requires factoring the - * numerator and denominator, then cancelling. It is more accurate - * than the algorithm used here, but the cancellation requires more - * time than the algorithm used here. - * - * W. Feller. An Introduction to Probability Theory and Its Applications, - * third edition. 1968. Chapter 2, section 6. - */ -#include -#include -#include -#include -#include -#include "gsl-extras.h" - -/* - * Pr (X <= k) - */ -double -gslextras_cdf_hypergeometric_P (const unsigned int k, - const unsigned int n0, - const unsigned int n1, - const unsigned int t) -{ - unsigned int i; - unsigned int mode; - double P; - double tmp; - double relerr; - - if( t > (n0+n1)) - { - GSLEXTRAS_CDF_ERROR("t larger than population size",GSL_EDOM); - } - else if( k >= n0 || k >= t) - { - P = 1.0; - } - else if (k < 0.0) - { - P = 0.0; - } - else - { - P = 0.0; - mode = (int) t*n0 / (n0+n1); - relerr = 1.0; - if( k < mode ) - { - i = k; - relerr = 1.0; - while(i != UINT_MAX && relerr > GSL_DBL_EPSILON && P < 1.0) - { - tmp = gsl_ran_hypergeometric_pdf(i, n0, n1, t); - P += tmp; - relerr = tmp / P; - i--; - } - } - else - { - i = mode; - relerr = 1.0; - while(i <= k && relerr > GSL_DBL_EPSILON && P < 1.0) - { - tmp = gsl_ran_hypergeometric_pdf(i, n0, n1, t); - P += tmp; - relerr = tmp / P; - i++; - } - i = mode - 1; - relerr = 1.0; - while( i != UINT_MAX && relerr > GSL_DBL_EPSILON && P < 1.0) - { - tmp = gsl_ran_hypergeometric_pdf(i, n0, n1, t); - P += tmp; - relerr = tmp / P; - i--; - } - } - /* - * Hack to get rid of a pesky error when the sum - * gets slightly above 1.0. - */ - P = GSL_MIN_DBL (P, 1.0); - } - return P; -} - -/* - * Pr (X > k) - */ -double -gslextras_cdf_hypergeometric_Q (const unsigned int k, - const unsigned int n0, - const unsigned int n1, - const unsigned int t) -{ - unsigned int i; - unsigned int mode; - double P; - double relerr; - double tmp; - - if( t > (n0+n1)) - { - GSLEXTRAS_CDF_ERROR("t larger than population size",GSL_EDOM); - } - else if( k >= n0 || k >= t) - { - P = 0.0; - } - else if (k < 0.0) - { - P = 1.0; - } - else - { - P = 0.0; - mode = (int) t*n0 / (n0+n1); - relerr = 1.0; - - if(k < mode) - { - i = mode; - while( i <= t && relerr > GSL_DBL_EPSILON && P < 1.0) - { - tmp = gsl_ran_hypergeometric_pdf(i, n0, n1, t); - P += tmp; - relerr = tmp / P; - i++; - } - i = mode - 1; - relerr = 1.0; - while ( i > k && relerr > GSL_DBL_EPSILON && P < 1.0) - { - tmp = gsl_ran_hypergeometric_pdf(i, n0, n1, t); - P += tmp; - relerr = tmp / P; - i--; - } - } - else - { - i = k+1; - while(i <= t && relerr > GSL_DBL_EPSILON && P < 1.0) - { - tmp = gsl_ran_hypergeometric_pdf(i, n0, n1, t); - P += tmp; - relerr = tmp / P; - i++; - } - } - /* - * Hack to get rid of a pesky error when the sum - * gets slightly above 1.0. - */ - P = GSL_MIN_DBL(P, 1.0); - } - return P; -} diff --git a/lib/gsl-extras/negbinom.c b/lib/gsl-extras/negbinom.c deleted file mode 100644 index b991f739..00000000 --- a/lib/gsl-extras/negbinom.c +++ /dev/null @@ -1,91 +0,0 @@ -/* cdf/negbinom.c - * - * Copyright (C) 2004 Free Software Foundation, Inc. - * - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 2 of the License, or (at - * your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - */ - - -#include -#include -#include -#include -#include "gsl-extras.h" - -/* - * Pr(X <= n) for a negative binomial random variable X, i.e., - * the probability of n or fewer failuers before success k. - */ -double -gslextras_cdf_negative_binomial_P(const long n, const long k, const double p) -{ - double P; - double a; - double b; - - if(p > 1.0 || p < 0.0) - { - GSLEXTRAS_CDF_ERROR("p < 0 or p > 1",GSL_EDOM); - } - if ( k < 0 ) - { - GSLEXTRAS_CDF_ERROR ("k < 0",GSL_EDOM); - } - if ( n < 0 ) - { - P = 0.0; - } - else - { - a = (double) k; - b = (double) n+1; - P = gsl_cdf_beta_P(p, a, b); - } - - return P; -} -/* - * Pr ( X > n ). - */ -double -gslextras_cdf_negative_binomial_Q(const long n, const long k, const double p) -{ - double P; - double a; - double b; - - if(p > 1.0 || p < 0.0) - { - GSLEXTRAS_CDF_ERROR("p < 0 or p > 1",GSL_EDOM); - } - if ( k < 0 ) - { - GSLEXTRAS_CDF_ERROR ("k < 0",GSL_EDOM); - } - if ( n < 0 ) - { - P = 1.0; - } - else - { - a = (double) k; - b = (double) n+1; - P = gsl_cdf_beta_Q(p, a, b); - } - - return P; -} - diff --git a/lib/gsl-extras/poisson.c b/lib/gsl-extras/poisson.c deleted file mode 100644 index 3ce2bf5a..00000000 --- a/lib/gsl-extras/poisson.c +++ /dev/null @@ -1,90 +0,0 @@ -/* cdf/poisson.c - * - * Copyright (C) 2004 Free Software Foundation, Inc. - * - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 2 of the License, or (at - * your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - */ -/* - * Computes the cumulative distribution function for a Poisson - * random variable. For a Poisson random variable X with parameter - * lambda, - * - * Pr( X <= k ) = Pr( Y >= p ) - * - * where Y is a gamma random variable with parameters k+1 and 1. - * - * Reference: - * - * W. Feller, "An Introduction to Probability and Its - * Applications," volume 1. Wiley, 1968. Exercise 46, page 173, - * chapter 6. - */ -#include -#include -#include -#include -#include "gsl-extras.h" - -/* - * Pr (X <= k) for a Poisson random variable X. - */ -double -gslextras_cdf_poisson_P (const long k, const double lambda) -{ - double P; - double a; - - if ( lambda <= 0.0 ) - { - GSLEXTRAS_CDF_ERROR ("lambda <= 0", GSL_EDOM); - } - if ( k < 0 ) - { - P = 0.0; - } - else - { - a = (double) k+1; - P = gsl_cdf_gamma_Q ( lambda, a, 1.0); - } - return P; -} - -/* - * Pr ( X > k ) for a Possion random variable X. - */ -double -gslextras_cdf_poisson_Q (const long k, const double lambda) -{ - double P; - double a; - - if ( lambda <= 0.0 ) - { - GSLEXTRAS_CDF_ERROR ("lambda <= 0", GSL_EDOM); - } - if ( k < 0 ) - { - P = 1.0; - } - else - { - a = (double) k+1; - P = gsl_cdf_gamma_P ( lambda, a, 1.0); - } - return P; -} -