From 2d05be528ac9ae20949c93c565f63716b4f330b3 Mon Sep 17 00:00:00 2001 From: Karan Anand Date: Sun, 5 Jan 2025 04:17:30 -0800 Subject: [PATCH 01/21] feat: add the C src files --- .../stats/base/dists/hypergeometric/pmf.h | 44 +++++++++++ .../dists/hypergeometric/pmf/src/Makefile | 70 ++++++++++++++++ .../base/dists/hypergeometric/pmf/src/addon.c | 23 ++++++ .../base/dists/hypergeometric/pmf/src/main.c | 79 +++++++++++++++++++ 4 files changed, 216 insertions(+) create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/include/stdlib/stats/base/dists/hypergeometric/pmf.h create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/Makefile create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/addon.c create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/main.c diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/include/stdlib/stats/base/dists/hypergeometric/pmf.h b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/include/stdlib/stats/base/dists/hypergeometric/pmf.h new file mode 100644 index 000000000000..893ee3039d08 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/include/stdlib/stats/base/dists/hypergeometric/pmf.h @@ -0,0 +1,44 @@ +/** + * @license Apache-2.0 + * + * Copyright (c) 2025 The Stdlib Authors. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +#ifndef STDLIB_STATS_BASE_DISTS_HYPERGEOMETRIC_PMF_H +#define STDLIB_STATS_BASE_DISTS_HYPERGEOMETRIC_PMF_H + +/* + * If C++, prevent name mangling so that the compiler emits a binary file having undecorated names, thus mirroring the behavior of a C compiler. + */ +#ifdef __cplusplus +extern "C" { +#endif + +/** + * Evaluates the probability mass function (PMF) for a hypergeometric distribution with population size `N`, subpopulation size `K`, and number of draws `n`. + * + * @param x input value + * @param N population size + * @param K subpopulation size + * @param n number of draws + * @return evaluated PMF + */ +double stdlib_base_dists_hypergeometric_pmf( const double x, const double N, const double K, const double n ); + +#ifdef __cplusplus +} +#endif + +#endif // !STDLIB_STATS_BASE_DISTS_HYPERGEOMETRIC_PMF_H diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/Makefile b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/Makefile new file mode 100644 index 000000000000..7733b6180cb4 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/Makefile @@ -0,0 +1,70 @@ +#/ +# @license Apache-2.0 +# +# Copyright (c) 2025 The Stdlib Authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +#/ + +# VARIABLES # + +ifndef VERBOSE + QUIET := @ +else + QUIET := +endif + +# Determine the OS ([1][1], [2][2]). +# +# [1]: https://en.wikipedia.org/wiki/Uname#Examples +# [2]: http://stackoverflow.com/a/27776822/2225624 +OS ?= $(shell uname) +ifneq (, $(findstring MINGW,$(OS))) + OS := WINNT +else +ifneq (, $(findstring MSYS,$(OS))) + OS := WINNT +else +ifneq (, $(findstring CYGWIN,$(OS))) + OS := WINNT +else +ifneq (, $(findstring Windows_NT,$(OS))) + OS := WINNT +endif +endif +endif +endif + + +# RULES # + +#/ +# Removes generated files for building an add-on. +# +# @example +# make clean-addon +#/ +clean-addon: + $(QUIET) -rm -f *.o *.node + +.PHONY: clean-addon + +#/ +# Removes generated files. +# +# @example +# make clean +#/ +clean: clean-addon + +.PHONY: clean diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/addon.c b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/addon.c new file mode 100644 index 000000000000..bdd253a68744 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/addon.c @@ -0,0 +1,23 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2025 The Stdlib Authors. +* +* Licensed under the Apache License, Version 2.0 (the "License"); +* you may not use this file except in compliance with the License. +* You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, software +* distributed under the License is distributed on an "AS IS" BASIS, +* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +* See the License for the specific language governing permissions and +* limitations under the License. +*/ + +#include "stdlib/math/base/napi/quaternary.h" +#include "stdlib/stats/base/dists/hypergeometric/pmf.h" + +// cppcheck-suppress shadowFunction +STDLIB_MATH_BASE_NAPI_MODULE_DDDD_D( stdlib_base_dists_hypergeometric_pmf ) diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/main.c b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/main.c new file mode 100644 index 000000000000..924b08d20e2a --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/src/main.c @@ -0,0 +1,79 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2025 The Stdlib Authors. +* +* Licensed under the Apache License, Version 2.0 (the "License"); +* you may not use this file except in compliance with the License. +* You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, software +* distributed under the License is distributed on an "AS IS" BASIS, +* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +* See the License for the specific language governing permissions and +* limitations under the License. +*/ + +#include "stdlib/math/base/assert/is_nonnegative_integer.h" +#include "stdlib/math/base/assert/is_nan.h" +#include "stdlib/math/base/special/exp.h" +#include "stdlib/math/base/special/factorialln.h" +#include "stdlib/math/base/special/max.h" +#include "stdlib/math/base/special/min.h" +#include "stdlib/constants/float64/pinf.h" + +/** +* Evaluates the probability mass function (PMF) for a hypergeometric distribution with population size `N`, subpopulation size `K`, and number of draws `n`. +* +* @param x input value +* @param N population size +* @param K subpopulation size +* @param n number of draws +* @return evaluated PMF, or NaN if inputs are invalid +* +* @example +* double sd = stdlib_base_dists_hypergeometric_pmf( 1.0, 8, 4, 2 ); +* // returns ~0.571 +* +* @example +* double sd = stdlib_base_dists_hypergeometric_pmf( 0.0, 8, 4, 2 ); +* // returns ~0.214 +* +* @example +* double sd = stdlib_base_dists_hypergeometric_pmf( NaN, 10, 5, 2 ); +* // returns NaN +*/ +double stdlib_base_dists_hypergeometric_pmf ( const double x, const double N, const double K, const double n ) { + if ( + stdlib_base_is_nan(x) || + stdlib_base_is_nan(N) || + stdlib_base_is_nan(K) || + stdlib_base_is_nan(n) || + !stdlib_base_is_nonnegative_integer(N) || + !stdlib_base_is_nonnegative_integer(K) || + !stdlib_base_is_nonnegative_integer(n) || + N == STDLIB_CONSTANT_FLOAT64_PINF || + K == STDLIB_CONSTANT_FLOAT64_PINF || + K > N || + n > N + ) { + return NAN; + } + + double mins = stdlib_base_max(0, n + K - N); + double maxs = stdlib_base_min(K, n); + + if (stdlib_base_is_nonnegative_integer(x) && mins <= x && x <= maxs) { + double lnum = stdlib_base_factorialln(n) + stdlib_base_factorialln(K) + + stdlib_base_factorialln(N - n) + stdlib_base_factorialln(N - K); + double ldenom = stdlib_base_factorialln(N) + stdlib_base_factorialln(x) + + stdlib_base_factorialln(n - x) + + stdlib_base_factorialln(K - x) + + stdlib_base_factorialln(N - K + x - n); + double lpmf = lnum - ldenom; + return stdlib_base_exp(lpmf); + } + return 0.0; +} From 6e8eb2d4f409a14fa72ea1dee60c82a2934e2d27 Mon Sep 17 00:00:00 2001 From: Karan Anand Date: Sun, 5 Jan 2025 04:17:54 -0800 Subject: [PATCH 02/21] feat: add the C benchmark and example files --- .../hypergeometric/pmf/benchmark/c/Makefile | 146 ++++++++++++++++++ .../pmf/benchmark/c/benchmark.c | 145 +++++++++++++++++ .../hypergeometric/pmf/examples/c/Makefile | 146 ++++++++++++++++++ .../hypergeometric/pmf/examples/c/example.c | 48 ++++++ 4 files changed, 485 insertions(+) create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/c/Makefile create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/c/benchmark.c create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/examples/c/Makefile create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/examples/c/example.c diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/c/Makefile b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/c/Makefile new file mode 100644 index 000000000000..a4bd7b38fd74 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/c/Makefile @@ -0,0 +1,146 @@ +#/ +# @license Apache-2.0 +# +# Copyright (c) 2025 The Stdlib Authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +#/ + +# VARIABLES # + +ifndef VERBOSE + QUIET := @ +else + QUIET := +endif + +# Determine the OS ([1][1], [2][2]). +# +# [1]: https://en.wikipedia.org/wiki/Uname#Examples +# [2]: http://stackoverflow.com/a/27776822/2225624 +OS ?= $(shell uname) +ifneq (, $(findstring MINGW,$(OS))) + OS := WINNT +else +ifneq (, $(findstring MSYS,$(OS))) + OS := WINNT +else +ifneq (, $(findstring CYGWIN,$(OS))) + OS := WINNT +else +ifneq (, $(findstring Windows_NT,$(OS))) + OS := WINNT +endif +endif +endif +endif + +# Define the program used for compiling C source files: +ifdef C_COMPILER + CC := $(C_COMPILER) +else + CC := gcc +endif + +# Define the command-line options when compiling C files: +CFLAGS ?= \ + -std=c99 \ + -O3 \ + -Wall \ + -pedantic + +# Determine whether to generate position independent code ([1][1], [2][2]). +# +# [1]: https://gcc.gnu.org/onlinedocs/gcc/Code-Gen-Options.html#Code-Gen-Options +# [2]: http://stackoverflow.com/questions/5311515/gcc-fpic-option +ifeq ($(OS), WINNT) + fPIC ?= +else + fPIC ?= -fPIC +endif + +# List of includes (e.g., `-I /foo/bar -I /beep/boop/include`): +INCLUDE ?= + +# List of source files: +SOURCE_FILES ?= + +# List of libraries (e.g., `-lopenblas -lpthread`): +LIBRARIES ?= + +# List of library paths (e.g., `-L /foo/bar -L /beep/boop`): +LIBPATH ?= + +# List of C targets: +c_targets := benchmark.out + + +# RULES # + +#/ +# Compiles source files. +# +# @param {string} [C_COMPILER] - C compiler (e.g., `gcc`) +# @param {string} [CFLAGS] - C compiler options +# @param {(string|void)} [fPIC] - compiler flag determining whether to generate position independent code (e.g., `-fPIC`) +# @param {string} [INCLUDE] - list of includes (e.g., `-I /foo/bar -I /beep/boop/include`) +# @param {string} [SOURCE_FILES] - list of source files +# @param {string} [LIBPATH] - list of library paths (e.g., `-L /foo/bar -L /beep/boop`) +# @param {string} [LIBRARIES] - list of libraries (e.g., `-lopenblas -lpthread`) +# +# @example +# make +# +# @example +# make all +#/ +all: $(c_targets) + +.PHONY: all + +#/ +# Compiles C source files. +# +# @private +# @param {string} CC - C compiler (e.g., `gcc`) +# @param {string} CFLAGS - C compiler options +# @param {(string|void)} fPIC - compiler flag determining whether to generate position independent code (e.g., `-fPIC`) +# @param {string} INCLUDE - list of includes (e.g., `-I /foo/bar`) +# @param {string} SOURCE_FILES - list of source files +# @param {string} LIBPATH - list of library paths (e.g., `-L /foo/bar`) +# @param {string} LIBRARIES - list of libraries (e.g., `-lopenblas`) +#/ +$(c_targets): %.out: %.c + $(QUIET) $(CC) $(CFLAGS) $(fPIC) $(INCLUDE) -o $@ $(SOURCE_FILES) $< $(LIBPATH) -lm $(LIBRARIES) + +#/ +# Runs compiled benchmarks. +# +# @example +# make run +#/ +run: $(c_targets) + $(QUIET) ./$< + +.PHONY: run + +#/ +# Removes generated files. +# +# @example +# make clean +#/ +clean: + $(QUIET) -rm -f *.o *.out + +.PHONY: clean diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/c/benchmark.c b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/c/benchmark.c new file mode 100644 index 000000000000..93cf983eaea1 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/c/benchmark.c @@ -0,0 +1,145 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2025 The Stdlib Authors. +* +* Licensed under the Apache License, Version 2.0 (the "License"); +* you may not use this file except in compliance with the License. +* You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, software +* distributed under the License is distributed on an "AS IS" BASIS, +* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +* See the License for the specific language governing permissions and +* limitations under the License. +*/ + +#include "stdlib/stats/base/dists/hypergeometric/pmf.h" +#include "stdlib/math/base/special/round.h" +#include +#include +#include +#include +#include + +#define NAME "hypergeometric-pmf" +#define ITERATIONS 1000000 +#define REPEATS 3 + +/** +* Prints the TAP version. +*/ +static void print_version( void ) { + printf( "TAP version 13\n" ); +} + +/** +* Prints the TAP summary. +* +* @param total total number of tests +* @param passing total number of passing tests +*/ +static void print_summary( int total, int passing ) { + printf( "#\n" ); + printf( "1..%d\n", total ); // TAP plan + printf( "# total %d\n", total ); + printf( "# pass %d\n", passing ); + printf( "#\n" ); + printf( "# ok\n" ); +} + +/** +* Prints benchmarks results. +* +* @param elapsed elapsed time in seconds +*/ +static void print_results( double elapsed ) { + double rate = (double)ITERATIONS / elapsed; + printf( " ---\n" ); + printf( " iterations: %d\n", ITERATIONS ); + printf( " elapsed: %0.9f\n", elapsed ); + printf( " rate: %0.9f\n", rate ); + printf( " ...\n" ); +} + +/** +* Returns a clock time. +* +* @return clock time +*/ +static double tic( void ) { + struct timeval now; + gettimeofday( &now, NULL ); + return (double)now.tv_sec + (double)now.tv_usec/1.0e6; +} + +/** +* Generates a random number on the interval [min,max). +* +* @param min minimum value (inclusive) +* @param max maximum value (exclusive) +* @return random number +*/ +static double random_uniform( const double min, const double max ) { + double v = (double)rand() / ( (double)RAND_MAX + 1.0 ); + return min + ( v*(max-min) ); +} + +/** +* Runs a benchmark. +* +* @return elapsed time in seconds +*/ +static double benchmark( void ) { + double elapsed; + double N[ 100 ]; + double K[ 100 ]; + double n[ 100 ]; + double x[ 100 ]; + double pmf; + double t; + int i; + + for ( i = 0; i < 100; i++ ) { + N[i] = stdlib_base_round(random_uniform(1.0, 100.0)); + K[i] = stdlib_base_round(random_uniform(0.0, N[i])); + n[i] = stdlib_base_round(random_uniform(0.0, N[i])); + x[i] = stdlib_base_round(random_uniform(0.0, n[i])); + } + + t = tic(); + for ( i = 0; i < ITERATIONS; i++ ) { + pmf = stdlib_base_dists_hypergeometric_pmf( x[ i % 100 ], N[ i % 100 ], K[ i % 100 ], n[ i % 100 ] ); + if ( pmf != pmf ) { + printf( "should not return NaN\n" ); + break; + } + } + elapsed = tic() - t; + if ( pmf != pmf ) { + printf( "should not return NaN\n" ); + } + return elapsed; +} + +/** +* Main execution sequence. +*/ +int main( void ) { + double elapsed; + int i; + + // Use the current time to seed the random number generator: + srand( time( NULL ) ); + + print_version(); + for ( i = 0; i < REPEATS; i++ ) { + printf( "# c::%s\n", NAME ); + elapsed = benchmark(); + print_results( elapsed ); + printf( "ok %d benchmark finished\n", i+1 ); + } + print_summary( REPEATS, REPEATS ); +} diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/examples/c/Makefile b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/examples/c/Makefile new file mode 100644 index 000000000000..25ced822f96a --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/examples/c/Makefile @@ -0,0 +1,146 @@ +#/ +# @license Apache-2.0 +# +# Copyright (c) 2025 The Stdlib Authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +#/ + +# VARIABLES # + +ifndef VERBOSE + QUIET := @ +else + QUIET := +endif + +# Determine the OS ([1][1], [2][2]). +# +# [1]: https://en.wikipedia.org/wiki/Uname#Examples +# [2]: http://stackoverflow.com/a/27776822/2225624 +OS ?= $(shell uname) +ifneq (, $(findstring MINGW,$(OS))) + OS := WINNT +else +ifneq (, $(findstring MSYS,$(OS))) + OS := WINNT +else +ifneq (, $(findstring CYGWIN,$(OS))) + OS := WINNT +else +ifneq (, $(findstring Windows_NT,$(OS))) + OS := WINNT +endif +endif +endif +endif + +# Define the program used for compiling C source files: +ifdef C_COMPILER + CC := $(C_COMPILER) +else + CC := gcc +endif + +# Define the command-line options when compiling C files: +CFLAGS ?= \ + -std=c99 \ + -O3 \ + -Wall \ + -pedantic + +# Determine whether to generate position independent code ([1][1], [2][2]). +# +# [1]: https://gcc.gnu.org/onlinedocs/gcc/Code-Gen-Options.html#Code-Gen-Options +# [2]: http://stackoverflow.com/questions/5311515/gcc-fpic-option +ifeq ($(OS), WINNT) + fPIC ?= +else + fPIC ?= -fPIC +endif + +# List of includes (e.g., `-I /foo/bar -I /beep/boop/include`): +INCLUDE ?= + +# List of source files: +SOURCE_FILES ?= + +# List of libraries (e.g., `-lopenblas -lpthread`): +LIBRARIES ?= + +# List of library paths (e.g., `-L /foo/bar -L /beep/boop`): +LIBPATH ?= + +# List of C targets: +c_targets := example.out + + +# RULES # + +#/ +# Compiles source files. +# +# @param {string} [C_COMPILER] - C compiler (e.g., `gcc`) +# @param {string} [CFLAGS] - C compiler options +# @param {(string|void)} [fPIC] - compiler flag determining whether to generate position independent code (e.g., `-fPIC`) +# @param {string} [INCLUDE] - list of includes (e.g., `-I /foo/bar -I /beep/boop/include`) +# @param {string} [SOURCE_FILES] - list of source files +# @param {string} [LIBPATH] - list of library paths (e.g., `-L /foo/bar -L /beep/boop`) +# @param {string} [LIBRARIES] - list of libraries (e.g., `-lopenblas -lpthread`) +# +# @example +# make +# +# @example +# make all +#/ +all: $(c_targets) + +.PHONY: all + +#/ +# Compiles C source files. +# +# @private +# @param {string} CC - C compiler (e.g., `gcc`) +# @param {string} CFLAGS - C compiler options +# @param {(string|void)} fPIC - compiler flag determining whether to generate position independent code (e.g., `-fPIC`) +# @param {string} INCLUDE - list of includes (e.g., `-I /foo/bar`) +# @param {string} SOURCE_FILES - list of source files +# @param {string} LIBPATH - list of library paths (e.g., `-L /foo/bar`) +# @param {string} LIBRARIES - list of libraries (e.g., `-lopenblas`) +#/ +$(c_targets): %.out: %.c + $(QUIET) $(CC) $(CFLAGS) $(fPIC) $(INCLUDE) -o $@ $(SOURCE_FILES) $< $(LIBPATH) -lm $(LIBRARIES) + +#/ +# Runs compiled examples. +# +# @example +# make run +#/ +run: $(c_targets) + $(QUIET) ./$< + +.PHONY: run + +#/ +# Removes generated files. +# +# @example +# make clean +#/ +clean: + $(QUIET) -rm -f *.o *.out + +.PHONY: clean diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/examples/c/example.c b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/examples/c/example.c new file mode 100644 index 000000000000..3b7f83892f26 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/examples/c/example.c @@ -0,0 +1,48 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2025 The Stdlib Authors. +* +* Licensed under the Apache License, Version 2.0 (the "License"); +* you may not use this file except in compliance with the License. +* You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, software +* distributed under the License is distributed on an "AS IS" BASIS, +* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +* See the License for the specific language governing permissions and +* limitations under the License. +*/ + +#include "stdlib/stats/base/dists/hypergeometric/pmf.h" +#include "stdlib/math/base/special/round.h" +#include +#include + +static double random_uniform( const double min, const double max ) { + double v = (double)rand() / ( (double)RAND_MAX + 1.0 ); + return min + ( v*(max-min) ); +} + +int main( void ) { + double N; + double K; + double n; + double x; + double pmf; + int i; + + for ( i = 0; i < 10; i++ ) { + N = stdlib_base_round(random_uniform(1.0, 20.0)); + K = stdlib_base_round(random_uniform(0.0, N)); + n = stdlib_base_round(random_uniform(0.0, N)); + x = stdlib_base_round(random_uniform(0.0, n)); + pmf = stdlib_base_dists_hypergeometric_pmf( x, N, K, n ); + + printf( "N: %lf, K: %lf, n: %lf, x: %lf, PMF: %lf\n", N, K, n, x, pmf ); + } + + return 0; +} From 8daa9eec6ffb8ebe9f0b3f27b7e21d2d1f7b7107 Mon Sep 17 00:00:00 2001 From: Karan Anand Date: Sun, 5 Jan 2025 04:35:56 -0800 Subject: [PATCH 03/21] feat: add the JS native files --- .../pmf/benchmark/benchmark.native.js | 77 ++++++++++++ .../dists/hypergeometric/pmf/lib/native.js | 49 ++++++++ .../hypergeometric/pmf/test/test.native.js | 119 ++++++++++++++++++ 3 files changed, 245 insertions(+) create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/benchmark.native.js create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/lib/native.js create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/test/test.native.js diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/benchmark.native.js b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/benchmark.native.js new file mode 100644 index 000000000000..19a409ca2958 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/benchmark/benchmark.native.js @@ -0,0 +1,77 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2025 The Stdlib Authors. +* +* Licensed under the Apache License, Version 2.0 (the "License"); +* you may not use this file except in compliance with the License. +* You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, software +* distributed under the License is distributed on an "AS IS" BASIS, +* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +* See the License for the specific language governing permissions and +* limitations under the License. +*/ + +'use strict'; + +// MODULES // + +var resolve = require( 'path' ).resolve; +var bench = require( '@stdlib/bench' ); +var Float64Array = require( '@stdlib/array/float64' ); +var randu = require( '@stdlib/random/base/randu' ); +var isnan = require( '@stdlib/math/base/assert/is-nan' ); +var tryRequire = require( '@stdlib/utils/try-require' ); +var round = require( '@stdlib/math/base/special/round' ); +var pkg = require( './../package.json' ).name; + + +// VARIABLES // + +var pmf = tryRequire( resolve( __dirname, './../lib/native.js' ) ); +var opts = { + 'skip': ( pmf instanceof Error ) +}; + + +// MAIN // + +bench( pkg+'::native', opts, function benchmark( b ) { + var len; + var N; + var K; + var n; + var x; + var y; + var i; + + len = 100; + N = new Float64Array( len ); + K = new Float64Array( len ); + n = new Float64Array( len ); + x = new Float64Array( len ); + for ( i = 0; i < len; i++ ) { + N[ i ] = round( ( randu() * 90.0 ) + 10.0 ); + K[ i ] = round( randu() * N[ i ] ); + n[ i ] = round( randu() * N[ i ] ); + x[ i ] = round( randu() * n[ i ] ); + } + + b.tic(); + for ( i = 0; i < b.iterations; i++ ) { + y = pmf( x[ i % len ], N[ i % len ], K[ i % len ], n[ i % len ] ); + if ( isnan( y ) ) { + b.fail( 'should not return NaN' ); + } + } + b.toc(); + if ( isnan( y ) ) { + b.fail( 'should not return NaN' ); + } + b.pass( 'benchmark finished' ); + b.end(); +}); diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/lib/native.js b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/lib/native.js new file mode 100644 index 000000000000..e055e13f9cd3 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/lib/native.js @@ -0,0 +1,49 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2025 The Stdlib Authors. +* +* Licensed under the Apache License, Version 2.0 (the "License"); +* you may not use this file except in compliance with the License. +* You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, software +* distributed under the License is distributed on an "AS IS\" BASIS, +* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +* See the License for the specific language governing permissions and +* limitations under the License. +*/ + +'use strict'; + +// MODULES // + +var addon = require( './../src/addon.node' ); + + +// MAIN // + +/** +* Evaluates the probability mass function (PMF) for a hypergeometric distribution. +* +* @private +* @param {number} x - number of successes +* @param {number} N - population size +* @param {number} K - subpopulation size +* @param {number} n - number of draws +* @returns {number} evaluated PMF +* +* @example +* var p = pmf( 2, 10, 5, 4 ); +* // returns ~0.238 +*/ +function pmf( x, N, K, n ) { + return addon( x, N, K, n ); +} + + +// EXPORTS // + +module.exports = pmf; diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/test/test.native.js b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/test/test.native.js new file mode 100644 index 000000000000..22a42fe7a34a --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/test/test.native.js @@ -0,0 +1,119 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2025 The Stdlib Authors. +* +* Licensed under the Apache License, Version 2.0 (the "License"); +* you may not use this file except in compliance with the License. +* You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, software +* distributed under the License is distributed on an "AS IS" BASIS, +* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +* See the License for the specific language governing permissions and +* limitations under the License. +*/ + +'use strict'; + +// MODULES // + +var resolve = require( 'path' ).resolve; +var tape = require( 'tape' ); +var tryRequire = require( '@stdlib/utils/try-require' ); +var isnan = require( '@stdlib/math/base/assert/is-nan' ); +var abs = require( '@stdlib/math/base/special/abs' ); + + +// VARIABLES // + +var pmf = tryRequire(resolve(__dirname, './../lib/native.js')); +var opts = { + 'skip': (pmf instanceof Error) +}; + + +// TESTS // + +tape('main export is a function', opts, function test(t) { + t.ok(true, __filename); + t.strictEqual(typeof pmf, 'function', 'main export is a function'); + t.end(); +}); + +tape('if provided `NaN` for any parameter, the function returns `NaN`', opts, function test(t) { + var v; + + v = pmf(NaN, 10, 5, 2); + t.equal(isnan(v), true, 'returns NaN'); + + v = pmf(2, NaN, 5, 2); + t.equal(isnan(v), true, 'returns NaN'); + + v = pmf(2, 10, NaN, 2); + t.equal(isnan(v), true, 'returns NaN'); + + v = pmf(2, 10, 5, NaN); + t.equal(isnan(v), true, 'returns NaN'); + + t.end(); +}); + +tape('if provided invalid inputs, the function returns `NaN`', opts, function test(t) { + var v; + + v = pmf(2, -10, 5, 2); + t.equal(isnan(v), true, 'returns NaN'); + + v = pmf(2, 10.5, 5, 2); + t.equal(isnan(v), true, 'returns NaN'); + + v = pmf(2, 10, -5, 2); + t.equal(isnan(v), true, 'returns NaN'); + + v = pmf(2, 10, 5.5, 2); + t.equal(isnan(v), true, 'returns NaN'); + + v = pmf(2, 10, 5, -2); + t.equal(isnan(v), true, 'returns NaN'); + + v = pmf(2, 10, 5, 2.5); + t.equal(isnan(v), true, 'returns NaN'); + + t.end(); +}); + +tape('the function evaluates the PMF for a hypergeometric distribution', opts, function test(t) { + var testCases = [{ + 'x': 1.0, + 'N': 8, + 'K': 4, + 'n': 2, + 'expected': 0.571 + }, + { + 'x': 2.0, + 'N': 8, + 'K': 4, + 'n': 2, + 'expected': 0.214 + }, + { + 'x': 0.0, + 'N': 8, + 'K': 4, + 'n': 2, + 'expected': 0.214 + }]; + var tol = 1e-3; + + testCases.forEach(function evaluateTestCase(testCase) { + var computedPMF = pmf(testCase.x, testCase.N, testCase.K, testCase.n); + var delta = abs(computedPMF - testCase.expected); + t.ok(delta <= tol, 'within tolerance. x: ' + testCase.x + ', N: ' + testCase.N + ', K: ' + testCase.K + ', n: ' + testCase.n + ', y: ' + computedPMF + ', expected: ' + testCase.expected + ', Δ: ' + delta + ', tol: ' + tol); + }); + + t.end(); +}); From f370792c9695be090792352069785595af90dcbc Mon Sep 17 00:00:00 2001 From: Karan Anand Date: Sun, 5 Jan 2025 04:36:17 -0800 Subject: [PATCH 04/21] build: added the json and gyp dependency files --- .../base/dists/hypergeometric/pmf/binding.gyp | 149 ++++++++++++++++++ .../dists/hypergeometric/pmf/include.gypi | 48 ++++++ .../dists/hypergeometric/pmf/manifest.json | 96 +++++++++++ .../dists/hypergeometric/pmf/package.json | 3 + 4 files changed, 296 insertions(+) create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/binding.gyp create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/include.gypi create mode 100644 lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/manifest.json diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/binding.gyp b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/binding.gyp new file mode 100644 index 000000000000..114dcb77c6aa --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/binding.gyp @@ -0,0 +1,149 @@ +# @license Apache-2.0 +# +# Copyright (c) 2025 The Stdlib Authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +# A `.gyp` file for building a Node.js native add-on. +# +# [1]: https://gyp.gsrc.io/docs/InputFormatReference.md +# [2]: https://gyp.gsrc.io/docs/UserDocumentation.md +{ + # List of files to include in this file: + "includes": [ + "./include.gypi", + ], + # Define variables to be used throughout the configuration for all targets: + "variables": { + # Target name should match the add-on export name: + "addon_target_name%": "addon", + # Set variables based on the host OS: + "conditions": [ + [ + 'OS=="win"', + { + # Define the object file suffix: + "obj": "obj", + }, + { + # Define the object file suffix: + "obj": "o", + }, + ], # end condition (OS=="win") + ], # end conditions + }, # end variables + # Define compile targets: + "targets": [ + # Target to generate an add-on: + { + # The target name should match the add-on export name: + "target_name": "<(addon_target_name)", + # Define dependencies: + "dependencies": [], + # Define directories which contain relevant include headers: + "include_dirs": [ + # Local include directory: + "<@(include_dirs)", + ], + # List of source files: + "sources": [ + "<@(src_files)", + "src/addon.c", + ], + # Settings which should be applied when a target's object files are used as linker input: + "link_settings": { + # Define libraries: + "libraries": [ + "<@(libraries)", + ], + # Define library directories: + "library_dirs": [ + "<@(library_dirs)", + ], + }, + # C/C++ compiler flags: + "cflags": [ + # Enable commonly used warning options: + "-Wall", + # Aggressive optimization: + "-O3", + ], + # C specific compiler flags: + "cflags_c": [ + # Specify the C standard to which a program is expected to conform: + "-std=c99", + ], + # C++ specific compiler flags: + "cflags_cpp": [ + # Specify the C++ standard to which a program is expected to conform: + "-std=c++11", + ], + # Linker flags: + "ldflags": [], + # Apply conditions based on the host OS: + "conditions": [ + [ + 'OS=="mac"', + { + # Linker flags: + "ldflags": [ + "-undefined dynamic_lookup", + "-Wl,-no-pie", + "-Wl,-search_paths_first", + ], + }, + ], # end condition (OS=="mac") + [ + 'OS!="win"', + { + # C/C++ flags: + "cflags": [ + # Generate platform-independent code: + "-fPIC", + ], + }, + ], # end condition (OS!="win") + ], # end conditions + }, # end target <(addon_target_name) + # Target to copy a generated add-on to a standard location: + { + "target_name": "copy_addon", + # Declare that the output of this target is not linked: + "type": "none", + # Define dependencies: + "dependencies": [ + # Require that the add-on be generated before building this target: + "<(addon_target_name)", + ], + # Define a list of actions: + "actions": [ + { + "action_name": "copy_addon", + "message": "Copying addon...", + # Explicitly list the inputs in the command-line invocation below: + "inputs": [], + # Declare the expected outputs: + "outputs": [ + "<(addon_output_dir)/<(addon_target_name).node", + ], + # Define the command-line invocation: + "action": [ + "cp", + "<(PRODUCT_DIR)/<(addon_target_name).node", + "<(addon_output_dir)/<(addon_target_name).node", + ], + }, + ], # end actions + }, # end target copy_addon + ], # end targets +} diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/include.gypi b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/include.gypi new file mode 100644 index 000000000000..235be47d6d3b --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/include.gypi @@ -0,0 +1,48 @@ +# @license Apache-2.0 +# +# Copyright (c) 2025 The Stdlib Authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +# A GYP include file for building a Node.js native add-on. +# +# Main documentation: +# +# [1]: https://gyp.gsrc.io/docs/InputFormatReference.md +# [2]: https://gyp.gsrc.io/docs/UserDocumentation.md +{ + # Define variables to be used throughout the configuration for all targets: + "variables": { + # Source directory: + "src_dir": "./src", + # Include directories: + "include_dirs": [ + " Date: Sun, 5 Jan 2025 04:36:31 -0800 Subject: [PATCH 05/21] docs: update README with C API documentation --- .../base/dists/hypergeometric/pmf/README.md | 105 ++++++++++++++++++ 1 file changed, 105 insertions(+) diff --git a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/README.md b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/README.md index 29f90e9aaf98..240e4b761083 100644 --- a/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/README.md +++ b/lib/node_modules/@stdlib/stats/base/dists/hypergeometric/pmf/README.md @@ -157,6 +157,111 @@ for ( i = 0; i < 10; i++ ) { + + +* * * + +
+ +## C APIs + + + +
+ +
+ + + + + +
+ +### Usage + +```c +#include "stdlib/stats/base/dists/hypergeometric/pmf.h" +``` + +#### stdlib_base_dists_hypergeometric_pmf( x, N, K, n ) + +Evaluates the probability mass function (PMF) for a hypergeometric distribution with population size `N`, subpopulation size `K`, and number of draws `n`. + +```c +double out = stdlib_base_dists_hypergeometric_stdev( 16, 11, 4 ); +// returns ~0.829 +``` + +The function accepts the following arguments: + +- **x**: `[in] double` input value. +- **N**: `[in] double` population size. +- **K**: `[in] double` subpopulation size. +- **n**: `[in] double` number of draws. + +```c +double stdlib_base_dists_hypergeometric_pmf ( const double x, const double N, const double K, const double n ); +``` + +
+ + + + + +
+ +
+ + + + + +
+ +### Examples + +```c +#include "stdlib/stats/base/dists/hypergeometric/pmf.h" +#include "stdlib/math/base/special/round.h" +#include +#include + +static double random_uniform( const double min, const double max ) { + double v = (double)rand() / ( (double)RAND_MAX + 1.0 ); + return min + ( v*(max-min) ); +} + +int main( void ) { + double N; + double K; + double n; + double x; + double pmf; + int i; + + for ( i = 0; i < 10; i++ ) { + N = stdlib_base_round(random_uniform(1.0, 20.0)); + K = stdlib_base_round(random_uniform(0.0, N)); + n = stdlib_base_round(random_uniform(0.0, N)); + x = stdlib_base_round(random_uniform(0.0, n)); + pmf = stdlib_base_dists_hypergeometric_pmf( x, N, K, n ); + + printf( "N: %lf, K: %lf, n: %lf, x: %lf, PMF: %lf\n", N, K, n, x, pmf ); + } + + return 0; +} +``` + +
+ + + +
+ + +