From f40c20c4def7b56eedacb3c46bc418fc9ae198da Mon Sep 17 00:00:00 2001 From: Philipp Burckhardt Date: Fri, 28 Aug 2026 00:14:10 -0500 Subject: [PATCH] feat: add C implementation for `stats/base/dists/negative-binomial/logpmf` PR-URL: https://github.com/stdlib-js/stdlib/pull/10132 Co-authored-by: nirmaljb Co-Authored-By: Claude Fable 5 --- .../dists/negative-binomial/logpmf/README.md | 111 +++++++++- .../logpmf/benchmark/benchmark.js | 3 +- .../logpmf/benchmark/benchmark.native.js | 72 ++++++ .../logpmf/benchmark/c/Makefile | 146 +++++++++++++ .../logpmf/benchmark/c/benchmark.c | 145 +++++++++++++ .../negative-binomial/logpmf/binding.gyp | 170 +++++++++++++++ .../logpmf/examples/c/Makefile | 146 +++++++++++++ .../logpmf/examples/c/example.c | 44 ++++ .../negative-binomial/logpmf/include.gypi | 53 +++++ .../base/dists/negative-binomial/logpmf.h | 38 ++++ .../negative-binomial/logpmf/lib/native.js | 96 ++++++++ .../negative-binomial/logpmf/manifest.json | 90 ++++++++ .../negative-binomial/logpmf/package.json | 3 + .../negative-binomial/logpmf/src/Makefile | 70 ++++++ .../negative-binomial/logpmf/src/addon.c | 22 ++ .../dists/negative-binomial/logpmf/src/main.c | 58 +++++ .../logpmf/test/test.factory.js | 10 +- .../test/{test.logpmf.js => test.main.js} | 10 +- .../logpmf/test/test.native.js | 205 ++++++++++++++++++ 19 files changed, 1479 insertions(+), 13 deletions(-) create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/benchmark.native.js create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/c/Makefile create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/c/benchmark.c create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/binding.gyp create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/examples/c/Makefile create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/examples/c/example.c create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/include.gypi create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/include/stdlib/stats/base/dists/negative-binomial/logpmf.h create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/lib/native.js create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/manifest.json create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/src/Makefile create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/src/addon.c create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/src/main.c rename lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/{test.logpmf.js => test.main.js} (90%) create mode 100644 lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.native.js diff --git a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/README.md b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/README.md index 0143acf5f34a..0fdf34540615 100644 --- a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/README.md +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/README.md @@ -2,7 +2,7 @@ @license Apache-2.0 -Copyright (c) 2018 The Stdlib Authors. +Copyright (c) 2026 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. @@ -157,6 +157,115 @@ logEachMap( 'x: %d, r: %0.4f, p: %0.4f, ln(P(X=x;r,p)): %0.4f', x, r, p, logpmf + + +* * * + +
+ +## C APIs + + + +
+ +
+ + + + + +
+ +### Usage + +```c +#include "stdlib/stats/base/dists/negative-binomial/logpmf.h" +``` + +#### stdlib_base_dists_negative_binomial_logpmf( x, r, p ) + +Evaluates the natural logarithm of the probability mass function (PMF) for a negative binomial distribution with number of successes until experiment is stopped `r` and success probability `p`. + +```c +double out = stdlib_base_dists_negative_binomial_logpmf( 5.0, 20.0, 0.8 ); +// returns ~-1.853 +``` + +The function accepts the following arguments: + +- **x**: `[in] double` input value. +- **r**: `[in] double` number of successes until experiment is stopped. +- **p**: `[in] double` success probability. + +```c +double stdlib_base_dists_negative_binomial_logpmf( const double x, const double r, const double p ); +``` + +
+ + + + + +
+ +
+ + + + + +
+ +### Examples + +```c +#include "stdlib/stats/base/dists/negative-binomial/logpmf.h" +#include "stdlib/math/base/special/ceil.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 r; + double p; + double x; + double y; + int i; + + for ( i = 0; i < 10; i++ ) { + x = stdlib_base_ceil( random_uniform( 0.0, 30.0 ) ); + r = random_uniform( 0.0, 50.0 ); + p = random_uniform( 0.0, 1.0 ); + y = stdlib_base_dists_negative_binomial_logpmf( x, r, p ); + printf( "x: %lf, r: %lf, p: %lf, ln(P(X=x;r,p)): %lf\n", x, r, p, y ); + } + + return 0; +} +``` + +
+ + + +
+ + + + + +
+ +
+ + +
diff --git a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/benchmark.js b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/benchmark.js index 53dfd9f2a70a..ef27451ebf46 100644 --- a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/benchmark.js +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/benchmark.js @@ -25,7 +25,6 @@ var uniform = require( '@stdlib/random/array/uniform' ); var discreteUniform = require( '@stdlib/random/array/discrete-uniform' ); var isnan = require( '@stdlib/math/base/assert/is-nan' ); var EPS = require( '@stdlib/constants/float64/eps' ); -var format = require( '@stdlib/string/format' ); var pkg = require( './../package.json' ).name; var logpmf = require( './../lib' ); @@ -62,7 +61,7 @@ bench( pkg, function benchmark( b ) { b.end(); }); -bench( format( '%s::factory', pkg ), function benchmark( b ) { +bench( pkg+':factory', function benchmark( b ) { var mylogpmf; var opts; var r; diff --git a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/benchmark.native.js b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/benchmark.native.js new file mode 100644 index 000000000000..a5244d6e66d2 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/benchmark.native.js @@ -0,0 +1,72 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2026 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 tryRequire = require( '@stdlib/utils/try-require' ); +var bench = require( '@stdlib/bench' ); +var uniform = require( '@stdlib/random/array/uniform' ); +var discreteUniform = require( '@stdlib/random/array/discrete-uniform' ); +var isnan = require( '@stdlib/math/base/assert/is-nan' ); +var format = require( '@stdlib/string/format' ); +var EPS = require( '@stdlib/constants/float64/eps' ); +var pkg = require( './../package.json' ).name; + + +// VARIABLES // + +var logpmf = tryRequire( resolve( __dirname, './../lib/native.js' ) ); +var opts = { + 'skip': ( logpmf instanceof Error ) +}; + + +// MAIN // + +bench( format( '%s::native', pkg ), opts, function benchmark( b ) { + var arrayOpts; + var r; + var p; + var x; + var y; + var i; + + arrayOpts = { + 'dtype': 'float64' + }; + x = discreteUniform( 100, 1, 100, arrayOpts ); + r = discreteUniform( 100, 1, 100, arrayOpts ); + p = uniform( 100, EPS, 1.0, arrayOpts ); + + b.tic(); + for ( i = 0; i < b.iterations; i++ ) { + y = logpmf( x[ i % x.length ], r[ i % r.length ], p[ i % p.length ] ); + 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/negative-binomial/logpmf/benchmark/c/Makefile b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/c/Makefile new file mode 100644 index 000000000000..979768abbcec --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/c/Makefile @@ -0,0 +1,146 @@ +#/ +# @license Apache-2.0 +# +# Copyright (c) 2026 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/negative-binomial/logpmf/benchmark/c/benchmark.c b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/c/benchmark.c new file mode 100644 index 000000000000..2b833fd4f5e6 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/benchmark/c/benchmark.c @@ -0,0 +1,145 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2026 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/negative-binomial/logpmf.h" +#include "stdlib/constants/float64/eps.h" +#include "stdlib/math/base/special/ceil.h" +#include +#include +#include +#include +#include +#include + +#define NAME "negative-binomial-logpmf" +#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 r[ 100 ]; + double p[ 100 ]; + double x[ 100 ]; + double elapsed; + double y; + double t; + int32_t i; + + for ( i = 0; i < 100; i++ ) { + x[ i ] = stdlib_base_ceil( random_uniform( 1.0, 100.0 ) ); + r[ i ] = stdlib_base_ceil( random_uniform( 1.0, 100.0 ) ); + p[ i ] = random_uniform( STDLIB_CONSTANT_FLOAT64_EPS, 1.0 ); + } + + t = tic(); + for ( i = 0; i < ITERATIONS; i++ ) { + y = stdlib_base_dists_negative_binomial_logpmf( x[ i%100 ], r[ i%100 ], p[ i%100 ]); + if ( y != y ) { + printf( "should not return NaN\n" ); + break; + } + } + elapsed = tic() - t; + if ( y != y ) { + 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/negative-binomial/logpmf/binding.gyp b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/binding.gyp new file mode 100644 index 000000000000..0d6508a12e99 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/binding.gyp @@ -0,0 +1,170 @@ +# @license Apache-2.0 +# +# Copyright (c) 2026 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)', + ], + + # 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/negative-binomial/logpmf/examples/c/Makefile b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/examples/c/Makefile new file mode 100644 index 000000000000..c8f8e9a1517b --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/examples/c/Makefile @@ -0,0 +1,146 @@ +#/ +# @license Apache-2.0 +# +# Copyright (c) 2026 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/negative-binomial/logpmf/examples/c/example.c b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/examples/c/example.c new file mode 100644 index 000000000000..0246ebeba528 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/examples/c/example.c @@ -0,0 +1,44 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2026 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/negative-binomial/logpmf.h" +#include "stdlib/math/base/special/ceil.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 r; + double p; + double x; + double y; + int i; + + for ( i = 0; i < 10; i++ ) { + x = stdlib_base_ceil( random_uniform( 0.0, 30.0 ) ); + r = random_uniform( 0.0, 50.0 ); + p = random_uniform( 0.0, 1.0 ); + y = stdlib_base_dists_negative_binomial_logpmf( x, r, p ); + printf( "x: %lf, r: %lf, p: %lf, ln(P(X;r,p)): %lf\n", x, r, p, y ); + } + return 0; +} diff --git a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/include.gypi b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/include.gypi new file mode 100644 index 000000000000..bee8d41a2caf --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/include.gypi @@ -0,0 +1,53 @@ +# @license Apache-2.0 +# +# Copyright (c) 2026 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': [ + ' + +/** +* Evaluates the natural logarithm of the probability mass function (PMF) for a negative binomial distribution with number of successes until experiment is stopped `r` and success probability `p` at a value `x`. +* +* @param x input value +* @param r number of successes until experiment is stopped +* @param p success probability +* @return evaluated logPMF +* +* @example +* double y = stdlib_base_dists_negative_binomial_logpmf( 5.0, 20.0, 0.8 ); +* // returns ~-1.853 +*/ +double stdlib_base_dists_negative_binomial_logpmf( const double x, const double r, const double p ) { + double derivative; + double out; + if ( + stdlib_base_is_nan( x ) || + stdlib_base_is_nan( r ) || + stdlib_base_is_nan( p ) || + r <= 0.0 || + p <= 0.0 || + p > 1.0 + ) { + return 0.0 / 0.0; // NaN + } + if ( !stdlib_base_is_nonnegative_integer( x ) || p == 0.0 ) { + return STDLIB_CONSTANT_FLOAT64_NINF; + } + // Compute the derivative of the regularized incomplete beta function: + stdlib_base_kernel_betainc( p, r, x + 1.0, true, false, &out, &derivative ); + return stdlib_base_ln( p ) - stdlib_base_ln( r + x ) + stdlib_base_ln( derivative ); +} diff --git a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.factory.js b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.factory.js index 6f08b7e9e619..38a9146ee08e 100644 --- a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.factory.js +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.factory.js @@ -21,8 +21,8 @@ // MODULES // var tape = require( 'tape' ); -var isAlmostSameValue = require( '@stdlib/assert/is-almost-same-value' ); var isnan = require( '@stdlib/math/base/assert/is-nan' ); +var isAlmostSameValue = require( '@stdlib/assert/is-almost-same-value' ); var PINF = require( '@stdlib/constants/float64/pinf' ); var NINF = require( '@stdlib/constants/float64/ninf' ); var factory = require( './../lib/factory.js' ); @@ -187,7 +187,7 @@ tape( 'the created function evaluates the logpmf for `x` given large `r` and `p` for ( i = 0; i < x.length; i++ ) { logpmf = factory( r[i], p[i] ); y = logpmf( x[i] ); - t.strictEqual( isAlmostSameValue( y, expected[i], 109 ), true, 'returns expected value' ); + t.strictEqual( isAlmostSameValue( y, expected[i], 160 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); } t.end(); }); @@ -208,7 +208,7 @@ tape( 'the created function evaluates the logpmf for `x` given a large parameter for ( i = 0; i < x.length; i++ ) { logpmf = factory( r[i], p[i] ); y = logpmf( x[i] ); - t.strictEqual( isAlmostSameValue( y, expected[i], 9 ), true, 'returns expected value' ); + t.strictEqual( isAlmostSameValue( y, expected[i], 10 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); } t.end(); }); @@ -229,7 +229,7 @@ tape( 'the created function evaluates the logpmf for `x` given small `r` and lar for ( i = 0; i < x.length; i++ ) { logpmf = factory( r[i], p[i] ); y = logpmf( x[i] ); - t.strictEqual( isAlmostSameValue( y, expected[i], 57 ), true, 'returns expected value' ); + t.strictEqual( isAlmostSameValue( y, expected[i], 60 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); } t.end(); }); @@ -250,7 +250,7 @@ tape( 'the created function evaluates the logpmf for `x` given small `r` and `p` for ( i = 0; i < x.length; i++ ) { logpmf = factory( r[i], p[i] ); y = logpmf( x[i] ); - t.strictEqual( isAlmostSameValue( y, expected[i], 6 ), true, 'returns expected value' ); + t.strictEqual( isAlmostSameValue( y, expected[i], 6 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); } t.end(); }); diff --git a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.logpmf.js b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.main.js similarity index 90% rename from lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.logpmf.js rename to lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.main.js index c86877ebcc66..79a64d4806dd 100644 --- a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.logpmf.js +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.main.js @@ -21,8 +21,8 @@ // MODULES // var tape = require( 'tape' ); -var isAlmostSameValue = require( '@stdlib/assert/is-almost-same-value' ); var isnan = require( '@stdlib/math/base/assert/is-nan' ); +var isAlmostSameValue = require( '@stdlib/assert/is-almost-same-value' ); var PINF = require( '@stdlib/constants/float64/pinf' ); var NINF = require( '@stdlib/constants/float64/ninf' ); var logpmf = require( './../lib' ); @@ -133,7 +133,7 @@ tape( 'the function evaluates the logpmf for `x` given large `r` and `p`', funct p = highHigh.p; for ( i = 0; i < x.length; i++ ) { y = logpmf( x[i], r[i], p[i] ); - t.strictEqual( isAlmostSameValue( y, expected[i], 109 ), true, 'returns expected value' ); + t.strictEqual( isAlmostSameValue( y, expected[i], 160 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); } t.end(); }); @@ -152,7 +152,7 @@ tape( 'the function evaluates the logpmf for `x` given large parameter `r` and s p = highSmall.p; for ( i = 0; i < x.length; i++ ) { y = logpmf( x[i], r[i], p[i] ); - t.strictEqual( isAlmostSameValue( y, expected[i], 9 ), true, 'returns expected value' ); + t.strictEqual( isAlmostSameValue( y, expected[i], 10 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); } t.end(); }); @@ -171,7 +171,7 @@ tape( 'the function evaluates the logpmf for `x` given small `r` and large `p`', p = smallHigh.p; for ( i = 0; i < x.length; i++ ) { y = logpmf( x[i], r[i], p[i] ); - t.strictEqual( isAlmostSameValue( y, expected[i], 57 ), true, 'returns expected value' ); + t.strictEqual( isAlmostSameValue( y, expected[i], 60 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); } t.end(); }); @@ -190,7 +190,7 @@ tape( 'the function evaluates the logpmf for `x` given small `r` and `p`', funct p = smallSmall.p; for ( i = 0; i < x.length; i++ ) { y = logpmf( x[i], r[i], p[i] ); - t.strictEqual( isAlmostSameValue( y, expected[i], 6 ), true, 'returns expected value' ); + t.strictEqual( isAlmostSameValue( y, expected[i], 6 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); } t.end(); }); diff --git a/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.native.js b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.native.js new file mode 100644 index 000000000000..c64488099106 --- /dev/null +++ b/lib/node_modules/@stdlib/stats/base/dists/negative-binomial/logpmf/test/test.native.js @@ -0,0 +1,205 @@ +/** +* @license Apache-2.0 +* +* Copyright (c) 2026 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 isAlmostSameValue = require( '@stdlib/assert/is-almost-same-value' ); +var PINF = require( '@stdlib/constants/float64/pinf' ); +var NINF = require( '@stdlib/constants/float64/ninf' ); + + +// VARIABLES // + +var logpmf = tryRequire( resolve( __dirname, './../lib/native.js' ) ); +var opts = { + 'skip': ( logpmf instanceof Error ) +}; + + +// FIXTURES // + +var smallSmall = require( './fixtures/julia/small_small.json' ); +var smallHigh = require( './fixtures/julia/small_high.json' ); +var highSmall = require( './fixtures/julia/high_small.json' ); +var highHigh = require( './fixtures/julia/high_high.json' ); + + +// TESTS // + +tape( 'main export is a function', opts, function test( t ) { + t.ok( true, __filename ); + t.strictEqual( typeof logpmf, 'function', 'main export is a function' ); + t.end(); +}); + +tape( 'if provided `NaN` for any parameter, the function returns `NaN`', opts, function test( t ) { + var y = logpmf( NaN, 20.0, 0.5 ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + y = logpmf( 0.0, NaN, 0.5 ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + y = logpmf( 0.0, 20.0, NaN ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + t.end(); +}); + +tape( 'if provided a negative integer for `x` and a valid `r` and `p`, the function returns `-Infinity`', opts, function test( t ) { + var y = logpmf( NINF, 20, 0.5 ); + t.strictEqual( y, NINF, 'returns expected value' ); + + y = logpmf( -20.0, 20, 0.5 ); + t.strictEqual( y, NINF, 'returns expected value' ); + + y = logpmf( -100.0, 20, 0.5 ); + t.strictEqual( y, NINF, 'returns expected value' ); + + y = logpmf( -1.0, 20, 0.5 ); + t.strictEqual( y, NINF, 'returns expected value' ); + + t.end(); +}); + +tape( 'if provided a non-integer for `x` and a valid `r` and `p`, the function returns `-Infinity`', opts, function test( t ) { + var y = logpmf( -1.5, 20.0, 0.5 ); + t.strictEqual( y, NINF, 'returns expected value' ); + + y = logpmf( -0.5, 20.0, 0.5 ); + t.strictEqual( y, NINF, 'returns expected value' ); + + y = logpmf( 1.5, 20.0, 0.5 ); + t.strictEqual( y, NINF, 'returns expected value' ); + + y = logpmf( 2.5, 20.0, 0.5 ); + t.strictEqual( y, NINF, 'returns expected value' ); + + t.end(); +}); + +tape( 'if provided `r` which is not a positive number, the function returns `NaN`', opts, function test( t ) { + var y; + + y = logpmf( 2.0, -0.5, 0.5 ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + + y = logpmf( 0.0, -1.0, 0.5 ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + + y = logpmf( 2.0, NINF, 0.5 ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + + t.end(); +}); + +tape( 'if provided a success probability `p` outside of `[0,1]`, the function returns `NaN`', opts, function test( t ) { + var y; + + y = logpmf( 2.0, 20, -1.0 ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + + y = logpmf( 0.0, 20, 1.5 ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + + y = logpmf( 2.0, 20, NINF ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + + y = logpmf( 2.0, 20, PINF ); + t.strictEqual( isnan( y ), true, 'returns expected value' ); + + t.end(); +}); + +tape( 'the function evaluates the logpmf for `x` given large `r` and `p`', opts, function test( t ) { + var expected; + var i; + var r; + var p; + var x; + var y; + + expected = highHigh.expected; + x = highHigh.x; + r = highHigh.r; + p = highHigh.p; + for ( i = 0; i < x.length; i++ ) { + y = logpmf( x[i], r[i], p[i] ); + t.strictEqual( isAlmostSameValue( y, expected[i], 160 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); + } + t.end(); +}); + +tape( 'the function evaluates the logpmf for `x` given large parameter `r` and small `p`', opts, function test( t ) { + var expected; + var i; + var r; + var p; + var x; + var y; + + expected = highSmall.expected; + x = highSmall.x; + r = highSmall.r; + p = highSmall.p; + for ( i = 0; i < x.length; i++ ) { + y = logpmf( x[i], r[i], p[i] ); + t.strictEqual( isAlmostSameValue( y, expected[i], 10 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); + } + t.end(); +}); + +tape( 'the function evaluates the logpmf for `x` given small `r` and large `p`', opts, function test( t ) { + var expected; + var i; + var r; + var p; + var x; + var y; + + expected = smallHigh.expected; + x = smallHigh.x; + r = smallHigh.r; + p = smallHigh.p; + for ( i = 0; i < x.length; i++ ) { + y = logpmf( x[i], r[i], p[i] ); + t.strictEqual( isAlmostSameValue( y, expected[i], 60 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); + } + t.end(); +}); + +tape( 'the function evaluates the logpmf for `x` given small `r` and `p`', opts, function test( t ) { + var expected; + var i; + var r; + var p; + var x; + var y; + + expected = smallSmall.expected; + x = smallSmall.x; + r = smallSmall.r; + p = smallSmall.p; + for ( i = 0; i < x.length; i++ ) { + y = logpmf( x[i], r[i], p[i] ); + t.strictEqual( isAlmostSameValue( y, expected[i], 6 ), true, 'within tolerance. x: '+x[i]+'. r: '+r[i]+'. p: '+p[i]+'. y: '+y+'. E: '+expected[i]+'.' ); + } + t.end(); +});