sstat 0.0.10 → 0.0.11

data/ext/sstat/sstat.h

@@ -3,6 +3,7 @@
 #include <ruby.h>
 #include <stdio.h>
 #include <stdlib.h>
+
 #include "lib/survival/survival.h"
 #include "lib/survival/distribution.h"
 #include "lib/global_utility.h"
@@ -22,21 +23,33 @@ static VALUE rb_kaplan_meier_3p_extraploation(VALUE self, VALUE time, VALUE cens
 static VALUE rb_log_rank_test(VALUE self, VALUE time_1, VALUE censor_1,VALUE time_2, VALUE censor_2);
 
 static VALUE rb_cdf_unormal_Q(VALUE self, VALUE x);
+
+static VALUE rb_dist_chi_square_Q(VALUE self, VALUE index, VALUE degree);
+static VALUE rb_dist_chi_square_P(VALUE self, VALUE index, VALUE degree);
+
 static VALUE rb_hist_mean(VALUE self, VALUE bin, VALUE range);
 static VALUE rb_hist_median(VALUE self, VALUE bin, VALUE range);
 
+static VALUE rb_basic_(VALUE self, VALUE bin, VALUE range);
+
 void Init_sstat() {
     VALUE sstat_module = rb_define_module("SStat");
     VALUE surv_class = rb_define_class_under(sstat_module, "Surv", rb_cObject);
     VALUE dist_class = rb_define_class_under(sstat_module, "Dist", rb_cObject);
     VALUE hist_class = rb_define_class_under(sstat_module, "Hist", rb_cObject);
+
+    /* Functions for basic */
     rb_define_method(surv_class, "percentile_index", rb_percentile_index, 2);
     rb_define_method(surv_class, "percentile", rb_percentile, 2);
     rb_define_method(surv_class, "index_less_equal", rb_index_less_equal, 2);
     rb_define_method(surv_class, "kaplan_meier", rb_kaplan_meier, 2);
     rb_define_method(surv_class, "log_rank_test", rb_log_rank_test, 4);
     rb_define_method(surv_class, "kaplan_meier_3p_extraploation", rb_kaplan_meier_3p_extraploation, 2);
+
+    /* Functions for distribution */
     rb_define_method(dist_class, "cdf_unormal_Q", rb_cdf_unormal_Q, 1);
+
+    /* Functions for histogram */
     rb_define_method(hist_class, "hist_mean", rb_hist_mean, 2);
     rb_define_method(hist_class, "hist_median", rb_hist_median, 2);
 }

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sstat
 version: !ruby/object:Gem::Version
-  version: 0.0.10
+  version: 0.0.11
 platform: ruby
 authors:
 - Haipeng Li
@@ -10,30 +10,20 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-09-06 00:00:00.000000000 Z
+date: 2016-11-17 00:00:00.000000000 Z
 dependencies: []
 description: 
 email: haipeng3@ualberta.ca
 executables: []
 extensions:
-- ext/extconf.rb
 - ext/sstat/extconf.rb
 extra_rdoc_files: []
 files:
 - bin/#console#
 - bin/console
 - bin/setup
-- ext/extconf.rb
-- ext/lib/distribution.h
-- ext/lib/global_utility.h
-- ext/lib/survival.h
-- ext/lib/survival_def.h
-- ext/lib/survival_func.h
-- ext/lib/survival_utility.h
-- ext/lib/type_def.h
 - ext/sstat/Makefile
 - ext/sstat/extconf.rb
-- ext/sstat/lib/basic/log
 - ext/sstat/lib/basic/median.h
 - ext/sstat/lib/basic/median_test
 - ext/sstat/lib/basic/median_test.c
@@ -47,6 +37,7 @@ files:
 - ext/sstat/lib/histogram/histogram_type.h
 - ext/sstat/lib/histogram/log
 - ext/sstat/lib/histogram/test.sh
+- ext/sstat/lib/survival.tar.gz
 - ext/sstat/lib/survival/distribution.h
 - ext/sstat/lib/survival/global_utility.h
 - ext/sstat/lib/survival/survival.h
@@ -61,6 +52,7 @@ files:
 - ext/sstat/sstat.o
 - ext/sstat/sstat.so
 - lib/simple_statistics.rb
+- lib/sstat.o
 - lib/sstat.so
 homepage: 
 licenses:

data/ext/extconf.rb

@@ -1,4 +0,0 @@
-require 'mkmf'
-$CFLAGS << ' -std=gnu99 -Wno-declaration-after-statement'
-
-create_makefile('sstat')

data/ext/lib/distribution.h

@@ -1,274 +0,0 @@
-#ifndef _SSTAT_DISTRIBUTION_UTILITY_H_
-#define _SSTAT_DISTRIBUTION_UTILITY_H_
-#include "type_def.h"
-static double
-get_del (double x, double rational)
-{
-double xsq = 0.0;
-double del = 0.0;
-double result = 0.0;
- 
-xsq = floor (x * GAUSS_SCALE) / GAUSS_SCALE;
-del = (x - xsq) * (x + xsq);
-del *= 0.5;
- 
-result = exp (-0.5 * xsq * xsq) * exp (-1.0 * del) * rational;
- 
-return result;
-}
- 
-/*
- * Normal cdf for fabs(x) < 0.66291
- */
-static double
-gauss_small (const double x)
-{
-unsigned int i;
-double result = 0.0;
-double xsq;
-double xnum;
-double xden;
- 
-const double a[5] = {
-2.2352520354606839287,
-161.02823106855587881,
-1067.6894854603709582,
-18154.981253343561249,
-0.065682337918207449113
-};
-const double b[4] = {
-47.20258190468824187,
-976.09855173777669322,
-10260.932208618978205,
-45507.789335026729956
-};
- 
-xsq = x * x;
-xnum = a[4] * xsq;
-xden = xsq;
- 
-for (i = 0; i < 3; i++)
-{
-xnum = (xnum + a[i]) * xsq;
-xden = (xden + b[i]) * xsq;
-}
- 
-result = x * (xnum + a[3]) / (xden + b[3]);
- 
-return result;
-}
- 
-/*
- * Normal cdf for 0.66291 < fabs(x) < sqrt(32).
- */
-static double
-gauss_medium (const double x)
-{
-unsigned int i;
-double temp = 0.0;
-double result = 0.0;
-double xnum;
-double xden;
-double absx;
- 
-const double c[9] = {
-0.39894151208813466764,
-8.8831497943883759412,
-93.506656132177855979,
-597.27027639480026226,
-2494.5375852903726711,
-6848.1904505362823326,
-11602.651437647350124,
-9842.7148383839780218,
-1.0765576773720192317e-8
-};
-const double d[8] = {
-22.266688044328115691,
-235.38790178262499861,
-1519.377599407554805,
-6485.558298266760755,
-18615.571640885098091,
-34900.952721145977266,
-38912.003286093271411,
-19685.429676859990727
-};
- 
-absx = fabs (x);
- 
-xnum = c[8] * absx;
-xden = absx;
- 
-for (i = 0; i < 7; i++)
-{
-xnum = (xnum + c[i]) * absx;
-xden = (xden + d[i]) * absx;
-}
- 
-temp = (xnum + c[7]) / (xden + d[7]);
- 
-result = get_del (x, temp);
- 
-return result;
-}
- 
-/*
- * Normal cdf for
- * {sqrt(32) < x < GAUSS_XUPPER} union { GAUSS_XLOWER < x < -sqrt(32) }.
- */
-static double
-gauss_large (const double x)
-{
-int i;
-double result;
-double xsq;
-double temp;
-double xnum;
-double xden;
-double absx;
- 
-const double p[6] = {
-0.21589853405795699,
-0.1274011611602473639,
-0.022235277870649807,
-0.001421619193227893466,
-2.9112874951168792e-5,
-0.02307344176494017303
-};
-const double q[5] = {
-1.28426009614491121,
-0.468238212480865118,
-0.0659881378689285515,
-0.00378239633202758244,
-7.29751555083966205e-5
-};
- 
-absx = fabs (x);
-xsq = 1.0 / (x * x);
-xnum = p[5] * xsq;
-xden = xsq;
- 
-for (i = 0; i < 4; i++)
-{
-xnum = (xnum + p[i]) * xsq;
-xden = (xden + q[i]) * xsq;
-}
- 
-temp = xsq * (xnum + p[4]) / (xden + q[4]);
-temp = (M_1_SQRT2PI - temp) / absx;
- 
-result = get_del (x, temp);
- 
-return result;
-}
- 
-double
-gsl_cdf_ugaussian_P (const double x)
-{
-double result;
-double absx = fabs (x);
- 
-if (absx < GAUSS_EPSILON)
-{
-result = 0.5;
-return result;
-}
-else if (absx < 0.66291)
-{
-result = 0.5 + gauss_small (x);
-return result;
-}
-else if (absx < SQRT32)
-{
-result = gauss_medium (x);
- 
-if (x > 0.0)
-{
-result = 1.0 - result;
-}
- 
-return result;
-}
-else if (x > GAUSS_XUPPER)
-{
-result = 1.0;
-return result;
-}
-else if (x < GAUSS_XLOWER)
-{
-result = 0.0;
-return result;
-}
-else
-{
-result = gauss_large (x);
- 
-if (x > 0.0)
-{
-result = 1.0 - result;
-}
-}
- 
-return result;
-}
-
-double
-cdf_ugaussian_Q (const double x)
-{
-double result;
-double absx = fabs (x);
- 
-if (absx < GAUSS_EPSILON)
-{
-result = 0.5;
-return result;
-}
-else if (absx < 0.66291)
-{
-result = gauss_small (x);
- 
-if (x < 0.0)
-{
-result = fabs (result) + 0.5;
-}
-else
-{
-result = 0.5 - result;
-}
- 
-return result;
-}
-else if (absx < SQRT32)
-{
-result = gauss_medium (x);
- 
-if (x < 0.0)
-{
-result = 1.0 - result;
-}
- 
-return result;
-}
-else if (x > -(GAUSS_XLOWER))
-{
-result = 0.0;
-return result;
-}
-else if (x < -(GAUSS_XUPPER))
-{
-result = 1.0;
-return result;
-}
-else
-{
-result = gauss_large (x);
- 
-if (x < 0.0)
-{
-result = 1.0 - result;
-}
- 
-}
- 
-return result;
-}
-#endif

data/ext/lib/global_utility.h

@@ -1,17 +0,0 @@
-#ifndef _SSTAT_GLOBAL_UTILITY_H_
-#define _SSTAT_GLOBAL_UTILITY_H_
-#include <stdio.h>
-#include <stdlib.h>
-#include "type_def.h"
-
-int compare_double (const void * a, const void * b)
-{
-   return *((double*)a) > *((double*)b)? 1 : 0;
-}
-
-int point_compare_x (const void * a, const void * b)
-{
-	return ((struct point*)a)->x - ((struct point*)b)->x;
-}
-
-#endif

data/ext/lib/survival.h

@@ -1,6 +0,0 @@
-#ifndef _SURVIVAL_STAT_H_
-#define _SURVIVAL_STAT_H_
-
-#include "survival_func.h"
-
-#endif

data/ext/lib/survival_def.h

@@ -1,49 +0,0 @@
-#ifndef _SURVIVAL_STAT_DEF_H_
-#define _SURVIVAL_STAT_DEF_H_
-
-#include "type_def.h"
-#include <stdio>
-#include <stdlib>
-
-/* Define survival stat data structure */
-typedef struct Group_N
-{
-	/* Time stands for the event time */
-	double* time;
-
-	/* How many people died at different event times */
-	int * uncensored;
-
-	/* How many people censored at different event times */
-	int * censored;
-
-	int size;
-
-} Group_N;
-
-void free_Group_N(struct Group_N* grp_n)
-{
-	if(grp_n->time != NULL)
-		free(grp_n->time);
-
-	if(grp_n->uncensored != NULL )
-		free(grp_n->uncensored);
-
-	if(grp_n->censored != NULL )
-		free(grp_n->censored);
-}
-
-void put_Group_N(struct Group_N * grp_n)
-{
-	int i;
-	puts("Start to print out Group N");
-	for( i = 0; i < grp_n->size; i++ )
-	{
-		printf("Time : %f -- Uncensored : %f -- Censored : %f \n", 
-			grp_n-> time[i],
-			grp_n-> uncensored[i],
-			grp_n-> censored[i]);
-	}
-}
-
-#endif