sstat 0.0.7 → 0.0.8

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: df2e4f59b250fc4871f7e51bddf5a3cf1a3981cf
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+  data.tar.gz: c5ebfe534e122751870fc4fda46481ec8b11b6f0
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+  data.tar.gz: fef20644b53955330ff25c23b3dc6e21939d02f28586b4f86407ae53116a4f288c0b6e262b3ee22592dcf410a75a171f342139897a09c0c0e73787826a26c262

data/ext/sstat/lib/basic/basic.c

@@ -0,0 +1,4 @@
+#ifndef _BASIC_STAT_H_
+#define _BASIC_STAT_H_
+
+#endif

data/ext/sstat/lib/distribution.h

@@ -16,7 +16,7 @@ result = exp (-0.5 * xsq * xsq) * exp (-1.0 * del) * rational;
  
 return result;
 }
- 
+
 /*
  * Normal cdf for fabs(x) < 0.66291
  */

data/ext/sstat/lib/histogram/histogram_stat.h

@@ -3,71 +3,73 @@
 #include "histogram_type.h"
 
 /*
-*
+* Mean of a histogram
+* Compute the bin-weighted arithmetic mean M of a histogram using the recurrence relation
+* M(n) = M(n-1) + (x[n] - M(n-1)) (w(n)/(W(n-1) + w(n))) 
+* W(n) = W(n-1) + w(n)
 */
-int histogram_mean(const histogram* h, f_T* res)
+int histogram_mean(const struct histogram* h, double* hmean)
 {
-	int i, n;
-	f_T xi, wi;
-	f_T hmean = 0;
-	f_T W = 0;
-	n = h->n;
+    int i, n;
+    double xi, wi;
+    (*hmean) = 0;
+    double W = 0;
+    n = h->n;
 
-	for(i = 0; i < n; i++)
-	{
-		//make sure size of h->range is n + 1
-		xi = (h->range[i+1] + h->range[i]) / 2;
-		wi = h->bin[i];
-		if(wi > 0)
-		{
-			W += wi;
-			hmean += (hmean - xi) * wi / W;
-		}
-	}
+    for(i = 0; i < n; i++)
+    {
+        //make sure size of h->range is n + 1
 
-	(*res) = hmean;
-	return 0;
+        xi = (h->range[i+1] + h->range[i]) / 2;
+        wi = h->bin[i];
+        if(wi > 0)
+        {
+            W += wi;
+            (*hmean) += (xi - (*hmean)) * wi / W;
+        }
+    }
+
+    return 0;
 }
 
-int histogram_bin_sum(const histogram* h, f_T* res)
+int histogram_bin_sum(const struct histogram* h, double* sum)
 {
-	size_t i, n;
-	f_T sum = 0;
-	n = h->n;
-	for(i = 0; i < n; i++)
-	{
-		sum += h->bin[i];
-	}
+    size_t i, n;
+    (*sum) = 0;
+    n = h->n;
+    for(i = 0; i < n; i++)
+    {
+        (*sum) += h->bin[i];
+    }
 
-	(*res) = sum;
-	return 0;
+    return 0;
 }
 
-int histogram_median(const histogram* h, f_T* res)
+int histogram_median(const struct histogram* h, double* hmedian)
 {
-	size_t i, n;
-	f_T sum, sum_50;
-	int proc_flag = histogram_bin_sum(h, &sum);
+    size_t i, n;
+    double sum, sum_50;
+    int proc_flag = histogram_bin_sum(h, &sum);
 
-	n = h->n;
+    n = h->n;
 
-	if(proc_flag != 0)
-		return -1; //unexpected error
+    if(proc_flag != 0)
+        return -1;
 
-	sum_50 = sum / 2.0;
-	sum = 0;
-	for(i = 0; i < n; i++)
-	{
-		sum += h->bin[i];
+    sum_50 = sum / 2.0;
+    sum = 0;
+    for(i = 0; i < n; i++)
+    {
+        sum += h->bin[i];
 
-		if(sum >= sum_50)
-		{
-			(*res) = (h->range[i] + h->range[i+1]) / 2;
-			break;
-		}
-	}
+        if(sum >= sum_50)
+        {
+            (*hmedian) = (h->range[i] + h->range[i+1]) / 2;
+            break;
+        }
+    }
 
-	return 0;
+    return 0;
 }
 
 #endif

data/ext/sstat/lib/histogram/histogram_test.c

@@ -0,0 +1,36 @@
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "histogram.h"
+
+int main(int argc, char const *argv[])
+{
+    int n = 5;
+    int i = 0;
+    double hmean = 0;
+    double hmedian = 0;
+    struct histogram* h = (struct histogram*)malloc( sizeof(struct histogram));
+
+    h->range = malloc(sizeof(double) * (n + 1));
+    h->bin = malloc(sizeof(double) * (n));
+
+    for(i = 0; i < (n+1); i++)
+        h->range[i] = i;
+
+    h->bin[0] = 2;
+    h->bin[1] = 3;
+    h->bin[2] = 5;
+    h->bin[3] = 2;
+    h->bin[4] = 1;
+
+    h->n = n;
+    /* Test histogram mean */
+    histogram_mean(h, &hmean);
+    printf("histogram mean %f \n", hmean);
+
+    histogram_median(h, &hmedian);
+    printf("histogram median %f \n", hmedian);
+
+    free_histogram(h);
+    return 0;
+}

data/ext/sstat/lib/histogram/histogram_type.h

@@ -3,12 +3,24 @@
 /*
  * The contain of this file is modified based on GSL lib
  * */
-typedef double f_T;
-
-typedef struct {
+struct histogram {
     size_t n ;
-    double * range ;
+    double * range ; /* size of range should be size of bin + 1 */
     double * bin ;
-} histogram;
+};
+
+void free_histogram(struct histogram* h)
+{
+    if(h)
+    {
+        if(h->range)
+            free(h->range);
+
+        if(h->bin)
+            free(h->bin);
+
+        free(h);
+    }
+}
 
 #endif

data/ext/sstat/lib/histogram/test.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+gcc -Wall -g -o histogram_test histogram_test.c &>log
+valgrind --tool=memcheck ./histogram_test

data/ext/sstat/lib/survival_kaplan_meier.h

@@ -102,10 +102,9 @@ int censored_uncensred_each_time_range(double* time, int* censored, int size,  s
 			else
 				uncensored_num_at++;
 
-			//if the last sample is censored, follow block stores counting for last time unique uncensored period
+			/* If the last sample is censored, follow block stores counting for last time unique uncensored period */
 			if (i == size - 1)
 			{
-				count_at++;
 				(*cens_ucens_number)->uncensored[count_at] = uncensored_num_at;
 				(*cens_ucens_number)->censored[count_at] = censored_num_at;
 			}
@@ -180,8 +179,6 @@ void calculate_kaplan_meier(int size, const struct CENS_UC_NUM* cens_ucens_numbe
  */
 int kaplan_meier(double* time, int* censored, int size, curve* KM_curve)
 {
-
-	int i, N;
 	struct CENS_UC_NUM* cens_ucens_number;
 
 	censored_uncensred_each_time_range(time, censored, size, &cens_ucens_number);
@@ -282,7 +279,7 @@ int kaplan_meier_3p_extrapolation(double* time, int* censored, int size, struct
 {
 	int proc_state = 0;
 	struct CENS_UC_NUM* cens_ucens_number;
-	censored_uncensred_each_time_range(time, censored, size, &cens_ucens_number);
+	proc_state = censored_uncensred_each_time_range(time, censored, size, &cens_ucens_number);
 	struct point* KM =  alloc_points(size);
 
 	/* If the length of the inital KM curve is less than or equal to 7, we will not apply extrapolation */
@@ -304,7 +301,7 @@ int kaplan_meier_3p_extrapolation(double* time, int* censored, int size, struct
 
 	free_CENS_UC_NUM(&cens_ucens_number);
 
-	return 0;
+	return proc_state;
 }
 
 #endif

data/ext/sstat/lib/test_kaplan_meier.c

@@ -1,14 +1,21 @@
+/*
+* This content of this file is used to generate binary to test kaplan meier
+*/
 #include "survival_kaplan_meier.h"
 
 int main(int argc, char const *argv[])
 {
 	struct curve KM_curve;
+	struct curve KM_curve_3p;
 
 	double _time[14] = {1.0, 2.1, 3.2, 4.5, 5.5, 6.2, 7.4, 8.5, 9.1, 10.4, 11.3, 12.5, 13.2, 14.7};
 	int _censored[14] = {1, 0 , 0, 0, 1, 1, 1, 0 , 1, 1,0,1,0,1};
-
-	kaplan_meier_3p_extrapolation(_time, _censored, 14, &KM_curve);
+	kaplan_meier(_time, _censored, 14, &KM_curve);
+	
 	free(KM_curve.point_array);
 
+	kaplan_meier_3p_extrapolation(_time, _censored, 14, &KM_curve_3p);
+	free(KM_curve_3p.point_array);
+
 	return 0;
 }

data/ext/sstat/sstat.c

@@ -52,6 +52,62 @@ static VALUE rb_index_less_equal(VALUE self, VALUE array, VALUE target)
   return INT2NUM(_index);
 }
 
+static VALUE rb_hist_mean(VALUE self, VALUE bin, VALUE range)
+{
+  int bin_size = RARRAY_LEN(bin);
+  int range_size = RARRAY_LEN(range);
+  int i;
+
+  if ((range_size - bin_size) != 1)
+    rb_raise(rb_eTypeError, "Size of range should be 1 larger than size of bin.");
+
+  double hmean = 0;
+  struct histogram* h = (struct histogram*)malloc(sizeof(struct histogram));
+  h->n = bin_size;
+  h->range = malloc(sizeof(double) * ( h->n + 1));
+  h->bin = malloc(sizeof(double) * (h->n));
+
+  for (i = 0; i < bin_size; i++) {
+    h->bin[i] = NUM2DBL(rb_ary_entry(bin, i));
+  }
+
+  for (i = 0; i < range_size; i++) {
+    h->range[i] = NUM2DBL(rb_ary_entry(range, i));
+  }
+
+  histogram_mean(h, &hmean);
+  free_histogram(h);
+  return DBL2NUM(hmean);
+}
+
+static VALUE rb_hist_median(VALUE self, VALUE bin, VALUE range)
+{
+  int bin_size = RARRAY_LEN(bin);
+  int range_size = RARRAY_LEN(range);
+  int i;
+
+  if ((range_size - bin_size) != 1)
+    rb_raise(rb_eTypeError, "Size of range should be 1 larger than size of bin.");
+
+  double hmedian = 0;
+  struct histogram* h = (struct histogram*)malloc(sizeof(struct histogram));
+  h->n = bin_size;
+  h->range = malloc(sizeof(double) * ( h->n + 1));
+  h->bin = malloc(sizeof(double) * (h->n));
+
+  for (i = 0; i < bin_size; i++) {
+    h->bin[i] = NUM2DBL(rb_ary_entry(bin, i));
+  }
+
+  for (i = 0; i < range_size; i++) {
+    h->range[i] = NUM2DBL(rb_ary_entry(range, i));
+  }
+
+  histogram_median(h, &hmedian);
+  free_histogram(h);
+  return DBL2NUM(hmedian);
+}
+
 static VALUE rb_kaplan_meier(VALUE self, VALUE time, VALUE censored)
 {
   int size = RARRAY_LEN(time);

data/ext/sstat/sstat.h

@@ -22,18 +22,24 @@ 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_hist_mean(VALUE self, VALUE bin, VALUE range);
+static VALUE rb_hist_median(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);
-	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);
-	rb_define_method(dist_class, "cdf_unormal_Q", rb_cdf_unormal_Q, 1);
+    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);
+    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);
+    rb_define_method(dist_class, "cdf_unormal_Q", rb_cdf_unormal_Q, 1);
+    rb_define_method(hist_class, "hist_mean", rb_hist_mean, 2);
+    rb_define_method(hist_class, "hist_median", rb_hist_median, 2);
+
 }
 
 #endif

data/lib/simple_statistics.rb

@@ -1,5 +0,0 @@
-require "simple_statistics/version"
-
-module SimpleStatistics
-  # Your code goes here...
-end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sstat
 version: !ruby/object:Gem::Version
-  version: 0.0.7
+  version: 0.0.8
 platform: ruby
 authors:
 - Haipeng Li
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-07-13 00:00:00.000000000 Z
+date: 2016-08-17 00:00:00.000000000 Z
 dependencies: []
 description: 
 email: haipeng3@ualberta.ca
@@ -33,12 +33,17 @@ files:
 - ext/lib/type_def.h
 - ext/sstat/Makefile
 - ext/sstat/extconf.rb
+- ext/sstat/lib/basic/basic.c
 - ext/sstat/lib/distribution.h
 - ext/sstat/lib/global_utility.h
 - ext/sstat/lib/histogram/histogram.h
 - ext/sstat/lib/histogram/histogram_error.h
 - ext/sstat/lib/histogram/histogram_stat.h
+- ext/sstat/lib/histogram/histogram_test
+- ext/sstat/lib/histogram/histogram_test.c
 - ext/sstat/lib/histogram/histogram_type.h
+- ext/sstat/lib/histogram/log
+- ext/sstat/lib/histogram/test.sh
 - ext/sstat/lib/km
 - ext/sstat/lib/survival.h
 - ext/sstat/lib/survival_def.h
@@ -52,7 +57,6 @@ files:
 - ext/sstat/sstat.o
 - ext/sstat/sstat.so
 - lib/simple_statistics.rb
-- lib/simple_statistics/version.rb
 - lib/sstat.so
 homepage: 
 licenses: []

data/lib/simple_statistics/version.rb

@@ -1,3 +0,0 @@
-module SimpleStatistics
-  VERSION = "0.0.6"
-end