sstat 0.0.8 → 0.0.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: c5ebfe534e122751870fc4fda46481ec8b11b6f0
+  metadata.gz: 843d3d96c90916264fd977b3adc810b232350c98
+  data.tar.gz: 8c585198944119c3981eb3c76fed0db7f6f2f35f
 SHA512:
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+  data.tar.gz: 107902e5f175e919ea220fa3b222e16a468dfaa95c29afc942dbee89f7aee29e79ca43c5a3c15d24c1e0b74872e1ef506ff68271cb3a9fa22655363cea54fe65

data/ext/lib/survival_func.h

@@ -136,6 +136,7 @@ double log_rank_test(double* time_1, int* censored_1, double* time_2, int* censo
 	}
 
 	Z = Z / sqrt(V_i_sum);
+
 	free(Group_N_1.uncensored);
 	free(Group_N_1.censored);
 	free(Group_N_2.uncensored);

data/ext/lib/survival_utility.h

@@ -18,6 +18,7 @@ struct array create_sorted_unique_array(double* array, int size)
 	qsort(array, size, sizeof(double), &compare_double);
 
 	count = 1;
+	
 	//calcualte number of unique
 	for(i = 1; i < size; ++i)
 	{

data/ext/sstat/lib/basic/log

@@ -0,0 +1,4 @@
+median_test.c: In function ‘main’:
+median_test.c:7:9: warning: unused variable ‘proc’ [-Wunused-variable]
+     int proc = median(data, 14, &m);
+         ^

data/ext/sstat/lib/basic/median.h

@@ -0,0 +1,47 @@
+#ifndef _BASIC_MEDIAN_H_
+#define _BASIC_MEDIAN_H_
+
+#include "utility.h"
+#include <stdio.h>
+#include <stdlib.h>
+
+int median_for_sorted_data(const double* sorted_data, int n, double* median)
+{
+    const int lhs = (n - 1) / 2 ;
+    const int rhs = n / 2 ;
+
+    if(n == 0)
+    {
+        (*median) = 0;
+        return 0;
+    }
+
+    if (lhs == rhs)
+    {
+        (*median) = sorted_data[lhs] ;
+    }
+    else 
+    {
+        (*median) = (sorted_data[lhs] + sorted_data[rhs])/2.0 ;
+    }
+
+    return 0;
+}
+
+int median(const double* data, int n, double* median)
+{
+    int i;
+    double* data_cpy = (double *) malloc(sizeof(double) * n);
+    for(i = 0; i < n; i++)
+    {
+        data_cpy[i] = data[i];
+    }
+
+    qsort(data_cpy, n, sizeof(double), &compare_double);
+
+    median_for_sorted_data(data_cpy, n, median);
+    free(data_cpy);
+    return 0;
+}
+
+#endif

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

@@ -0,0 +1,11 @@
+#include "median.h"
+
+int main(int argc, char const *argv[])
+{
+    double data[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 };
+    double m;
+    int proc = median(data, 14, &m);
+    printf("Median %f \n", m);
+
+    return 0;
+}

data/ext/sstat/lib/basic/utility.h

@@ -0,0 +1,42 @@
+#ifndef _BASIC_MEDIAN_H_
+#define _BASIC_MEDIAN_H_
+
+/* error macro */
+#include <stdlib>
+#include <stdio.h>
+#include <errno.h>
+#include <string.h>
+
+#ifdef NDEBUG
+#define debug(M, ...)
+#else
+#define debug(M, ...) fprintf(stderr, "DEBUG %s:%d: " M "\n", __FILE__, __LINE__, ##__VA_ARGS__)
+#endif
+
+#define clean_errno() (errno == 0 ? "None" : strerror(errno))
+
+#define log_err(M, ...) fprintf(stderr, "[ERROR] (%s:%d: errno: %s) " M "\n", __FILE__, __LINE__, clean_errno(), ##__VA_ARGS__)
+
+#define log_warn(M, ...) fprintf(stderr, "[WARN] (%s:%d: errno: %s) " M "\n", __FILE__, __LINE__, clean_errno(), ##__VA_ARGS__)
+
+#define log_info(M, ...) fprintf(stderr, "[INFO] (%s:%d) " M "\n", __FILE__, __LINE__, ##__VA_ARGS__)
+
+#define check(A, M, ...) if(!(A)) { log_err(M, ##__VA_ARGS__); errno=0; goto error; }
+
+#define sentinel(M, ...)  { log_err(M, ##__VA_ARGS__); errno=0; goto error; }
+
+#define check_mem(A) check((A), "Out of memory.")
+
+#define check_debug(A, M, ...) if(!(A)) { debug(M, ##__VA_ARGS__); errno=0; goto error; }
+
+#endif
+
+int compare_double (const void * a, const void * b)
+{
+   return *((double*)a) > *((double*)b)? 1 : 0;
+}
+
+enum ERRORS {
+    OUTOF_MEMORY_ERROR = 1,
+    NOT_EMPTY_ERROR = 2,
+};

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

@@ -24,6 +24,7 @@ int main(int argc, char const *argv[])
     h->bin[4] = 1;
 
     h->n = n;
+    
     /* Test histogram mean */
     histogram_mean(h, &hmean);
     printf("histogram mean %f \n", hmean);

data/ext/sstat/lib/{distribution.h → survival/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/survival/global_utility.h

@@ -0,0 +1,21 @@
+#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)
+{
+	double diff = (double)(((struct point*)a)->x) - (double)(((struct point*)b)->x);
+	if(diff > 0)
+		return 1;
+	else
+		return 0;
+}
+
+#endif

data/ext/sstat/lib/{survival_func.h → survival/survival_func.h}

@@ -51,7 +51,7 @@ double log_rank_test(double* time_1, int* censored_1, double* time_2, int* censo
 {
 	int i, time_pnt_size;
 	int index;
-
+	
 	array merged_time_pnts = merge_two_array(time_1, size_1, time_2, size_2);
 	array merged_uniq_time_pnts = create_sorted_unique_array(merged_time_pnts.D_ptr, merged_time_pnts.size);
 
@@ -126,9 +126,14 @@ double log_rank_test(double* time_1, int* censored_1, double* time_2, int* censo
 
 	for (i = 0; i < time_pnt_size; ++i)
 	{
-		N_i[i] = N1_at_risk[i] + N2_at_risk[i];
+
+		N_i[i] = (N1_at_risk[i] + N2_at_risk[i]);
+
 		O_i[i] = (combined_Group_N_1.uncensored[i] + combined_Group_N_2.uncensored[i]);
-		E_i[i] = 1.0 * N1_at_risk[i] * O_i[i] / N_i[i];
+
+		if(N_i[i] != 0)
+		{
+			E_i[i] = 1.0 * N1_at_risk[i] * O_i[i] / N_i[i];
 
 		if (N_i[i] > 1)
 		{
@@ -140,10 +145,12 @@ double log_rank_test(double* time_1, int* censored_1, double* time_2, int* censo
 			V_i_sum += V_i[i];
 		}
 
-		Z += (combined_Group_N_1.uncensored[i] - E_i[i]);
+			Z += (combined_Group_N_1.uncensored[i] - E_i[i]);
+		}
 	}
 
 	Z = Z / sqrt(V_i_sum);
+
 	free(Group_N_1.uncensored);
 	free(Group_N_1.censored);
 	free(Group_N_2.uncensored);

data/ext/sstat/lib/{survival_kaplan_meier.h → survival/survival_kaplan_meier.h}

@@ -234,7 +234,7 @@ int KM_3p_extrapolation(struct CENS_UC_NUM** cens_uc_num, struct CENS_UC_NUM** u
 	mean_last_uncensored = mean_last_uncensored / 3;
 	mean_last_censored = mean_last_censored / 3;
 	time_interval_mean = time_interval_mean / 3;
-
+	
 	/* Calculate how many points we should extrapolate */
 	extrapolation_size = ceil((double)num_left / (mean_last_uncensored + mean_last_censored));
 	updated_cens_uc_num_size = (*cens_uc_num)->size + extrapolation_size;

data/ext/sstat/sstat.c

@@ -202,7 +202,6 @@ static VALUE rb_log_rank_test(VALUE self, VALUE _time_1, VALUE _cens_1, VALUE _t
   double* time_2 = (double *)malloc(sizeof(double) * size_2);
   int* cens_1 = (int *)malloc(sizeof(int) * size_1);
   int* cens_2 = (int *)malloc(sizeof(int) * size_2);
-
   for (i = 0; i < size_1; i++) {
     time_1[i] = NUM2DBL(rb_ary_entry(_time_1, i));
     cens_1[i] = NUM2INT(rb_ary_entry(_cens_1, i));
@@ -212,6 +211,7 @@ static VALUE rb_log_rank_test(VALUE self, VALUE _time_1, VALUE _cens_1, VALUE _t
     time_2[i] = NUM2DBL(rb_ary_entry(_time_2, i));
     cens_2[i] = NUM2INT(rb_ary_entry(_cens_2, i));
   }
+
   _Z = log_rank_test(time_1, cens_1, time_2, cens_2, size_1, size_2);
 
   free(time_1);

data/ext/sstat/sstat.h

@@ -3,9 +3,9 @@
 #include <ruby.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include "lib/survival.h"
+#include "lib/survival/survival.h"
+#include "lib/survival/distribution.h"
 #include "lib/global_utility.h"
-#include "lib/distribution.h"
 #include "lib/histogram/histogram.h"
 
 static VALUE rb_percentile(VALUE self, VALUE arg, VALUE target);
@@ -39,7 +39,6 @@ void Init_sstat() {
     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

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sstat
 version: !ruby/object:Gem::Version
-  version: 0.0.8
+  version: 0.0.9
 platform: ruby
 authors:
 - Haipeng Li
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-08-17 00:00:00.000000000 Z
+date: 2016-09-06 00:00:00.000000000 Z
 dependencies: []
 description: 
 email: haipeng3@ualberta.ca
@@ -33,8 +33,11 @@ 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/basic/log
+- ext/sstat/lib/basic/median.h
+- ext/sstat/lib/basic/median_test
+- ext/sstat/lib/basic/median_test.c
+- ext/sstat/lib/basic/utility.h
 - ext/sstat/lib/global_utility.h
 - ext/sstat/lib/histogram/histogram.h
 - ext/sstat/lib/histogram/histogram_error.h
@@ -44,14 +47,15 @@ files:
 - 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
-- ext/sstat/lib/survival_func.h
-- ext/sstat/lib/survival_kaplan_meier.h
-- ext/sstat/lib/survival_utility.h
-- ext/sstat/lib/test_kaplan_meier.c
-- ext/sstat/lib/type_def.h
+- ext/sstat/lib/survival/distribution.h
+- ext/sstat/lib/survival/global_utility.h
+- ext/sstat/lib/survival/survival.h
+- ext/sstat/lib/survival/survival_def.h
+- ext/sstat/lib/survival/survival_func.h
+- ext/sstat/lib/survival/survival_kaplan_meier.h
+- ext/sstat/lib/survival/survival_utility.h
+- ext/sstat/lib/survival/test_kaplan_meier.c
+- ext/sstat/lib/survival/type_def.h
 - ext/sstat/sstat.c
 - ext/sstat/sstat.h
 - ext/sstat/sstat.o

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

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