update

util/evaluation.py

@@ -3,23 +3,37 @@ import numpy as np
 from scipy import stats
 from scipy.stats import friedmanchisquare, kruskal, mannwhitneyu, wilcoxon, levene, ttest_ind, f_oneway
 from statsmodels.stats.multicomp import MultiComparison
-
 from scipy.stats import spearmanr, pearsonr, kendalltau, entropy
 from scipy.spatial.distance import jensenshannon
-from scipy.stats import ttest_ind, friedmanchisquare, rankdata
+from scipy.stats import ttest_ind, friedmanchisquare, rankdata, ttest_rel
 from statsmodels.stats.multicomp import pairwise_tukeyhsd
 
+# def bootstrap_t_test(data1, data2, num_bootstrap=1000):
+#     """Perform a bootstrapped t-test."""
+#     observed_t_stat, _ = ttest_ind(data1, data2)
+#     combined = np.concatenate([data1, data2])
+#     t_stats = []
+#
+#     for _ in range(num_bootstrap):
+#         np.random.shuffle(combined)
+#         new_data1 = combined[:len(data1)]
+#         new_data2 = combined[len(data1):]
+#         t_stat, _ = ttest_ind(new_data1, new_data2)
+#         t_stats.append(t_stat)
+#
+#     p_value = np.sum(np.abs(t_stats) >= np.abs(observed_t_stat)) / num_bootstrap
+#     return observed_t_stat, p_value
+
 def bootstrap_t_test(data1, data2, num_bootstrap=1000):
-    """Perform a bootstrapped t-test."""
-    observed_t_stat, _ = ttest_ind(data1, data2)
-    combined = np.concatenate([data1, data2])
+    """Perform a bootstrapped paired t-test."""
+    observed_t_stat, _ = ttest_rel(data1, data2)
+    differences = data1 - data2
     t_stats = []
 
     for _ in range(num_bootstrap):
-        np.random.shuffle(combined)
-        new_data1 = combined[:len(data1)]
-        new_data2 = combined[len(data1):]
-        t_stat, _ = ttest_ind(new_data1, new_data2)
+        # Resample with replacement
+        resampled_diffs = np.random.choice(differences, size=len(differences), replace=True)
+        t_stat, _ = ttest_rel(resampled_diffs, np.zeros(len(resampled_diffs)))
         t_stats.append(t_stat)
 
     p_value = np.sum(np.abs(t_stats) >= np.abs(observed_t_stat)) / num_bootstrap