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#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
from cogent.maths.stats.ks import pkolmogorov1x, pkolmogorov2x, pkstwo,\
psmirnov2x
from cogent.maths.stats.test import ks_test, ks_boot
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
class KSTests(TestCase):
"""Tests Kolmogorov-Smirnov."""
def setUp(self):
self.x1 = [0.09916191, 0.29732882, 0.41475044, 0.68816838, 0.20841367,
0.46129887, 0.22074544, 0.06889561, 0.88264852, 0.87726406, 0.76905072,
0.86178033, 0.42596777, 0.59443782, 0.68852176, 0.66032130, 0.72683791,
0.02363118, 0.82384762, 0.32759965, 0.69231127, 0.50848596, 0.67500888,
0.84919139, 0.70774136, 0.97847465, 0.59784714, 0.82033663, 0.45640039,
0.13054766, 0.01227875, 0.21229238, 0.37054602, 0.80905622, 0.26056527,
0.01662457, 0.76277188, 0.76892495, 0.39186350, 0.61468789, 0.83247770,
0.69946238, 0.80550609, 0.22336814, 0.62491296, 0.03413056, 0.74500251,
0.36008309, 0.19443889, 0.06808133]
self.x2 = [1.1177760, 0.9984325, 0.8113576, 0.7247507, 0.9473543, 1.1192222,
1.2577115, 0.6168244, 0.9616475, 1.0677138, 0.5106196, 1.2334833,
0.3750225, 0.9788191, 1.1366872, 0.8212352, 0.7665240, 0.4409294,
0.4447418, 1.1381901, 0.7299300, 1.1307991, 0.5356031, 0.3193794,
1.2476867, 0.7909454, 0.7781800, 0.8438637, 1.1814135, 1.0117055,
0.7433708, 0.7917239, 0.5080752, 0.9014003, 0.5960710, 0.9646521,
0.9263595, 0.7969784, 1.2847108, 0.6393015, 0.6828791, 1.0817340,
0.6586887, 0.7314203, 0.3998812, 0.9988478, 1.0225579, 1.2721428,
0.6465969, 0.9133413]
def test_pk1x(self):
"""1 sample 1-sided should match answers from R"""
self.assertFloatEqual(pkolmogorov1x(0.06, 30), 0.2248113)
def test_pk2x(self):
"""1 sample 2-sided should match answers from R"""
self.assertFloatEqual(pkolmogorov2x(0.7199, 50), (1-6.661e-16))
self.assertFloatEqual(pkolmogorov2x(0.08, 30), 0.01754027)
self.assertFloatEqual(pkolmogorov2x(0.03, 300), 0.05753413)
def test_ps2x(self):
"""2 sample 2-sided smirnov should match answers from R"""
self.assertFloatEqual(psmirnov2x(0.48, 20, 50), 0.9982277)
self.assertFloatEqual(psmirnov2x(0.28, 20, 50), 0.8161612)
self.assertFloatEqual(psmirnov2x(0.28, 50, 20), 0.8161612)
def tes_pk2x(self):
"""2 sample 2-sided kolmogorov should match answers from R"""
self.assertFloatEqual(pkolmogorov1x(0.058, 50), 0.007530237)
self.assertFloatEqual(pkolmogorov1x(0.018, 50), 4.887356e-26)
self.assertFloatEqual(pkolmogorov1x(0.018, 5000), 0.922618)
def test_pkstwo(self):
"""kolmogorov asymptotic should match answers from R"""
self.assertFloatEqual(pkstwo(2.3),[1-5.084e-05],eps=1e-5)
def test_ks2x(self):
"""KS two-sample, 2-sided should match answers from R"""
D, Pval = ks_test(self.x1, self.x2)
self.assertFloatEqual((D, Pval), (0.46, 3.801e-05), eps=1e-4)
D, Pval = ks_test(self.x1, self.x2, exact=False)
self.assertFloatEqual((D, Pval), (0.46, 5.084e-05), eps=1e-4)
D, Pval = ks_test(self.x1, self.x2[:20])
self.assertFloatEqual((D,Pval), (0.53, 0.0003576), eps=1e-4)
D, Pval = ks_test(self.x2[:20], self.x1)
self.assertFloatEqual((D,Pval), (0.53, 0.0003576), eps=1e-4)
D, Pval = ks_test(self.x1[:20], self.x2)
self.assertFloatEqual((D,Pval), (0.48, 0.001772), eps=1e-4)
D, Pval = ks_test(self.x1, self.x2, alt="greater")
self.assertFloatEqual((D,Pval), (0.46, 2.542e-05), eps=1e-4)
D, Pval = ks_test(self.x1, self.x2, alt="g")
self.assertFloatEqual((D,Pval), (0.46, 2.542e-05), eps=1e-4)
D, Pval = ks_test(self.x1, self.x2, alt="less")
self.assertFloatEqual((D,Pval), (6.9388939039072284e-18, 1.), eps=1e-4)
D, Pval = ks_test(self.x2, self.x1, alt="l")
self.assertFloatEqual((D,Pval), (0.46, 2.542e-05), eps=1e-4)
def test_ks_boot(self):
"""excercising the bootstrapped version of KS"""
D, Pval = ks_boot(self.x1[:10], self.x2[:10], num_reps=10)
if __name__ == "__main__":
main()
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