def testGTestYates(self):
"""Verify computation of G-test with Yates' continuity correction"""
from stamp.plugins.samples.statisticalTests.GTestYates import GTestYates
gTestYates = GTestYates(preferences)
# Ground truth obtained from Peter L. Hurd's R script (http://www.psych.ualberta.ca/~phurd/cruft/g.test.r)
oneSided, twoSided, _ = gTestYates.hypothesisTest(table1[0], table1[1], table1[2], table1[3])
self.assertEqual(oneSided, float('inf'))
self.assertAlmostEqual(twoSided, 0.325502240010)
oneSided, twoSided, _ = gTestYates.hypothesisTest(table2[0], table2[1], table2[2], table2[3])
self.assertEqual(oneSided, float('inf'))
self.assertAlmostEqual(twoSided, 2.220446049e-16)
class GTestFisher(AbstractSampleStatsTestPlugin): ''' Perform G-test w/ Yates' correction or Fisher's exact test. ''' def __init__(self, preferences): AbstractSampleStatsTestPlugin.__init__(self, preferences) self.name = 'G-test (w/ Yates\') + Fisher\'s' self.fishers = Fishers(self.preferences) self.gTestYates = GTestYates(self.preferences) def hypothesisTest(self, seq1, seq2, totalSeq1, totalSeq2): a = seq1 b = seq2 c = totalSeq1 - seq1 d = totalSeq2 - seq2 if a < 20 or b < 20 or c < 20 or d < 20: return self.fishers.hypothesisTest(seq1, seq2, totalSeq1, totalSeq2) else: return self.gTestYates.hypothesisTest(seq1, seq2, totalSeq1, totalSeq2)
class GTestFisher(AbstractSampleStatsTestPlugin):
'''
Perform G-test w/ Yates' correction or Fisher's exact test.
'''
def __init__(self, preferences):
AbstractSampleStatsTestPlugin.__init__(self, preferences)
self.name = 'G-test (w/ Yates\') + Fisher\'s'
self.fishers = Fishers(self.preferences)
self.gTestYates = GTestYates(self.preferences)
def hypothesisTest(self, seq1, seq2, totalSeq1, totalSeq2):
a = seq1
b = seq2
c = totalSeq1 - seq1
d = totalSeq2 - seq2
if a < 20 or b < 20 or c < 20 or d < 20:
return self.fishers.hypothesisTest(seq1, seq2, totalSeq1,
totalSeq2)
else:
return self.gTestYates.hypothesisTest(seq1, seq2, totalSeq1,
totalSeq2)
def __init__(self, preferences):
AbstractSampleStatsTestPlugin.__init__(self, preferences)
self.name = 'G-test (w/ Yates\') + Fisher\'s'
self.fishers = Fishers(self.preferences)
self.gTestYates = GTestYates(self.preferences)
def __init__(self, preferences): AbstractSampleStatsTestPlugin.__init__(self, preferences) self.name = 'G-test (w/ Yates\') + Fisher\'s' self.fishers = Fishers(self.preferences) self.gTestYates = GTestYates(self.preferences)
