def test_chi_square_from_Dict2D(self):
"""chi_square_from_Dict2D calcs a Chi-Square and p value from Dict2D"""
#test1
obs_matrix = Dict2D({'rest_of_tree': {'env1': 2, 'env3': 1, 'env2': 0},
'b': {'env1': 1, 'env3': 1, 'env2': 3}})
input_matrix = calc_contingency_expected(obs_matrix)
test, csp = chi_square_from_Dict2D(input_matrix)
self.assertFloatEqual(test, 3.0222222222222221)
#test2
test_matrix_2 = Dict2D({'Marl': {'val':[2, 5.2]},
'Chalk': {'val':[10, 5.2]},
'Sandstone':{'val':[8, 5.2]},
'Clay':{'val':[2, 5.2]},
'Limestone':{'val':[4, 5.2]}
})
test2, csp2 = chi_square_from_Dict2D(test_matrix_2)
self.assertFloatEqual(test2, 10.1538461538)
self.assertFloatEqual(csp2, 0.0379143890013)
#test3
matrix3_obs = Dict2D({'AIDS':{'Males':4, 'Females':2, 'Both':3},
'No_AIDS':{'Males':3, 'Females':16, 'Both':2}
})
matrix3 = calc_contingency_expected(matrix3_obs)
test3, csp3 = chi_square_from_Dict2D(matrix3)
self.assertFloatEqual(test3, 7.6568405139833722)
self.assertFloatEqual(csp3, 0.0217439383468)
def test_chi_square_from_Dict2D(self):
"""chi_square_from_Dict2D calcs a Chi-Square and p value from Dict2D"""
#test1
obs_matrix = Dict2D({
'rest_of_tree': {
'env1': 2,
'env3': 1,
'env2': 0
},
'b': {
'env1': 1,
'env3': 1,
'env2': 3
}
})
input_matrix = calc_contingency_expected(obs_matrix)
test, csp = chi_square_from_Dict2D(input_matrix)
self.assertFloatEqual(test, 3.0222222222222221)
#test2
test_matrix_2 = Dict2D({
'Marl': {
'val': [2, 5.2]
},
'Chalk': {
'val': [10, 5.2]
},
'Sandstone': {
'val': [8, 5.2]
},
'Clay': {
'val': [2, 5.2]
},
'Limestone': {
'val': [4, 5.2]
}
})
test2, csp2 = chi_square_from_Dict2D(test_matrix_2)
self.assertFloatEqual(test2, 10.1538461538)
self.assertFloatEqual(csp2, 0.0379143890013)
#test3
matrix3_obs = Dict2D({
'AIDS': {
'Males': 4,
'Females': 2,
'Both': 3
},
'No_AIDS': {
'Males': 3,
'Females': 16,
'Both': 2
}
})
matrix3 = calc_contingency_expected(matrix3_obs)
test3, csp3 = chi_square_from_Dict2D(matrix3)
self.assertFloatEqual(test3, 7.6568405139833722)
self.assertFloatEqual(csp3, 0.0217439383468)
def run_single_G_test(OTU_name, category_info, otu_table, category_values,
suppress_warnings=False):
"""run the G test on a single OTU
If suppress_warnings=True, doesn't warn when sample in map but not otu table
"""
contingency_matrix = make_contingency_matrix(OTU_name, category_info, \
otu_table, category_values, suppress_warnings=suppress_warnings)
contingency_matrix = calc_contingency_expected(contingency_matrix)
g_val, prob = G_fit_from_Dict2D(contingency_matrix)
return g_val, prob, contingency_matrix
def test_calc_contingency_expected(self):
"""calcContingencyExpected returns new matrix with expected freqs"""
matrix = Dict2D({'rest_of_tree': {'env1': 2, 'env3': 1, 'env2': 0},
'b': {'env1': 1, 'env3': 1, 'env2': 3}})
result = calc_contingency_expected(matrix)
self.assertFloatEqual(result['rest_of_tree']['env1'], [2, 1.125])
self.assertFloatEqual(result['rest_of_tree']['env3'], [1, 0.75])
self.assertFloatEqual(result['rest_of_tree']['env2'], [0, 1.125])
self.assertFloatEqual(result['b']['env1'], [1, 1.875])
self.assertFloatEqual(result['b']['env3'], [1, 1.25])
self.assertFloatEqual(result['b']['env2'], [3, 1.875])
def run_single_G_test(OTU_name,
category_info,
otu_sample_info,
category_values,
suppress_warnings=False):
"""run the G test on a single OTU
If suppress_warnings=True, doesn't warn when sample in map but not otu table
"""
contingency_matrix = make_contingency_matrix(OTU_name, category_info, \
otu_sample_info, category_values, suppress_warnings=suppress_warnings)
contingency_matrix = calc_contingency_expected(contingency_matrix)
g_val, prob = G_fit_from_Dict2D(contingency_matrix)
return g_val, prob, contingency_matrix
def test_calc_contingency_expected(self):
"""calcContingencyExpected returns new matrix with expected freqs"""
matrix = Dict2D({
'rest_of_tree': {
'env1': 2,
'env3': 1,
'env2': 0
},
'b': {
'env1': 1,
'env3': 1,
'env2': 3
}
})
result = calc_contingency_expected(matrix)
self.assertFloatEqual(result['rest_of_tree']['env1'], [2, 1.125])
self.assertFloatEqual(result['rest_of_tree']['env3'], [1, 0.75])
self.assertFloatEqual(result['rest_of_tree']['env2'], [0, 1.125])
self.assertFloatEqual(result['b']['env1'], [1, 1.875])
self.assertFloatEqual(result['b']['env3'], [1, 1.25])
self.assertFloatEqual(result['b']['env2'], [3, 1.875])