def test_procrustes_bad_dimensions(self):
self.other.samples = self.other.samples.iloc[:, :4]
self.other.eigvals = self.other.eigvals[:4]
self.other.proportion_explained = self.other.proportion_explained[:4]
with self.assertRaisesRegex(ValueError, 'The matrices cannot be '):
procrustes_analysis(self.reference, self.other)
def test_procrustes_bad_dimensions(self):
self.other.samples = self.other.samples.iloc[:, :4]
self.other.eigvals = self.other.eigvals[:4]
self.other.proportion_explained = self.other.proportion_explained[:4]
with self.assertRaisesRegex(ValueError, 'The matrices cannot be '):
procrustes_analysis(self.reference, self.other)
def test_non_zero_p(self):
# generated with np.random.seed(3); np.random.randn(4, 6)
noise = np.array([[
1.78862847, 0.43650985, 0.09649747, -1.8634927, -0.2773882,
-0.35475898
],
[
-0.08274148, -0.62700068, -0.04381817,
-0.47721803, -1.31386475, 0.88462238
],
[
0.88131804, 1.70957306, 0.05003364, -0.40467741,
-0.54535995, -1.54647732
],
[
0.98236743, -1.10106763, -1.18504653, -0.2056499,
1.48614836, 0.23671627
]])
self.other.samples += noise
ref, other, m2_results = procrustes_analysis(self.reference,
self.other)
true_m2 = m2_results['true M^2 value'][0]
true_p_value = m2_results['p-value for true M^2 value'][0]
skbio.util.assert_ordination_results_equal(ref, self.expected_ref)
skbio.util.assert_ordination_results_equal(other, self.expected_noise)
# the p value shouldn't be zero even in the presence of noise
self.assertAlmostEqual(true_m2, 0.7388121)
self.assertNotAlmostEqual(true_p_value, 0.001)
def test_procrustes(self):
ref, other, m2_results = procrustes_analysis(self.reference,
self.other)
true_m2 = m2_results['true M^2 value'][0]
true_p_value = m2_results['p-value for true M^2 value'][0]
skbio.util.assert_ordination_results_equal(ref, self.expected_ref)
skbio.util.assert_ordination_results_equal(other, self.expected_other)
self.assertAlmostEqual(true_m2, self.expected_m2)
self.assertNotAlmostEqual(true_p_value, self.expected_p)
def test_zero_permutations_nan_pvalue(self):
ref, other, m2_results = procrustes_analysis(self.reference,
self.other,
permutations='disable')
true_m2 = m2_results['true M^2 value'][0]
true_p_value = m2_results['p-value for true M^2 value'][0]
skbio.util.assert_ordination_results_equal(ref, self.expected_ref)
skbio.util.assert_ordination_results_equal(other, self.expected_other)
self.assertAlmostEqual(true_m2, self.expected_m2)
self.assertTrue(np.isnan(true_p_value))
def test_procrustes_id_mismatch(self):
msg = 'The ordinations represent two different sets of samples'
self.other.samples.index = pd.Index([':L', ':D', ':)', ':('])
with self.assertRaisesRegex(ValueError, msg):
procrustes_analysis(self.reference, self.other)
self.other.samples.index = pd.Index([':L', 'B', 'C', 'D'])
with self.assertRaisesRegex(ValueError, msg):
procrustes_analysis(self.reference, self.other)
self.other.samples.index = pd.Index(['a', 'b', 'c', 'd'])
with self.assertRaisesRegex(ValueError, msg):
procrustes_analysis(self.reference, self.other)
def test_procrustes_id_mismatch(self):
msg = 'The ordinations represent two different sets of samples'
self.other.samples.index = pd.Index([':L', ':D', ':)', ':('])
with self.assertRaisesRegex(ValueError, msg):
procrustes_analysis(self.reference, self.other)
self.other.samples.index = pd.Index([':L', 'B', 'C', 'D'])
with self.assertRaisesRegex(ValueError, msg):
procrustes_analysis(self.reference, self.other)
self.other.samples.index = pd.Index(['a', 'b', 'c', 'd'])
with self.assertRaisesRegex(ValueError, msg):
procrustes_analysis(self.reference, self.other)
def test_procrustes_over_dimensions(self):
with self.assertRaisesRegex(ValueError, 'Cannot fit fewer dimensions '
'than available'):
procrustes_analysis(self.reference, self.other, 11)
def test_procrustes(self):
ref, other = procrustes_analysis(self.reference, self.other)
skbio.util.assert_ordination_results_equal(ref, self.expected_ref)
skbio.util.assert_ordination_results_equal(other, self.expected_other)
def test_procrustes_over_dimensions(self):
with self.assertRaisesRegex(ValueError, 'Cannot fit fewer dimensions '
'than available'):
procrustes_analysis(self.reference, self.other, 11)
def test_procrustes(self):
ref, other = procrustes_analysis(self.reference, self.other)
skbio.util.assert_ordination_results_equal(ref, self.expected_ref)
skbio.util.assert_ordination_results_equal(other, self.expected_other)
