def setUp(self):
"""Define some sample data that will be used by the tests."""
self.colwell_data1 = asarray(colwell_data1)
self.colwell_data2 = asarray(colwell_data2)
self.est1 = AbstractPointEstimator(asarray([0, 1, 2, 3, 4, 5]))
self.est2 = AbstractPointEstimator(self.colwell_data1)
self.est3 = AbstractPointEstimator(self.colwell_data2)
class AbstractPointEstimatorTests(TestCase):
"""Tests for the AbstractPointEstimator class."""
def setUp(self):
"""Define some sample data that will be used by the tests."""
self.colwell_data1 = asarray(colwell_data1)
self.colwell_data2 = asarray(colwell_data2)
self.est1 = AbstractPointEstimator(asarray([0, 1, 2, 3, 4, 5]))
self.est2 = AbstractPointEstimator(self.colwell_data1)
self.est3 = AbstractPointEstimator(self.colwell_data2)
def test_constructor(self):
"""Test instantiating an AbstractPointEstimator instance."""
self.assertTrue(isinstance(self.est1, AbstractPointEstimator))
def test_constructor_empty_sample(self):
"""Test instantiating an estimator with a sample that has no obs."""
with self.assertRaises(EmptySampleError):
_ = AbstractPointEstimator(asarray([0, 0, 0, 0.0, 0, 0.0]))
def test_getTotalIndividualCount(self):
"""Returns correct total number of observed individuals."""
# Verified with iNEXT.
self.assertEqual(self.est1.getTotalIndividualCount(), 15)
# Verified against results in Colwell 2012 paper.
self.assertEqual(self.est2.getTotalIndividualCount(), 976)
self.assertEqual(self.est3.getTotalIndividualCount(), 237)
def test_getObservationCount(self):
"""Returns correct number of (observed) observations."""
# Verified with iNEXT.
self.assertEqual(self.est1.getObservationCount(), 5)
# Verified against results in Colwell 2012 paper.
self.assertEqual(self.est2.getObservationCount(), 140)
self.assertEqual(self.est3.getObservationCount(), 112)
def test_getAbundanceFrequencyCounts(self):
"""Returns correct abundance frequency counts."""
# Verified with iNEXT.
exp = defaultdict(int, {1: 1, 2: 1, 3: 1, 4: 1, 5: 1})
obs = self.est1.getAbundanceFrequencyCounts()
self.assertEqual(obs, exp)
# Verified against results in Colwell 2012 paper.
self.assertEqual(self.est2.getAbundanceFrequencyCounts(), colwell_fk1)
self.assertEqual(self.est3.getAbundanceFrequencyCounts(), colwell_fk2)
def test_call(self):
"""Test should raise error."""
with self.assertRaises(NotImplementedError):
self.est1(1)
def setUp(self):
"""Define some sample data that will be used by the tests."""
self.colwell_data1 = asarray(colwell_data1)
self.colwell_data2 = asarray(colwell_data2)
self.est1 = AbstractPointEstimator(asarray([0, 1, 2, 3, 4, 5]))
self.est2 = AbstractPointEstimator(self.colwell_data1)
self.est3 = AbstractPointEstimator(self.colwell_data2)
def test_constructor_empty_sample(self):
"""Test instantiating an estimator with a sample that has no obs."""
with self.assertRaises(EmptySampleError):
_ = AbstractPointEstimator(asarray([0, 0, 0, 0.0, 0, 0.0]))
