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)
Example #2
0
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]))