def test_dist_manhattan(self):
"""tests dist_manhattan
tests inputs of empty mtx, zeros, and dense1 compared with calcs done
by hand"""
assert_allclose(dist_manhattan(self.zeromtx), zeros((4, 4), "d"))
dense1expected = array(
[[0.0, 5.0, 019.9], [5.0, 0.0, 24.9], [19.9, 24.90, 0.0]], "d")
assert_allclose(dist_manhattan(self.dense1), dense1expected)
def test_dist_bray_curtis_faith(self):
"""tests dist_bray_curtis_faith
tests inputs of empty mtx, zeros, and mtx1 compared with calcs done
by hand"""
assert_allclose(dist_manhattan(self.zeromtx), zeros((4, 4) * 1, "d"))
mtx1expected = array([[0, 21.1 / 27.1], [21.1 / 27.1, 0]], "d")
assert_allclose(dist_bray_curtis_faith(self.mtx1), mtx1expected)
def test_dist_bray_curtis(self):
"""tests dist_bray_curtis
tests inputs of empty mtx, zeros, and mtx1 compared with calcs done
by hand"""
self.assertFloatEqual(dist_manhattan(self.zeromtx), zeros((4, 4) * 1, "d"))
mtx1expected = array([[0, 21.1 / 27.1], [21.1 / 27.1, 0]], "d")
self.assertFloatEqual(dist_bray_curtis(self.mtx1), mtx1expected)
def test_dist_soergel(self):
"""tests dist_soergel
tests inputs of empty mtx, zeros, and dense1 compared with calcs done
by hand/manhattan dist"""
assert_allclose(dist_soergel(self.zeromtx), zeros((4, 4) * 1, "d"))
dense1expected = dist_manhattan(self.dense1)
dense1norm = array([[1, 8, 23], [8, 1, 27], [23, 27, 1]], "d")
dense1expected /= dense1norm
assert_allclose(dist_soergel(self.dense1), dense1expected)
def test_binary_dist_jaccard(self):
"""tests binary_dist_jaccard
tests inputs of empty mtx, zeros, and sparse1 compared with calcs done
by hand"""
assert_allclose(binary_dist_jaccard(self.zeromtx), zeros((4, 4), "d"))
sparse1expected = array(
[[0, 0, 1.0, 1.0], [0, 0, 1, 1], [1, 1, 0, 1], [1, 1, 1, 0]], "d")
assert_allclose(binary_dist_jaccard(self.sparse1), sparse1expected)
sparse1expected = dist_manhattan(self.sparse1.astype(bool))
sparse1norm = array(
[[1, 1, 2, 1], [1, 1, 2, 1], [2, 2, 1, 1], [1, 1, 1, 100]], "d")
sparse1expected /= sparse1norm
assert_allclose(binary_dist_jaccard(self.sparse1), sparse1expected)