code stringlengths 3 6.57k |
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self.assertRaises(TreeSimulatorError) |
bd_sim.simulate_tree() |
self.assertRaises(TreeSimulatorError) |
bd_sim.simulate_tree() |
self.assertRaises(TreeSimulatorError) |
bd_sim.simulate_tree() |
test_bad_stopping_conditions(self) |
self.assertRaises(TreeSimulatorError) |
BirthDeathFitnessSimulator(lambda _: 1, 1, lambda: 2) |
self.assertRaises(TreeSimulatorError) |
self.assertRaises(TreeSimulatorError) |
self.assertRaises(TreeSimulatorError) |
self.assertRaises(TreeSimulatorError) |
self.assertRaises(TreeSimulatorError) |
test_dead_at_start(self) |
self.assertRaises(TreeSimulatorError) |
bd_sim.simulate_tree() |
self.assertRaises(TreeSimulatorError) |
bd_sim.simulate_tree() |
test_dead_before_end(self) |
np.random.exponential(scale) |
np.random.exponential(0.6) |
self.assertRaises(TreeSimulatorError) |
bd_sim.simulate_tree() |
self.assertRaises(TreeSimulatorError) |
bd_sim.simulate_tree() |
test_single_lineage(self) |
BirthDeathFitnessSimulator(lambda _: 1, 1, num_extant=1) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertEqual(results[1], 1) |
self.assertEqual(tree.get_branch_length("0", "1") |
self.assertEqual(results[0], [1]) |
BirthDeathFitnessSimulator(lambda _: 1, 1, experiment_time=1) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertEqual(results[1], 1) |
self.assertEqual(tree.get_branch_length("0", "1") |
self.assertEqual(results[0], [1]) |
test_constant_yule(self) |
BirthDeathFitnessSimulator(lambda _: 1, 1, num_extant=32) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertEqual(i, 6) |
self.assertEqual(results[1], 32) |
self.assertTrue(results[2]) |
BirthDeathFitnessSimulator(lambda _: 1, 1, experiment_time=6) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertEqual(i, 6) |
self.assertEqual(results[1], 32) |
self.assertTrue(results[2]) |
test_nonconstant_yule(self) |
np.random.exponential(scale) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertTrue(all(np.isclose(x, results[0][0]) |
self.assertEqual(results[1], 16) |
self.assertTrue(results[2]) |
self.assertEqual(max([int(i) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertEqual(i, 2) |
self.assertTrue(results[2]) |
test_nonconstant_birth_death(self) |
np.random.exponential(scale) |
np.random.exponential(1.5) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertTrue(all(np.isclose(x, results[0][0]) |
self.assertEqual(results[1], 8) |
self.assertTrue(results[2]) |
self.assertNotIn("9", tree.nodes) |
self.assertNotIn("2", tree.nodes) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertTrue(np.isclose(i, 2) |
self.assertTrue(results[2]) |
self.assertNotIn("9", tree.nodes) |
self.assertNotIn("2", tree.nodes) |
test_nonconstant_birth_death_no_unifurcation_collapsing(self) |
np.random.exponential(scale) |
np.random.exponential(1.5) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertTrue(all(np.isclose(x, results[0][0]) |
self.assertEqual(results[1], 8) |
self.assertFalse(results[2]) |
self.assertNotIn("3", tree.nodes) |
self.assertIn("2", tree.nodes) |
self.assertIn("6", tree.nodes) |
bd_sim.simulate_tree() |
extract_tree_statistics(tree) |
self.assertTrue(np.isclose(i, 1.3) |
self.assertFalse(results[2]) |
self.assertNotIn("3", tree.nodes) |
self.assertIn("2", tree.nodes) |
self.assertIn("6", tree.nodes) |
test_nonconstant_birth_death_both_stopping_conditions(self) |
np.random.exponential(scale) |
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