def test_increment_from_node(self):
node = Patch(0, [self.compartment])
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.compartment, 12)
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 12)
def setUp(self):
self.probability = 0.1
self.compartment = 'a'
self.new_compartment = 'z'
self.edge_type = 'edge1'
EDGE_ID = 'edgeid'
self.event = TranslocateAndChange([Patch], self.probability,
self.compartment, self.edge_type,
self.new_compartment)
self.nodes = [
Patch(0, [self.compartment]),
Patch(1, [self.compartment]),
Patch(2, [self.compartment]),
Patch(3, [self.compartment])
]
self.edges = [(self.nodes[0], self.nodes[1], {
EDGE_TYPE: self.edge_type,
EDGE_ID: 1
}),
(self.nodes[0], self.nodes[2], {
EDGE_TYPE: self.edge_type,
EDGE_ID: 2
}),
(self.nodes[2], self.nodes[3], {
EDGE_TYPE: 'edge2',
EDGE_ID: 3
})]
self.network = MetapopulationNetwork([self.compartment], self.nodes,
self.edges, [self.event])
def test_update_rate(self):
nodes = [Patch(0, ['a']), Patch(1, ['a'])]
nodes[0].update_subpopulation('a', 1)
nodes[1].update_subpopulation('a', 2)
self.non_abstract_event.attach_nodes(nodes)
self.non_abstract_event.update_rate(None)
self.assertEqual(self.non_abstract_event.state_variable, 3)
self.assertEqual(self.non_abstract_event.rate, 3 * self.prob)
def test_increment_from_node(self):
node = Patch(0, [self.mac_heal, self.mac_inf, self.bac])
self.assertEqual(self.event.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.bac, 4)
self.assertEqual(self.event.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.mac_inf, 5)
node.update_subpopulation(self.bac, -4)
self.assertEqual(self.event.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.bac, 4)
self.assertEqual(self.event.increment_state_variable_from_node(node, None), 5)
class PatchTestCase(unittest.TestCase):
def setUp(self):
self.node_id = 90
self.compartments = ['a', 'b', 'c']
self.position = (6, 7)
self.patch = Patch(self.node_id, self.compartments, self.position)
def test_initialise(self):
self.assertItemsEqual(self.patch.subpopulations.keys(),
self.compartments)
for key in self.patch.subpopulations:
self.assertEqual(self.patch.subpopulations[key], 0)
self.assertSequenceEqual(self.patch.position, self.position)
self.assertEqual(self.patch.node_id, self.node_id)
def test_update_subpopulation(self):
self.patch.update_subpopulation(self.compartments[0], 1)
self.assertEqual(self.patch.subpopulations[self.compartments[0]], 1)
# Fail wrong key
with self.assertRaises(AssertionError) as context:
self.patch.update_subpopulation('FAIL', 1)
self.assertEqual('Invalid compartment FAIL for update',
str(context.exception))
def test_compartment_per_compartment(self):
self.patch.update_subpopulation(self.compartments[0], 10)
self.patch.update_subpopulation(self.compartments[1], 3)
self.assertEqual(
self.patch.compartment_per_compartment(self.compartments[0],
self.compartments[1]), 3)
def test_destroy_internals_functions(self):
node = Patch(0, ['a', 'b', 'c'])
node.subpopulations['a'] = 5
node.subpopulations['b'] = 10
node.subpopulations['c'] = 18
destroy_internals(['b', 'c'], 'a', node)
self.assertEqual(node.subpopulations['a'], 5)
self.assertEqual(node.subpopulations['b'], 8)
self.assertEqual(node.subpopulations['c'], 15)
def test_update_network(self):
np.random.seed(101)
nodes = [Patch(0, ['a']), Patch(1, ['a'])]
nodes[0].update_subpopulation('a', 1)
nodes[1].update_subpopulation('a', 2)
self.non_abstract_event.attach_nodes(nodes)
self.non_abstract_event.update_rate(None)
self.non_abstract_event.update_network(None)
self.assertEqual(nodes[0].subpopulations['a'], 1)
self.assertEqual(nodes[1].subpopulations['a'], 3)
def setUp(self):
self.probability = 0.1
self.compartment = 'a'
self.internal_compartment = 'b'
self.edge_type = 'edge1'
EDGE_ID = 'edgeid'
self.event_no_internals = Translocate([Patch], self.probability,
self.compartment, self.edge_type)
self.event_with_internals = Translocate(
[Patch],
self.probability,
self.compartment,
self.edge_type,
internal_compartments=[self.internal_compartment])
self.event_not_affected_by_degree = Translocate(
[Patch],
self.probability,
self.compartment,
self.edge_type,
probability_increases_with_edges=False)
self.nodes = [
Patch(0, [self.compartment]),
Patch(1, [self.compartment]),
Patch(2, [self.compartment]),
Patch(3, [self.compartment])
]
self.edges = [(self.nodes[0], self.nodes[1], {
EDGE_TYPE: self.edge_type,
EDGE_ID: 1
}),
(self.nodes[0], self.nodes[2], {
EDGE_TYPE: self.edge_type,
EDGE_ID: 2
}),
(self.nodes[2], self.nodes[3], {
EDGE_TYPE: 'edge2',
EDGE_ID: 3
})]
events = [self.event_no_internals]
self.network = MetapopulationNetwork([self.compartment], self.nodes,
self.edges, events)
def test_update_node(self):
node = Patch(0, [self.comp_from, self.comp_to])
node.update_subpopulation(self.comp_from, 6)
self.event.update_node(node, None)
self.assertEqual(node.subpopulations[self.comp_from], 5)
self.assertEqual(node.subpopulations[self.comp_to], 1)
node = Patch(0, [
self.comp_from, self.comp_to, self.internal_comps[0],
self.internal_comps[1]
])
node.update_subpopulation(self.comp_from, 6)
node.update_subpopulation(self.internal_comps[0], 12)
node.update_subpopulation(self.internal_comps[1], 33)
self.event_with_internals.update_node(node, None)
self.assertEqual(node.subpopulations[self.comp_from], 5)
self.assertEqual(node.subpopulations[self.comp_to], 1)
self.assertEqual(node.subpopulations[self.internal_comps[0]], 10)
self.assertEqual(node.subpopulations[self.internal_comps[1]], 28)
def test_update_node(self):
node = Patch(0, [
self.compartment, self.influencing_comps[0],
self.influencing_comps[1], self.new_comp
])
node.subpopulations[self.compartment] = 5
node.subpopulations[self.influencing_comps[0]] = 3
node.subpopulations[self.influencing_comps[1]] = 8
self.event.update_node(node, None)
self.assertEqual(node.subpopulations[self.compartment], 4)
self.assertEqual(node.subpopulations[self.influencing_comps[0]], 3)
self.assertEqual(node.subpopulations[self.influencing_comps[1]], 8)
self.assertEqual(node.subpopulations[self.new_comp], 0)
node = Patch(0, [
self.compartment, self.influencing_comps[0],
self.influencing_comps[1], self.new_comp
])
node.subpopulations[self.compartment] = 5
node.subpopulations[self.influencing_comps[0]] = 3
node.subpopulations[self.influencing_comps[1]] = 8
self.event_destroy_influencer.update_node(node, None)
self.assertEqual(node.subpopulations[self.compartment], 4)
self.assertEqual(node.subpopulations[self.influencing_comps[0]], 2)
self.assertEqual(node.subpopulations[self.influencing_comps[1]], 8)
self.assertEqual(node.subpopulations[self.new_comp], 0)
node = Patch(0, [
self.compartment, self.influencing_comps[0],
self.influencing_comps[1], self.new_comp
])
node.subpopulations[self.compartment] = 5
node.subpopulations[self.influencing_comps[0]] = 3
node.subpopulations[self.influencing_comps[1]] = 8
self.event_change_influencer.update_node(node, None)
self.assertEqual(node.subpopulations[self.compartment], 4)
self.assertEqual(node.subpopulations[self.influencing_comps[0]], 3)
self.assertEqual(node.subpopulations[self.influencing_comps[1]], 7)
self.assertEqual(node.subpopulations[self.new_comp], 1)
def test_increment_from_node(self):
node = Patch(0, [self.comp_from, self.comp_to] + self.externals)
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.comp_from, 10)
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.externals[0], 1)
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 10 * 1)
node.update_subpopulation(self.externals[1], 2)
self.assertEqual(
self.event.increment_state_variable_from_node(node, None),
10 * (1 + 2))
def test_increment_from_node(self):
node = Patch(0, [self.bac_original, self.bac_new, self.mac_original, self.mac_new])
self.assertEqual(self.event_no_change.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.bac_original, 13)
self.assertEqual(self.event_no_change.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.mac_original, 5)
self.assertEqual(self.event_no_change.increment_state_variable_from_node(node, None), 13 * 5)
def test_increment_from_node(self):
node = Patch(0, [self.comp_from, self.comp_to] + self.inf_comps)
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.comp_from, 10)
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 0)
node.update_subpopulation(self.inf_comps[0], 3)
self.assertEqual(
self.event.increment_state_variable_from_node(node, None),
10.0 * 3.0 / 13.0)
def test_increment_from_node(self):
node = Patch(0, [
self.compartment, self.influencing_comps[0],
self.influencing_comps[1], self.new_comp
])
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 0)
node.subpopulations[self.compartment] = 12
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 0)
node.subpopulations[self.compartment] = 0
node.subpopulations[self.influencing_comps[0]] = 12
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 0)
node.subpopulations[self.compartment] = 3
node.subpopulations[self.influencing_comps[0]] = 4
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 12)
node.subpopulations[self.influencing_comps[1]] = 2
self.assertEqual(
self.event.increment_state_variable_from_node(node, None), 18)
def __init__(self, compartments, events):
node = Patch(0, compartments)
MetapopulationNetwork.__init__(self, compartments, [node], [], events)
def test_update_node(self):
node = Patch(0, [self.compartment])
self.event.update_node(node, None)
self.assertEqual(node.subpopulations[self.compartment], 1)
def setUp(self):
self.node_id = 90
self.compartments = ['a', 'b', 'c']
self.position = (6, 7)
self.patch = Patch(self.node_id, self.compartments, self.position)
def test_update_node(self):
node = Patch(0, [
self.compartment, self.internal_comp_destroy,
self.internal_comp_from, self.internal_comp_to
])
node.update_subpopulation(self.compartment, 5)
node.update_subpopulation(self.internal_comp_destroy, 10)
node.update_subpopulation(self.internal_comp_from, 18)
node.update_subpopulation(self.internal_comp_to, 0)
self.event.update_node(node, None)
self.assertEqual(node.subpopulations[self.compartment], 4)
self.assertEqual(node.subpopulations[self.internal_comp_destroy], 10)
self.assertEqual(node.subpopulations[self.internal_comp_from], 18)
self.assertEqual(node.subpopulations[self.internal_comp_to], 0)
node = Patch(0, [
self.compartment, self.internal_comp_destroy,
self.internal_comp_from, self.internal_comp_to
])
node.update_subpopulation(self.compartment, 5)
node.update_subpopulation(self.internal_comp_destroy, 10)
node.update_subpopulation(self.internal_comp_from, 18)
node.update_subpopulation(self.internal_comp_to, 0)
self.event_with_internals_destroyed.update_node(node, None)
self.assertEqual(node.subpopulations[self.compartment], 4)
self.assertEqual(node.subpopulations[self.internal_comp_destroy], 8)
self.assertEqual(node.subpopulations[self.internal_comp_from], 18)
self.assertEqual(node.subpopulations[self.internal_comp_to], 0)
node = Patch(0, [
self.compartment, self.internal_comp_destroy,
self.internal_comp_from, self.internal_comp_to
])
node.update_subpopulation(self.compartment, 5)
node.update_subpopulation(self.internal_comp_destroy, 10)
node.update_subpopulation(self.internal_comp_from, 18)
node.update_subpopulation(self.internal_comp_to, 0)
self.event_with_internals_changed.update_node(node, None)
self.assertEqual(node.subpopulations[self.compartment], 4)
self.assertEqual(node.subpopulations[self.internal_comp_destroy], 10)
self.assertEqual(node.subpopulations[self.internal_comp_from], 15)
self.assertEqual(node.subpopulations[self.internal_comp_to], 3)
def test_update_node(self):
node = Patch(0, [self.comp_from, self.comp_to, self.new_external] +
self.externals)
node.update_subpopulation(self.comp_from, 10)
node.update_subpopulation(self.externals[0], 5)
node.update_subpopulation(self.externals[1], 3)
self.event.update_node(node, None)
self.assertEqual(node.subpopulations[self.comp_from], 9)
self.assertEqual(node.subpopulations[self.comp_to], 1)
self.assertEqual(node.subpopulations[self.externals[0]], 5)
self.assertEqual(node.subpopulations[self.externals[1]], 3)
self.assertEqual(node.subpopulations[self.new_external], 0)
node = Patch(0, [self.comp_from, self.comp_to, self.new_external] +
self.externals)
node.update_subpopulation(self.comp_from, 10)
node.update_subpopulation(self.externals[0], 5)
node.update_subpopulation(self.externals[1], 3)
self.event_change_internals.update_node(node, None)
self.assertEqual(node.subpopulations[self.comp_from], 9)
self.assertEqual(node.subpopulations[self.comp_to], 1)
self.assertEqual(node.subpopulations[self.externals[0]], 4)
self.assertEqual(node.subpopulations[self.externals[1]], 3)
self.assertEqual(node.subpopulations[self.new_external], 1)
def test_update_node(self):
node = Patch(0, [self.mac_heal, self.mac_inf, self.bac])
node.update_subpopulation(self.bac, 20)
node.update_subpopulation(self.mac_inf, 4)
self.event.update_node(node, None)
self.assertEqual(node.subpopulations[self.mac_inf], 4)
self.assertEqual(node.subpopulations[self.bac], 19)
self.assertEqual(node.subpopulations[self.mac_heal], 0)
node = Patch(0, [self.mac_heal, self.mac_inf, self.bac])
node.update_subpopulation(self.bac, 4)
node.update_subpopulation(self.mac_inf, 4)
self.event.update_node(node, None)
self.assertEqual(node.subpopulations[self.mac_inf], 3)
self.assertEqual(node.subpopulations[self.bac], 3)
self.assertEqual(node.subpopulations[self.mac_heal], 1)
def test_attach_nodes(self):
nodes = [Patch(0, ['a']), Patch(1, ['b'])]
self.event.attach_nodes(nodes)
self.assertItemsEqual(self.event.nodes_impacted, nodes)
def test_update_node(self):
node = Patch(0, [self.bac_original, self.bac_new, self.mac_original, self.mac_new])
node.update_subpopulation(self.bac_original, 2)
node.update_subpopulation(self.mac_original, 2)
self.event_no_change.update_node(node, None)
self.assertEqual(node.subpopulations[self.bac_original], 1)
self.assertEqual(node.subpopulations[self.mac_original], 2)
self.assertEqual(node.subpopulations[self.bac_new], 0)
self.assertEqual(node.subpopulations[self.mac_new], 0)
node = Patch(0, [self.bac_original, self.bac_new, self.mac_original, self.mac_new])
node.update_subpopulation(self.bac_original, 2)
node.update_subpopulation(self.mac_original, 2)
self.event_bac_change.update_node(node, None)
self.assertEqual(node.subpopulations[self.bac_original], 1)
self.assertEqual(node.subpopulations[self.mac_original], 2)
self.assertEqual(node.subpopulations[self.bac_new], 1)
self.assertEqual(node.subpopulations[self.mac_new], 0)
node = Patch(0, [self.bac_original, self.bac_new, self.mac_original, self.mac_new])
node.update_subpopulation(self.bac_original, 2)
node.update_subpopulation(self.mac_original, 2)
self.event_mac_change.update_node(node, None)
self.assertEqual(node.subpopulations[self.bac_original], 1)
self.assertEqual(node.subpopulations[self.mac_original], 1)
self.assertEqual(node.subpopulations[self.bac_new], 0)
self.assertEqual(node.subpopulations[self.mac_new], 1)
node = Patch(0, [self.bac_original, self.bac_new, self.mac_original, self.mac_new])
node.update_subpopulation(self.bac_original, 2)
node.update_subpopulation(self.mac_original, 2)
self.event_both_change.update_node(node, None)
self.assertEqual(node.subpopulations[self.bac_original], 1)
self.assertEqual(node.subpopulations[self.mac_original], 1)
self.assertEqual(node.subpopulations[self.bac_new], 1)
self.assertEqual(node.subpopulations[self.mac_new], 1)