def test_simulate(self):
treat_all = self.granich(False)
treat_deferred = self.granich(True)
results_treat = macro.simulate([treat_all])
results_deferred = macro.simulate([treat_deferred])
totals_before_t = macro.calc_totals(results_treat[0][0])
totals_after_t = macro.calc_totals(results_treat[-1][0])
n_before = sum(
[value for key, value in totals_before_t.items() if key != 'N'])
n_after = sum(
[value for key, value in totals_after_t.items() if key != 'N'])
self.assertAlmostEqual(n_before, n_after, 6)
self.assertAlmostEqual(n_after, 36000000, 6)
totals_before_d = macro.calc_totals(results_deferred[0][0])
totals_after_d = macro.calc_totals(results_deferred[-1][0])
n_before = sum(
[value for key, value in totals_before_d.items() if key != 'N'])
n_after = sum(
[value for key, value in totals_after_d.items() if key != 'N'])
self.assertAlmostEqual(n_before, n_after, 5)
self.assertAlmostEqual(n_after, 36000000, 5)
self.assertGreater(totals_after_t['DI'], 1000)
self.assertGreater(totals_after_t['DT'], 1000)
self.assertGreater(totals_after_d['DI'], totals_after_t['DI'])
self.assertGreater(totals_after_d['DT'], totals_after_t['DT'])
self.assertGreater(totals_after_t['N'], totals_after_d['N'])
self.assertGreater(-totals_after_t['B'], -totals_after_d['B'])
def test_simulate(self):
res = macro.simulate([self.simple()])
self.assertEqual(res[0][0]['iteration'], 0)
self.assertEqual(res[1][0]['iteration'], 50)
self.assertEqual(res[-1][0]['iteration'], 365)
self.assertEqual(res[-2][0]['iteration'], 350)
self.assertEqual(len(res), 9)
self.assertEqual(len(res[0]), 1)
totals = macro.calc_totals(res[-2][0])
self.assertAlmostEqual(totals['N'],
57000001.0,
msg="Sum of compartments")
table = macro.modelList_to_table(res[-2], True)
self.assertEqual(table[0], ['iter', 'name_0', 'S', 'I', 'R'],
msg="Table header has correct column names")
self.assertEqual(table[1], [
350, 'Simple model', 65525.67886409864, 7.38650518227673e-07,
56934475.32113517
],
msg="Table row has correct values")
(_, filename) = tempfile.mkstemp()
macro.series_to_csv(res, filename)
with open(filename, newline='') as csvfile:
c = csv.reader(csvfile)
t = [r for r in c]
self.assertEqual(table[0], t[0])
for pair in zip(table[-1], t[-2]):
self.assertEqual(str(pair[0]), str(pair[1]))
def test_parallel(self):
resultSeries = macro.simulate_series(
[TestCorona().corona() for _ in range(10)])
self.assertEqual(len(resultSeries), 3660)
self.assertEqual(len(resultSeries[0]), 3)
self.assertEqual(len(resultSeries[3659]), 3)
results = [r for r in resultSeries if r[0]['iteration'] == 365]
N_0 = macro.calc_totals(results[0][0])['N']
N_1 = macro.calc_totals(results[1][0])['N']
self.assertNotEqual(N_0, N_1)
self.assertLess(abs(N_0 - N_1), 180000)
for i in range(10):
results = [r for r in resultSeries if r[0]['ident'] == i]
self.check_results(results)
results = [r for r in resultSeries if r[1]['ident'] == i]
self.check_results(results)
def check_results(self, results):
self.assertEqual(len(results), 366)
Nb = macro.grand_sum_totals([macro.calc_totals(m) for m in results[0]])
Na = macro.grand_sum_totals(
[macro.calc_totals(m) for m in results[-1]])
self.assertAlmostEqual(Nb, Na, 5)
totals = macro.sum_totals([macro.calc_totals(m) for m in results[-1]])
self.assertGreater(totals['D'], 100000)
self.assertLess(totals['D'], 160000)
# Check that informal settlement > urban > rural
proportions = [
t['D'] / t['N']
for t in [macro.calc_totals(m) for m in results[-1]]
]
self.assertTrue(proportions[0] > proportions[1])
self.assertTrue(proportions[1] > proportions[2])
self.assertGreater(proportions[2], 0.00015)
def test_simulate(self):
totals = macro.calc_totals(self.complicated())
self.assertAlmostEqual(totals['N'], 1091.0, msg="Sum of compartments")
res = macro.simulate([self.complicated()])
self.assertEqual(res[0][0]['iteration'], 0)
self.assertEqual(res[1][0]['iteration'], 50)
self.assertEqual(res[-1][0]['iteration'], 365)
self.assertEqual(res[-2][0]['iteration'], 350)
self.assertEqual(len(res), 9)
self.assertEqual(len(res[0]), 1)
totals = macro.calc_totals(res[-2][0])
self.assertAlmostEqual(totals['N'], 1091.0, msg="Sum of compartments")
table = macro.modelList_to_table(res[-2], True)
self.assertEqual(table[0],
['iter', 'name_0', 'name_1', 'name_2', 'S', 'I', 'R'],
msg="Table header has correct column names")
self.assertEqual(table[1], [
350, 'Van Wyks Dorp', 'Male', '0-50', 25.59087276881619,
6.371396740780498e-07, 265.4091265940443
],
msg="Table row has correct values")
(_, filename) = tempfile.mkstemp()
macro.series_to_csv(res, filename)
with open(filename, newline='') as csvfile:
c = csv.reader(csvfile)
t = [r for r in c]
self.assertEqual(table[0], t[0])
for pair in zip(table[-1], t[-5]):
self.assertEqual(str(pair[0]), str(pair[1]))
table = macro.modelList_to_table(res[-2], concat_names="|")
(_, filename) = tempfile.mkstemp()
macro.series_to_csv(res, filename, concat_names="|")
self.assertEqual(len(table[0]), 5)
self.assertEqual(len(table[0]), len(table[-1]))
with open(filename, newline='') as csvfile:
c = csv.reader(csvfile)
t = [r for r in c]
self.assertEqual(table[0], t[0])
for pair in zip(table[-1], t[-5]):
self.assertEqual(str(pair[0]), str(pair[1]))
def test_simulate(self):
res = macro.simulate([self.simple()])
self.assertEqual(res[0][0]['iteration'], 0)
self.assertEqual(res[1][0]['iteration'], 50)
self.assertEqual(res[-1][0]['iteration'], 365)
self.assertEqual(res[-2][0]['iteration'], 350)
totals = macro.calc_totals(res[-1][0])
self.assertAlmostEqual(totals['N'],
57000001.0,
1,
msg="Sum of compartments")
table = macro.modelList_to_table(res[-2], True)
self.assertEqual(table[0], ['iter', 'name_0', 'S', 'I', 'R'],
msg="Table header has correct column names")
self.assertGreater(table[1][2],
50000.0,
msg="Random fluctuations give reasonable result")
self.assertGreater(80000.0,
table[1][2],
msg="Random fluctuations give reasonable result")