def test_gelman_rubin_raise_error(self):
chains=setup_chains()
for _ in range(len(chains) - 1):
chains.pop(-1)
with self.assertRaises(ValueError,
msg='Must have multiple chains'):
CS.gelman_rubin(chains=chains)
def test_string_display(self):
capturedOutput = io.StringIO() # Create StringIO object
sys.stdout = capturedOutput # and redirect stdout.
CS.print_chain_acceptance_info(chain)
sys.stdout = sys.__stdout__ # Reset redirect.
self.assertTrue(isinstance(capturedOutput.getvalue(), str),
msg='Caputured string')
self.assertFalse('Results dictionary' in capturedOutput.getvalue(),
msg='Expect results dictionary not included')
def test_string_display_w_details(self):
capturedOutput = io.StringIO() # Create StringIO object
sys.stdout = capturedOutput # and redirect stdout.
CS.chainstats(chain, display_details=True)
sys.stdout = sys.__stdout__ # Reset redirect.
self.assertTrue(isinstance(capturedOutput.getvalue(), str),
msg='Caputured string')
self.assertFalse('Results dictionary' in capturedOutput.getvalue(),
msg='Expect results dictionary not included')
self.assertTrue('Definition for items displayed:' in capturedOutput.getvalue())
def test_string_display_with_results(self):
capturedOutput = io.StringIO() # Create StringIO object
sys.stdout = capturedOutput # and redirect stdout.
CS.print_chain_acceptance_info(
chain, results=dict(
nsimu=5000,
iacce=np.array([200, 800])
))
sys.stdout = sys.__stdout__ # Reset redirect.
self.assertTrue(isinstance(capturedOutput.getvalue(), str),
msg='Caputured string')
self.assertTrue('Results dictionary' in capturedOutput.getvalue(),
msg='Expect results dictionary included')
def test_gelman_rubin_with_pres(self):
chains = setup_chains()
pres = []
for _, chain in enumerate(chains):
pres.append(dict(chain=chain, nsimu=chain.shape[0]))
psrf = CS.gelman_rubin(chains=pres)
self.standard_check(psrf)
def test_gelman_rubin(self):
chains=setup_chains()
capturedOutput = io.StringIO() # Create StringIO object
sys.stdout = capturedOutput # and redirect stdout.
psrf = CS.gelman_rubin(chains=chains, display=True)
sys.stdout = sys.__stdout__ # Reset redirect.
self.assertTrue(isinstance(capturedOutput.getvalue(), str),
msg='Caputured string')
self.standard_check(psrf)
def test_calc_psrf(self):
x = np.concatenate((np.linspace(0, 1, 1000).reshape(1000, 1),
np.linspace(2.5, 3.3, 1000).reshape(1000, 1)),
axis=1)
psrf = CS.calculate_psrf(x, nsimu=1000, nchains=2)
self.assertTrue(isinstance(psrf, dict), msg='Expect dictionary output')
self.assertAlmostEqual(psrf['R'], 8.001818935964492, places=6,
msg=str('R: {} neq {}'.format(psrf['R'], 8.001818935964492)))
self.assertAlmostEqual(psrf['B'], 2879.9999999999964, places=6,
msg=str('R: {} neq {}'.format(psrf['B'], 2879.9999999999964)))
self.assertAlmostEqual(psrf['W'], 0.06853867547894903, places=6,
msg=str('R: {} neq {}'.format(psrf['W'], 0.06853867547894903)))
self.assertAlmostEqual(psrf['V'], 4.388470136803464, places=6,
msg=str('R: {} neq {}'.format(psrf['V'], 4.388470136803464)))
self.assertAlmostEqual(psrf['neff'], 3.047548706113521, places=6,
msg=str('R: {} neq {}'.format(psrf['neff'], 3.047548706113521)))
def test_too_few_batches(self):
with self.assertRaises(SystemExit, msg='too few batches'):
CS.batch_mean_standard_deviation(chain, b=chain.shape[0])
def test_len_s(self):
s = CS.batch_mean_standard_deviation(chain, b=None)
self.assertEqual(len(s), 2)
def test_cs_eval_with_no_chain(self):
stats = CS.chainstats(chain=None, returnstats=True)
self.assertTrue(isinstance(stats, str))
def test_cs_eval_with_no_return(self):
stats = CS.chainstats(chain=chain, returnstats=False)
self.assertEqual(stats, None)
def test_cs_eval_with_return(self):
stats = CS.chainstats(chain=chain, returnstats=True)
self.assertTrue(isinstance(stats, dict))
def test_gelman_rubin_with_names(self):
chains = setup_chains()
psrf = CS.gelman_rubin(chains=chains, names=['a', 'b'])
self.standard_check(psrf)
def test_nw_not_none(self):
x = chain[:, 0]
y = CS.power_spectral_density_using_hanning_window(x=x, nw=len(x))
nfft = min(len(x), 256)
n2 = int(np.floor(nfft/2))
self.assertEqual(n2, len(y))
def test_nfft_not_none_size(self):
x = chain[:, 0]
nfft = 100
y = CS.power_spectral_density_using_hanning_window(x=x, nfft=nfft)
n2 = int(np.floor(nfft/2))
self.assertEqual(n2, len(y))