def test_chain_not_accepted_within_bounds(self):
accept = 0
outsidebounds = 0
CL = {
'theta': np.array([1.0, 2.0]),
'ss': 1.0,
'prior': 0.0,
'sigma2': 0.0
}
parset = ParameterSet(theta=CL['theta'],
ss=CL['ss'],
prior=CL['prior'],
sigma2=CL['sigma2'])
mcstat = gf.setup_initialize_chains(CL)
mcstat._MCMC__rejected = {
'total': 10,
'in_adaptation_interval': 4,
'outside_bounds': 1
}
mcstat._MCMC__update_chain(accept=accept,
new_set=parset,
outsidebounds=outsidebounds)
self.assertTrue(np.array_equal(mcstat._MCMC__chain[-1, :],
mcstat._MCMC__old_set.theta),
msg=str('theta added to end of chain - {}'.format(
mcstat._MCMC__chain[-1, :])))
def test_initialize_chain_updatesigma_1_nsos_2(self):
CL = self.setup_CL()
mcstat = gf.setup_initialize_chains(CL, nsos=2)
self.assertEqual(mcstat._MCMC__chain.shape,
(mcstat.simulation_options.nsimu, 2),
msg=str('Shape should be (nsimu,2) -> {}'.format(
mcstat._MCMC__chain.shape)))
self.assertEqual(mcstat._MCMC__sschain.shape,
(mcstat.simulation_options.nsimu, 2),
msg=str('Shape should be (nsimu,2) -> {}'.format(
mcstat._MCMC__sschain.shape)))
self.assertEqual(mcstat._MCMC__s2chain.shape,
(mcstat.simulation_options.nsimu, 2),
msg=str('Shape should be (nsimu,2) -> {}'.format(
mcstat._MCMC__s2chain.shape)))
def test_initialize_chain_updatesigma_0(self):
CL = self.setup_CL()
mcstat = gf.setup_initialize_chains(CL, updatesigma=False)
self.assertEqual(mcstat._MCMC__chain.shape,
(mcstat.simulation_options.nsimu, 2),
msg=str('Shape should be (nsimu,2) -> {}'.format(
mcstat._MCMC__chain.shape)))
self.assertEqual(mcstat._MCMC__sschain.shape,
(mcstat.simulation_options.nsimu, 1),
msg=str('Shape should be (nsimu,1) -> {}'.format(
mcstat._MCMC__sschain.shape)))
self.assertEqual(mcstat._MCMC__s2chain,
None,
msg=str('s2chain should be None -> {}'.format(
mcstat._MCMC__s2chain)))
def test_expand_chain_updatesigma_1_nsos_2(self):
CL = self.setup_CL()
mcstat = gf.setup_initialize_chains(CL, nsos=2)
mcstat._MCMC__expand_chains(
nsimu=mcstat.simulation_options.nsimu,
npar=mcstat.parameters.npar,
nsos=mcstat.model_settings.nsos,
updatesigma=mcstat.simulation_options.updatesigma)
self.assertEqual(mcstat._MCMC__chain.shape,
(mcstat.simulation_options.nsimu * 2 - 1, 2),
msg=str('Shape should be (nsimu,2) -> {}'.format(
mcstat._MCMC__chain.shape)))
self.assertEqual(mcstat._MCMC__sschain.shape,
(mcstat.simulation_options.nsimu * 2 - 1, 2),
msg=str('Shape should be (nsimu,2) -> {}'.format(
mcstat._MCMC__sschain.shape)))
self.assertEqual(mcstat._MCMC__s2chain.shape,
(mcstat.simulation_options.nsimu * 2 - 1, 2),
msg=str('Shape should be (nsimu,2) -> {}'.format(
mcstat._MCMC__s2chain.shape)))
def test_chain_accepted(self):
accept = 1
outsidebounds = 0
CL = {
'theta': np.array([1.0, 2.0]),
'ss': 1.0,
'prior': 0.0,
'sigma2': 0.0
}
parset = ParameterSet(theta=CL['theta'],
ss=CL['ss'],
prior=CL['prior'],
sigma2=CL['sigma2'])
mcstat = gf.setup_initialize_chains(CL)
mcstat._MCMC__update_chain(accept=accept,
new_set=parset,
outsidebounds=outsidebounds)
self.assertTrue(np.array_equal(mcstat._MCMC__chain[-1, :],
parset.theta),
msg=str('theta added to end of chain - {}'.format(
mcstat._MCMC__chain[-1, :])))
self.assertEqual(mcstat._MCMC__old_set,
parset,
msg='old_set updated to new set')