def test_return_statdist(self):
C = np.loadtxt(testpath + 'C_1_lag.dat')
# dense
T, mu = apicall(C,
reversible=True,
method='dense',
return_statdist=True)
mu_manual = msmtools.analysis.stationary_distribution(T)
np.testing.assert_allclose(mu, mu_manual)
# sparse
T, mu = apicall(C,
reversible=True,
method='sparse',
return_statdist=True)
mu_manual = msmtools.analysis.stationary_distribution(T)
np.testing.assert_allclose(mu, mu_manual)
def test_mle_trev(self):
C = np.loadtxt(testpath + 'C_1_lag.dat')
T_impl_algo_sparse_type_sparse = impl_sparse(
scipy.sparse.csr_matrix(C)).toarray()
T_impl_algo_dense_type_dense = impl_dense(C)
T_api_algo_dense_type_dense = apicall(C,
reversible=True,
method='dense')
T_api_algo_sparse_type_dense = apicall(C,
reversible=True,
method='sparse')
T_api_algo_dense_type_sparse = apicall(scipy.sparse.csr_matrix(C),
reversible=True,
method='dense').toarray()
T_api_algo_sparse_type_sparse = apicall(scipy.sparse.csr_matrix(C),
reversible=True,
method='sparse').toarray()
T_api_algo_auto_type_dense = apicall(C, reversible=True, method='auto')
T_api_algo_auto_type_sparse = apicall(scipy.sparse.csr_matrix(C),
reversible=True,
method='auto').toarray()
assert_allclose(T_impl_algo_sparse_type_sparse,
T_impl_algo_dense_type_dense)
assert_allclose(T_api_algo_dense_type_dense,
T_impl_algo_dense_type_dense)
assert_allclose(T_api_algo_sparse_type_dense,
T_impl_algo_dense_type_dense)
assert_allclose(T_api_algo_dense_type_sparse,
T_impl_algo_dense_type_dense)
assert_allclose(T_api_algo_sparse_type_sparse,
T_impl_algo_dense_type_dense)
assert_allclose(T_api_algo_auto_type_dense,
T_impl_algo_dense_type_dense)
assert_allclose(T_api_algo_auto_type_sparse,
T_impl_algo_dense_type_dense)
def test_mle_trev_given_pi(self):
C = np.loadtxt(testpath + 'C_1_lag.dat')
pi = np.loadtxt(testpath + 'pi.dat')
T_impl_algo_dense_type_dense = impl_dense(C, pi)
T_impl_algo_sparse_type_sparse = impl_sparse(
scipy.sparse.csr_matrix(C), pi).toarray()
T_Frank = impl_dense_Frank(C, pi)
T_api_algo_dense_type_dense = apicall(C,
reversible=True,
mu=pi,
method='dense')
T_api_algo_sparse_type_dense = apicall(C,
reversible=True,
mu=pi,
method='sparse')
T_api_algo_dense_type_sparse = apicall(scipy.sparse.csr_matrix(C),
reversible=True,
mu=pi,
method='dense').toarray()
T_api_algo_sparse_type_sparse = apicall(scipy.sparse.csr_matrix(C),
reversible=True,
mu=pi,
method='sparse').toarray()
T_api_algo_auto_type_dense = apicall(C,
reversible=True,
mu=pi,
method='auto')
T_api_algo_auto_type_sparse = apicall(scipy.sparse.csr_matrix(C),
reversible=True,
mu=pi,
method='auto').toarray()
assert_allclose(T_impl_algo_dense_type_dense, T_Frank)
assert_allclose(T_impl_algo_sparse_type_sparse, T_Frank)
assert_allclose(T_api_algo_dense_type_dense, T_Frank)
assert_allclose(T_api_algo_sparse_type_dense, T_Frank)
assert_allclose(T_api_algo_dense_type_sparse, T_Frank)
assert_allclose(T_api_algo_sparse_type_sparse, T_Frank)
assert_allclose(T_api_algo_auto_type_dense, T_Frank)
assert_allclose(T_api_algo_auto_type_sparse, T_Frank)
assert is_transition_matrix(T_Frank)
assert is_transition_matrix(T_impl_algo_dense_type_dense)
assert is_transition_matrix(T_impl_algo_sparse_type_sparse)
assert is_transition_matrix(T_api_algo_dense_type_dense)
assert is_transition_matrix(T_api_algo_sparse_type_dense)
assert is_transition_matrix(T_api_algo_dense_type_sparse)
assert is_transition_matrix(T_api_algo_sparse_type_sparse)
assert is_transition_matrix(T_api_algo_auto_type_dense)
assert is_transition_matrix(T_api_algo_auto_type_sparse)
assert_allclose(statdist(T_Frank), pi)
assert_allclose(statdist(T_impl_algo_dense_type_dense), pi)
assert_allclose(statdist(T_impl_algo_sparse_type_sparse), pi)
assert_allclose(statdist(T_api_algo_dense_type_dense), pi)
assert_allclose(statdist(T_api_algo_sparse_type_dense), pi)
assert_allclose(statdist(T_api_algo_dense_type_sparse), pi)
assert_allclose(statdist(T_api_algo_sparse_type_sparse), pi)
assert_allclose(statdist(T_api_algo_auto_type_dense), pi)
assert_allclose(statdist(T_api_algo_auto_type_sparse), pi)