def test_noninteger_counts_dense(self):
C = np.loadtxt(testpath + 'C_1_lag.dat')
T_dense_reference = impl_dense(C)
T_dense_scaled_1 = impl_dense(C*10.0)
T_dense_scaled_2 = impl_dense(C*0.1)
assert_allclose(T_dense_reference, T_dense_scaled_1)
assert_allclose(T_dense_reference, T_dense_scaled_2)
def test_warnings(self):
C = np.loadtxt(testpath + 'C_1_lag.dat')
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('ignore')
warnings.simplefilter('always', category=NotConvergedWarning)
impl_sparse(scipy.sparse.csr_matrix(C), maxiter=1)
assert issubclass(w[-1].category, NotConvergedWarning)
impl_dense(C, maxiter=1)
assert len(w) == 2
assert issubclass(w[-1].category, NotConvergedWarning)
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(stationary_distribution(T_Frank), pi)
assert_allclose(stationary_distribution(T_impl_algo_dense_type_dense),
pi)
assert_allclose(
stationary_distribution(T_impl_algo_sparse_type_sparse), pi)
assert_allclose(stationary_distribution(T_api_algo_dense_type_dense),
pi)
assert_allclose(stationary_distribution(T_api_algo_sparse_type_dense),
pi)
assert_allclose(stationary_distribution(T_api_algo_dense_type_sparse),
pi)
assert_allclose(stationary_distribution(T_api_algo_sparse_type_sparse),
pi)
assert_allclose(stationary_distribution(T_api_algo_auto_type_dense),
pi)
assert_allclose(stationary_distribution(T_api_algo_auto_type_sparse),
pi)