def test_beta_gamma_eta_model(sfa_inputs):
data, X, Z, beta_true, gamma_true, eta_true = sfa_inputs
n_beta = len(beta_true)
with patch.object(ParameterSet, '__init__', lambda x: None):
param_set = ParameterSet()
param_set.reset()
param_set.num_fe = n_beta
param_set.num_re_var = 1
param_set.design_matrix_fe = X
param_set.design_matrix_re = Z
param_set.lb_fe = [-10.0] * n_beta
param_set.ub_fe = [10.0] * n_beta
param_set.lb_re_var = [0.0] * 1
param_set.ub_re_var = [10.0] * 1
param_set.constr_matrix_fe = np.zeros((1, n_beta))
param_set.constr_lb_fe = [0.0]
param_set.constr_ub_fe = [0.0]
param_set.constr_matrix_re_var = np.zeros((1, 1))
param_set.constr_lb_re_var = [0.0]
param_set.constr_ub_re_var = [0.0]
param_set.fe_priors = []
param_set.re_var_priors = []
model = SimpleBetaGammaEtaModel(param_set)
solver = IPOPTSolver(model)
x_init = np.random.rand(len(beta_true) + 2)
solver.fit(x_init, data, options=dict(solver_options=dict(max_iter=100)))
assert np.linalg.norm(solver.x_opt[:n_beta] - beta_true) / np.linalg.norm(beta_true) < 2e-2
def test_u_model(re_inputs):
data, Z, u_true, eta = re_inputs
n_groups = len(u_true)
with patch.object(ParameterSet, '__init__', lambda x: None):
with patch.object(ParameterSet, 'num_re', new_callable=PropertyMock) as mock_num_re:
param_set = ParameterSet()
param_set.reset()
param_set.num_fe = 1
mock_num_re.return_value = n_groups
param_set.design_matrix_re = Z
param_set.constr_matrix_re = np.zeros((1, n_groups))
param_set.constr_lb_re = [0.0]
param_set.constr_ub_re = [0.0]
param_set.lb_re = [-2.0] * n_groups
param_set.ub_re = [2.0] * n_groups
param_set.re_priors = [GaussianPrior(mean=[0.0], std=[eta])]
param_set.re_var_padding = np.ones((n_groups, 1))
model = UModel(param_set)
solver = ScipyOpt(model)
x_init = np.random.rand(n_groups)
solver.fit(x_init, data, options=dict(solver_options=dict(maxiter=100)))
assert np.linalg.norm(solver.x_opt - u_true) / np.linalg.norm(u_true) < 2e-2
u_model = UModel(param_set)
cf_solver = ClosedFormSolver(u_model)
cf_solver.fit(x_init, data)
assert np.linalg.norm(cf_solver.x_opt - u_true) / np.linalg.norm(u_true) < 2e-2
def SimpleParam():
return ParameterSet(parameters=[
Parameter(variables=[
Intercept(add_re=True, col_group='group', fe_prior=GaussianPrior())
],
link_fun=lambda x: x,
param_name='foo')
])
def SplineParam():
constr_cvx = SplineLinearConstr(order=2,
y_bounds=[0.0, np.inf],
grid_size=5)
spline_var = Spline(
covariate='cov1',
derivative_constr=[constr_cvx],
degree=2,
)
parameter = Parameter(
variables=[spline_var,
Intercept(add_re=True, col_group='group')],
param_name='foo')
return ParameterSet([parameter])
def make_parameter_set(self,
coefficient_priors: Optional[List[float]] = None,
coefficient_prior_var: Optional[float] = None):
if coefficient_priors is not None:
intercept = [
Intercept(
fe_prior=GaussianPrior(mean=[coefficient_priors.pop(0)],
std=[coefficient_prior_var**0.5]))
]
else:
intercept = [Intercept()]
if self.covariates is not None:
if coefficient_priors is None:
covariate_variables = [
Variable(covariate=cov) for cov in self.covariates
]
else:
covariate_variables = [
Variable(covariate=cov,
fe_prior=GaussianPrior(
mean=[coefficient_priors.pop(0)],
std=[coefficient_prior_var**0.5]))
for cov in self.covariates
]
else:
covariate_variables = list()
spline_variables = list()
if self.splines is not None:
spline_variables = make_spline_variables(self.splines,
coefficient_priors,
coefficient_prior_var)
parameter = Parameter(param_name='p',
variables=intercept + covariate_variables +
spline_variables,
link_fun=lambda x: expit(x))
self.parameter_set = ParameterSet(parameters=[parameter])
def __init__(self,
df: pd.DataFrame,
col_output: str,
col_se: str,
col_input: str,
increasing: bool = False,
decreasing: bool = False,
concave: bool = False,
convex: bool = False,
knots_type: str = 'domain',
knots_num: int = 4,
knots_degree: int = 3,
r_linear: bool = False,
l_linear: bool = False,
include_intercept: bool = True):
self.col_output = col_output
self.col_se = col_se
self.col_input = col_input
self.increasing = increasing
self.decreasing = decreasing
self.concave = concave
self.convex = convex
self.knots_num = knots_num
self.knots_type = knots_type
self.knots_degree = knots_degree
self.r_linear = r_linear
self.l_linear = l_linear
self.include_intercept = include_intercept
data = df.copy().reset_index(drop=True)
data['group'] = data.index
self.data_spec = DataSpecs(col_obs=self.col_output,
col_obs_se=self.col_se)
# Create derivative constraints including monotone constraints
# and shape constraints
derivative_constraints = []
if self.increasing or self.decreasing:
if self.increasing and self.decreasing:
raise RuntimeError(
"Cannot have both monotone increasing and decreasing.")
if self.increasing:
y_bounds = [0.0, np.inf]
else:
y_bounds = [-np.inf, 0.0]
derivative_constraints.append(
SplineLinearConstr(order=1, y_bounds=y_bounds, grid_size=20))
if self.convex or self.concave:
if self.convex and self.concave:
raise RuntimeError("Cannot have both convex and concave.")
if self.convex:
y_bounds = [0.0, np.inf]
else:
y_bounds = [-np.inf, 0.0]
derivative_constraints.append(
SplineLinearConstr(order=2, y_bounds=y_bounds, grid_size=20))
# Create the spline variable for the input
spline = Spline(covariate=self.col_input,
knots_type=self.knots_type,
knots_num=self.knots_num,
degree=self.knots_degree,
r_linear=self.r_linear,
l_linear=self.l_linear,
derivative_constr=derivative_constraints,
include_intercept=include_intercept)
# Create the parameter set to solve
# the marginal likelihood problem
param_set_marginal = ParameterSet(
parameters=[Parameter(param_name='beta', variables=[spline])])
process_all(param_set_marginal, data)
# Create the parameter set to solve
# for the inefficiencies
intercept = Intercept(add_re=True,
col_group='group',
re_prior=GaussianPrior(lower_bound=[0.0],
upper_bound=[np.inf]))
param_set_v = ParameterSet(
parameters=[Parameter(param_name='v', variables=[intercept])])
process_all(param_set_v, data)
# Process the data set
self.data = Data(data_specs=self.data_spec)
self.data.process(data)
# Build the two models
self.marginal_model = SimpleBetaEtaModel(param_set_marginal)
self.v_model = VModel(param_set_v)
# Create the solvers for the models
marginal_solver = IPOPTSolver(self.marginal_model)
v_solver = ClosedFormSolver(self.v_model)
self.solver = SimpleSolver([marginal_solver, v_solver])
# Randomly initialize parameter values
self.x_init = np.random.randn(marginal_solver.model.x_dim)
# Placeholder for inefficiencies
self.inefficiencies = np.zeros(len(data))
def test_parameter_set_duplicates(self, param1):
with pytest.raises(ParameterSetError):
ParameterSet(
parameters=[param1, param1]
)
def parameter_set(param1, param2, parameter_function):
return ParameterSet(
parameters=[param1, param2],
parameter_functions=[parameter_function],
)
def param_set(variable1, variable2, spline_variable):
return ParameterSet([
Parameter(param_name='foo',
variables=[variable1, variable2, spline_variable])
])