def test_set_parameters(pheno_path):
model = Model(pheno_path)
params = {
'THETA(1)': 0.75,
'THETA(2)': 0.5,
'THETA(3)': 0.25,
'OMEGA(1,1)': 0.1,
'OMEGA(2,2)': 0.2,
'SIGMA(1,1)': 0.3,
}
model.parameters = params
assert model.parameters['THETA(1)'] == Parameter('THETA(1)', 0.75, lower=0, upper=1000000)
assert model.parameters['THETA(2)'] == Parameter('THETA(2)', 0.5, lower=0, upper=1000000)
assert model.parameters['THETA(3)'] == Parameter('THETA(3)', 0.25, lower=-0.99, upper=1000000)
assert model.parameters['OMEGA(1,1)'] == Parameter('OMEGA(1,1)', 0.1, lower=0, upper=sympy.oo)
assert model.parameters['OMEGA(2,2)'] == Parameter('OMEGA(2,2)', 0.2, lower=0, upper=sympy.oo)
assert model.parameters['SIGMA(1,1)'] == Parameter('SIGMA(1,1)', 0.3, lower=0, upper=sympy.oo)
model.update_source()
thetas = model.control_stream.get_records('THETA')
assert str(thetas[0]) == '$THETA (0,0.75) ; PTVCL\n'
assert str(thetas[1]) == '$THETA (0,0.5) ; PTVV\n'
assert str(thetas[2]) == '$THETA (-.99,0.25)\n'
omegas = model.control_stream.get_records('OMEGA')
assert str(omegas[0]) == '$OMEGA DIAGONAL(2)\n 0.1 ; IVCL\n 0.2 ; IVV\n\n'
sigmas = model.control_stream.get_records('SIGMA')
assert str(sigmas[0]) == '$SIGMA 0.3\n'
model = Model(pheno_path)
params = model.parameters
params['THETA(1)'].init = 18
model.parameters = params
assert model.parameters['THETA(1)'] == Parameter('THETA(1)', 18, lower=0, upper=1000000)
assert model.parameters['THETA(2)'] == Parameter('THETA(2)', 1.00916, lower=0, upper=1000000)
def test_add_random_variables_and_statements(pheno_path):
model = Model(pheno_path)
rvs = model.random_variables
pset = model.parameters
eta = RandomVariable.normal('ETA_NEW', 'iiv', 0, S('omega'))
rvs.append(eta)
pset.append(Parameter('omega', 0.1))
eps = RandomVariable.normal('EPS_NEW', 'ruv', 0, S('sigma'))
rvs.append(eps)
pset.append(Parameter('sigma', 0.1))
model.random_variables = rvs
model.parameters = pset
sset = model.get_pred_pk_record().statements
statement_new = Assignment(S('X'), 1 + S(eps.name) + S(eta.name))
sset.append(statement_new)
model.get_pred_pk_record().statements = sset
model.update_source()
assert str(model.get_pred_pk_record()).endswith('X = 1 + ETA(3) + EPS(2)\n\n')
def test_add_random_variables(pheno_path, rv_new, buf_new):
model = Model(pheno_path)
rvs = model.random_variables
pset = model.parameters
eta = RandomVariable.normal('eta_new', 'iiv', 0, S(rv_new.name))
rvs.append(eta)
pset.append(rv_new)
model.random_variables = rvs
model.parameters = pset
model.update_source()
rec_ref = (
f'$OMEGA DIAGONAL(2)\n'
f' 0.0309626 ; IVCL\n'
f' 0.031128 ; IVV\n\n'
f'{buf_new} ; omega\n'
)
rec_mod = ''
for rec in model.control_stream.get_records('OMEGA'):
rec_mod += str(rec)
assert rec_mod == rec_ref
rv = model.random_variables['eta_new']
assert rv.sympy_rv.pspace.distribution.mean == 0
assert (rv.sympy_rv.pspace.distribution.std ** 2).name == 'omega'
def test_add_parameters_and_statements(pheno_path, param_new, statement_new, buf_new):
model = Model(pheno_path)
pset = model.parameters
pset.append(param_new)
model.parameters = pset
sset = model.statements
# Insert new statement before ODE system.
new_sset = ModelStatements()
for s in sset:
if isinstance(s, ODESystem):
new_sset.append(statement_new)
new_sset.append(s)
model.statements = new_sset
model.update_source()
rec = (
f'$PK\n'
f'IF(AMT.GT.0) BTIME=TIME\n'
f'TAD=TIME-BTIME\n'
f'TVCL=THETA(1)*WGT\n'
f'TVV=THETA(2)*WGT\n'
f'IF(APGR.LT.5) TVV=TVV*(1+THETA(3))\n'
f'CL=TVCL*EXP(ETA(1))\n'
f'V=TVV*EXP(ETA(2))\n'
f'S1=V\n'
f'{buf_new}\n\n'
)
assert str(model.get_pred_pk_record()) == rec
def test_add_parameters(pheno_path, param_new, init_expected, buf_new):
model = Model(pheno_path)
pset = model.parameters
assert len(pset) == 6
pset.append(param_new)
model.parameters = pset
model.update_source()
assert len(pset) == 7
assert model.parameters[param_new.name].init == init_expected
parser = NMTranParser()
stream = parser.parse(str(model))
assert str(model.control_stream) == str(stream)
rec_ref = (
f'$THETA (0,0.00469307) ; PTVCL\n'
f'$THETA (0,1.00916) ; PTVV\n'
f'$THETA (-.99,.1)\n'
f'{buf_new}\n'
)
rec_mod = ''
for rec in model.control_stream.get_records('THETA'):
rec_mod += str(rec)
assert rec_ref == rec_mod
def test_add_random_variables(pheno_path, rv_new, buf_new):
model = Model(pheno_path)
rvs = model.random_variables
pset = model.parameters
eta = sympy.stats.Normal('eta_new', 0, sympy.sqrt(S(rv_new.name)))
eta.variability_level = VariabilityLevel.IIV
rvs.add(eta)
pset.add(rv_new)
model.random_variables = rvs
model.parameters = pset
model.update_source()
rec_ref = (
f'$OMEGA DIAGONAL(2)\n'
f' 0.0309626 ; IVCL\n'
f' 0.031128 ; IVV\n\n'
f'{buf_new} ; omega\n'
)
rec_mod = ''
for rec in model.control_stream.get_records('OMEGA'):
rec_mod += str(rec)
assert rec_mod == rec_ref
rv = model.random_variables['eta_new']
assert rv.pspace.distribution.mean == 0
assert rv.pspace.distribution.std ** 2 == rv_new.symbol
def test_add_two_parameters(pheno_path):
model = Model(pheno_path)
pset = model.parameters
assert len(pset) == 6
param_1 = Parameter('COVEFF1', 0.2)
param_2 = Parameter('COVEFF2', 0.1)
pset.append(param_1)
pset.append(param_2)
model.parameters = pset
model.update_source()
assert len(pset) == 8
assert model.parameters[param_1.name].init == 0.2
assert model.parameters[param_2.name].init == 0.1
