def test_efron_computed_by_hand_examples(self, data_nus):
cox = CoxPHFitter()
X = data_nus['x'][:, None]
T = data_nus['t']
E = data_nus['E']
# Enforce numpy arrays
X = np.array(X)
T = np.array(T)
E = np.array(E)
# Want as bools
E = E.astype(bool)
# tests from http://courses.nus.edu.sg/course/stacar/internet/st3242/handouts/notes3.pdf
beta = np.array([[0]])
l, u = cox._get_efron_values(X, beta, T, E)
l = -l
assert np.abs(l[0][0] - 77.13) < 0.05
assert np.abs(u[0] - -2.51) < 0.05
beta = beta + u / l
assert np.abs(beta - -0.0326) < 0.05
l, u = cox._get_efron_values(X, beta, T, E)
l = -l
assert np.abs(l[0][0] - 72.83) < 0.05
assert np.abs(u[0] - -0.069) < 0.05
beta = beta + u / l
assert np.abs(beta - -0.0325) < 0.01
l, u = cox._get_efron_values(X, beta, T, E)
l = -l
assert np.abs(l[0][0] - 72.70) < 0.01
assert np.abs(u[0] - -0.000061) < 0.01
beta = beta + u / l
assert np.abs(beta - -0.0335) < 0.01
def test_efron_computed_by_hand_examples(self, data_nus):
cox = CoxPHFitter()
X = data_nus['x'][:, None]
T = data_nus['t']
E = data_nus['E']
# Enforce numpy arrays
X = np.array(X)
T = np.array(T)
E = np.array(E)
# Want as bools
E = E.astype(bool)
# tests from http://courses.nus.edu.sg/course/stacar/internet/st3242/handouts/notes3.pdf
beta = np.array([[0]])
l, u = cox._get_efron_values(X, beta, T, E)
l = -l
assert np.abs(l[0][0] - 77.13) < 0.05
assert np.abs(u[0] - -2.51) < 0.05
beta = beta + u / l
assert np.abs(beta - -0.0326) < 0.05
l, u = cox._get_efron_values(X, beta, T, E)
l = -l
assert np.abs(l[0][0] - 72.83) < 0.05
assert np.abs(u[0] - -0.069) < 0.05
beta = beta + u / l
assert np.abs(beta - -0.0325) < 0.01
l, u = cox._get_efron_values(X, beta, T, E)
l = -l
assert np.abs(l[0][0] - 72.70) < 0.01
assert np.abs(u[0] - -0.000061) < 0.01
beta = beta + u / l
assert np.abs(beta - -0.0335) < 0.01
