def test_add(self):
t1 = formula.term("t1")
t2 = formula.term("t2")
f = t1 + t2
self.assert_(isinstance(f, formula.formula))
self.assert_(f.hasterm(t1))
self.assert_(f.hasterm(t2))
def test_init(self):
t1 = formula.term("trivial")
sqr = lambda x: x*x
t2 = formula.term("not_so_trivial", sqr, "sqr")
self.assertRaises(ValueError, formula.term, "name", termname=0)
def test_termcolumns(self):
t1 = formula.term("A")
t2 = formula.term("B")
f = t1 + t2 + t1 * t2
def other(val):
return N.array([3.2*val,4.342*val**2, 5.234*val**3])
q = formula.quantitative(['other%d' % i for i in range(1,4)], termname='other', func=t1, transform=other)
f += q
q.namespace = f.namespace = self.formula.namespace
assert_almost_equal(q(), f()[f.termcolumns(q)])
def test_mul(self):
t1 = formula.term("t1")
t2 = formula.term("t2")
f = t1 * t2
self.assert_(isinstance(f, formula.formula))
intercept = formula.term("intercept")
f = t1 * intercept
self.assertEqual(str(f), str(formula.formula(t1)))
f = intercept * t1
self.assertEqual(str(f), str(formula.formula(t1)))
def test_contrast2(self):
dummy = formula.term('zero')
self.namespace['zero'] = N.zeros((40,), N.float64)
term = dummy + self.terms[2]
c = contrast.Contrast(term, self.formula)
c.getmatrix()
test = [0]*2 + [1] + [0]*7
assert_almost_equal(c.matrix, test)
def setUp(self):
self.X = R.standard_normal((40,10))
self.namespace = {}
self.terms = []
for i in range(10):
name = '%s' % string.uppercase[i]
self.namespace[name] = self.X[:,i]
self.terms.append(formula.term(name))
self.formula = self.terms[0]
for i in range(1, 10):
self.formula += self.terms[i]
self.formula.namespace = self.namespace
def test_contrast3(self):
X = self.formula.design()
P = N.dot(X, L.pinv(X))
dummy = formula.term('noise')
resid = N.identity(40) - P
self.namespace['noise'] = N.transpose(N.dot(resid, R.standard_normal((40,5))))
terms = dummy + self.terms[2]
terms.namespace = self.formula.namespace
c = contrast.Contrast(terms, self.formula)
c.getmatrix()
self.assertEquals(c.matrix.shape, (10,))
def test_namespace(self):
space1 = {'X':N.arange(50), 'Y':N.arange(50)*2}
space2 = {'X':N.arange(20), 'Y':N.arange(20)*2}
X = formula.term('X')
Y = formula.term('Y')
X.namespace = space1
assert_almost_equal(X(), N.arange(50))
Y.namespace = space2
assert_almost_equal(Y(), N.arange(20)*2)
f = X + Y
f.namespace = space1
self.assertEqual(f().shape, (2,50))
assert_almost_equal(Y(), N.arange(50)*2)
assert_almost_equal(X(), N.arange(50))
f.namespace = space2
self.assertEqual(f().shape, (2,20))
assert_almost_equal(Y(), N.arange(20)*2)
assert_almost_equal(X(), N.arange(20))
self._compute_sigma(ML=ML)
self._compute_D(ML=ML)
if not self.cont(ML=ML):
break
if __name__ == '__main__':
import numpy.random as R
nsubj = 400
units = []
n = 3
from scipy.sandbox.models.formula import term
fixed = term('f')
random = term('r')
response = term('y')
for i in range(nsubj):
d = R.standard_normal()
X = R.standard_normal((10,n))
Z = X[0:2]
Y = R.standard_normal((n,)) + d * 4
units.append(Unit({'f':X, 'r':Z, 'y':Y}))
#m = Mixed(units, response)#, fixed, random)
m = Mixed(units, response, fixed, random)
m.initialize()
m.fit()
def test_str(self):
t = formula.term("name")
s = str(t)
