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 np.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_namespace(self):
space1 = {'X':np.arange(50), 'Y':np.arange(50)*2}
space2 = {'X':np.arange(20), 'Y':np.arange(20)*2}
space3 = {'X':np.arange(30), 'Y':np.arange(30)*2}
X = formula.Term('X')
Y = formula.Term('Y')
X.namespace = space1
assert_almost_equal(X(), np.arange(50))
Y.namespace = space2
assert_almost_equal(Y(), np.arange(20)*2)
f = X + Y
f.namespace = space1
self.assertEqual(f().shape, (2,50))
assert_almost_equal(Y(), np.arange(20)*2)
assert_almost_equal(X(), np.arange(50))
f.namespace = space2
self.assertEqual(f().shape, (2,20))
assert_almost_equal(Y(), np.arange(20)*2)
assert_almost_equal(X(), np.arange(50))
f.namespace = space3
self.assertEqual(f().shape, (2,30))
assert_almost_equal(Y(), np.arange(20)*2)
assert_almost_equal(X(), np.arange(50))
xx = X**2
self.assertEqual(xx().shape, (50,))
xx.namespace = space3
self.assertEqual(xx().shape, (30,))
xx = X * formula.I
self.assertEqual(xx().shape, (50,))
xx.namespace = space3
self.assertEqual(xx().shape, (30,))
xx = X * X
self.assertEqual(xx.namespace, X.namespace)
xx = X + Y
self.assertEqual(xx.namespace, {})
Y.namespace = {'X':np.arange(50), 'Y':np.arange(50)*2}
xx = X + Y
self.assertEqual(xx.namespace, {})
Y.namespace = X.namespace
xx = X+Y
self.assertEqual(xx.namespace, Y.namespace)
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_interactions(self):
f = formula.interactions([formula.Term(l) for l in ['a', 'b', 'c']])
assert_equal(set(f.termnames()), set(['a', 'b', 'c', 'a*b', 'a*c', 'b*c']))
f = formula.interactions([formula.Term(l) for l in ['a', 'b', 'c', 'd']], order=3)
assert_equal(set(f.termnames()), set(['a', 'b', 'c', 'd', 'a*b', 'a*c', 'a*d', 'b*c', 'b*d', 'c*d', 'a*b*c', 'a*c*d', 'a*b*d', 'b*c*d']))
f = formula.interactions([formula.Term(l) for l in ['a', 'b', 'c', 'd']], order=[1,2,3])
assert_equal(set(f.termnames()), set(['a', 'b', 'c', 'd', 'a*b', 'a*c', 'a*d', 'b*c', 'b*d', 'c*d', 'a*b*c', 'a*c*d', 'a*b*d', 'b*c*d']))
f = formula.interactions([formula.Term(l) for l in ['a', 'b', 'c', 'd']], order=[3])
assert_equal(set(f.termnames()), set(['a*b*c', 'a*c*d', 'a*b*d', 'b*c*d']))
def test_contrast2(self):
dummy = formula.Term('zero')
self.namespace['zero'] = np.zeros((40,), np.float64)
term = dummy + self.terms[2]
c = contrast.Contrast(term, self.formula)
test = [0]*2 + [1] + [0]*7
assert_almost_equal(c.matrix, test)
def test_subtract(self):
f = formula.interactions([formula.Term(l) for l in ['a', 'b', 'c']])
ff = f - f['a*b']
assert_equal(set(ff.termnames()), set(['a', 'b', 'c', 'a*c', 'b*c']))
ff = f - f['a*b'] - f['a*c']
assert_equal(set(ff.termnames()), set(['a', 'b', 'c', 'b*c']))
ff = f - (f['a*b'] + f['a*c'])
assert_equal(set(ff.termnames()), set(['a', 'b', 'c', 'b*c']))
def test_contrast3(self):
X = self.formula.design()
P = np.dot(X, L.pinv(X))
dummy = formula.Term('noise')
resid = np.identity(40) - P
self.namespace['noise'] = np.transpose(np.dot(resid, R.standard_normal((40,5))))
terms = dummy + self.terms[2]
terms.namespace = self.formula.namespace
c = contrast.Contrast(terms, self.formula)
self.assertEquals(c.matrix.shape, (10,))
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
import string
import numpy as np
from scikits.statsmodels.sandbox import formula
from scikits.statsmodels.sandbox import contrast_old as contrast
#Example: Formula from tests, setup
X = np.random.standard_normal((40, 10))
namespace = {}
terms = []
for i in range(10):
name = '%s' % string.uppercase[i]
namespace[name] = X[:, i]
terms.append(formula.Term(name))
form = terms[0]
for i in range(1, 10):
form += terms[i]
form.namespace = namespace
form.design().shape
(40, 10)
'''
>>> dir(form)
['_Formula__namespace', '__add__', '__call__', '__class__',
'__delattr__', '__dict__', '__doc__', '__getattribute__',
'__getitem__', '__hash__', '__init__', '__module__', '__mul__',
'__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__',
'__str__', '__sub__', '__weakref__', '_del_namespace',
'_get_namespace', '_names', '_set_namespace', '_termnames',
def test_str(self):
t = formula.Term("name")
s = str(t)