[Scipy-svn] r2547 - in trunk/Lib/sandbox/models: . tests
scipy-svn at scipy.org
scipy-svn at scipy.org
Sun Jan 14 08:12:34 EST 2007
Author: jarrod.millman
Date: 2007-01-14 07:12:30 -0600 (Sun, 14 Jan 2007)
New Revision: 2547
Modified:
trunk/Lib/sandbox/models/bspline.py
trunk/Lib/sandbox/models/cox.py
trunk/Lib/sandbox/models/gam.py
trunk/Lib/sandbox/models/glm.py
trunk/Lib/sandbox/models/setup.py
trunk/Lib/sandbox/models/smoothers.py
trunk/Lib/sandbox/models/tests/test_robust.py
Log:
minor clean ups
Modified: trunk/Lib/sandbox/models/bspline.py
===================================================================
--- trunk/Lib/sandbox/models/bspline.py 2007-01-14 12:35:28 UTC (rev 2546)
+++ trunk/Lib/sandbox/models/bspline.py 2007-01-14 13:12:30 UTC (rev 2547)
@@ -1,10 +1,9 @@
-
import numpy as N
import numpy.linalg as L
+from scipy.linalg import solveh_banded
from scipy.optimize import golden
from scipy.sandbox.models import _bspline
-from scipy.linalg import solveh_banded
def _upper2lower(ub):
"""
Modified: trunk/Lib/sandbox/models/cox.py
===================================================================
--- trunk/Lib/sandbox/models/cox.py 2007-01-14 12:35:28 UTC (rev 2546)
+++ trunk/Lib/sandbox/models/cox.py 2007-01-14 13:12:30 UTC (rev 2547)
@@ -1,6 +1,8 @@
import shutil
import tempfile
+
import numpy as N
+
from scipy.sandbox.models import survival, model
class discrete:
@@ -197,7 +199,7 @@
for i in range(2*n):
subjects[i].X = X[i]
- import formula as F
+ import scipy.sandbox.models.formula as F
x = F.quantitative('X')
f = F.formula(x)
Modified: trunk/Lib/sandbox/models/gam.py
===================================================================
--- trunk/Lib/sandbox/models/gam.py 2007-01-14 12:35:28 UTC (rev 2546)
+++ trunk/Lib/sandbox/models/gam.py 2007-01-14 13:12:30 UTC (rev 2547)
@@ -1,9 +1,9 @@
import numpy as N
+
from scipy.sandbox.models import family
+from scipy.sandbox.models.bspline import SmoothingSpline
+from scipy.sandbox.models.glm import model as glm
-from glm import model as glm
-from bspline import SmoothingSpline
-
def default_smoother(x):
_x = x.copy()
_x.sort()
Modified: trunk/Lib/sandbox/models/glm.py
===================================================================
--- trunk/Lib/sandbox/models/glm.py 2007-01-14 12:35:28 UTC (rev 2546)
+++ trunk/Lib/sandbox/models/glm.py 2007-01-14 13:12:30 UTC (rev 2547)
@@ -25,11 +25,13 @@
"""
if results is None:
results = self.results
- if Y is None: Y = self.Y
+ if Y is None:
+ Y = self.Y
return self.family.deviance(Y, results.mu) / scale
def next(self):
- results = self.results; Y = self.Y
+ results = self.results
+ Y = self.Y
self.weights = self.family.weights(results.mu)
self.initialize(self.design)
Z = results.predict + self.family.link.deriv(results.mu) * (Y - results.mu)
Modified: trunk/Lib/sandbox/models/setup.py
===================================================================
--- trunk/Lib/sandbox/models/setup.py 2007-01-14 12:35:28 UTC (rev 2546)
+++ trunk/Lib/sandbox/models/setup.py 2007-01-14 13:12:30 UTC (rev 2547)
@@ -8,7 +8,7 @@
config.add_data_dir('tests')
try:
- from bspline_module import mod
+ from scipy.sandbox.models.bspline_module import mod
n, s, d = weave_ext(mod)
config.add_extension(n, s, **d)
except ImportError: pass
Modified: trunk/Lib/sandbox/models/smoothers.py
===================================================================
--- trunk/Lib/sandbox/models/smoothers.py 2007-01-14 12:35:28 UTC (rev 2546)
+++ trunk/Lib/sandbox/models/smoothers.py 2007-01-14 13:12:30 UTC (rev 2547)
@@ -7,13 +7,11 @@
import numpy as N
import numpy.linalg as L
-from scipy.optimize import golden
from scipy.linalg import solveh_banded
+from scipy.optimize import golden
-from bspline import bspline
-from utils import band2array
-
from scipy.sandbox.models import _bspline
+from scipy.sandbox.models.bspline import bspline, band2array
class poly_smoother:
@@ -96,7 +94,7 @@
mask = N.flatnonzero(1 - N.alltrue(N.equal(bt, 0), axis=0))
- bt = bt[:,mask]
+ bt = bt[:, mask]
y = y[mask]
self.df_total = y.shape[0]
@@ -115,9 +113,9 @@
nband, nbasis = self.g.shape
for i in range(nbasis):
for k in range(min(nband, nbasis-i)):
- self.btb[k,i] = (bt[i] * bt[i+k]).sum()
+ self.btb[k, i] = (bt[i] * bt[i+k]).sum()
- bty.shape = (1,bty.shape[0])
+ bty.shape = (1, bty.shape[0])
self.chol, self.coef = solveh_banded(self.btb +
pen*self.g,
bty, lower=1)
@@ -164,7 +162,6 @@
return self.rank
class smoothing_spline_fixeddf(smoothing_spline):
-
"""
Fit smoothing spline with approximately df degrees of freedom
used in the fit, i.e. so that self.trace() is approximately df.
@@ -172,7 +169,6 @@
In general, df must be greater than the dimension of the null space
of the Gram inner product. For cubic smoothing splines, this means
that df > 2.
-
"""
target_df = 5
Modified: trunk/Lib/sandbox/models/tests/test_robust.py
===================================================================
--- trunk/Lib/sandbox/models/tests/test_robust.py 2007-01-14 12:35:28 UTC (rev 2546)
+++ trunk/Lib/sandbox/models/tests/test_robust.py 2007-01-14 13:12:30 UTC (rev 2547)
@@ -1,8 +1,9 @@
-import scipy.sandbox.models as S
import unittest
+
import numpy.random as R
-import numpy as N
+import scipy.sandbox.models as S
+
W = R.standard_normal
class RegressionTest(unittest.TestCase):
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