def test_match_distribution(self):
"""Some really basic testing for match_distribution
"""
ds = datasets['uni2medium'] # large to get stable stats
data = ds.samples[:, ds.a.bogus_features[0]]
# choose bogus feature, which
# should have close to normal distribution
# Lets test ad-hoc rv_semifrozen
floc = rv_semifrozen(scipy.stats.norm, loc=0).fit(data)
self.assertTrue(floc[0] == 0)
fscale = rv_semifrozen(scipy.stats.norm, scale=1.0).fit(data)
self.assertTrue(fscale[1] == 1)
flocscale = rv_semifrozen(scipy.stats.norm, loc=0, scale=1.0).fit(data)
self.assertTrue(flocscale[1] == 1 and flocscale[0] == 0)
full = scipy.stats.norm.fit(data)
for res in [floc, fscale, flocscale, full]:
self.assertTrue(len(res) == 2)
data_mean = np.mean(data)
for loc in [None, data_mean]:
for test in ['p-roc', 'kstest']:
# some really basic testing
matched = match_distribution(data=data,
distributions=[
'scipy',
('norm', {
'name': 'norm_fixed',
'loc': 0.2,
'scale': 0.3
})
],
test=test,
loc=loc,
p=0.05)
# at least norm should be in there
names = [m[2] for m in matched]
if test == 'p-roc':
if cfg.getboolean('tests', 'labile', default='yes'):
# we can guarantee that only for norm_fixed
self.assertTrue('norm' in names)
self.assertTrue('norm_fixed' in names)
inorm = names.index('norm_fixed')
# and it should be at least in the first
# 30 best matching ;-)
self.assertTrue(inorm <= 30)
# Test plotting only once
if loc is None and externals.exists("pylab plottable"):
import pylab as pl
from mvpa2.clfs.stats import plot_distribution_matches
fig = pl.figure()
plot_distribution_matches(data,
matched,
legend=1,
nbest=5)
#pl.show()
pl.close(fig)
def test_match_distribution(self):
"""Some really basic testing for match_distribution
"""
ds = datasets['uni2medium'] # large to get stable stats
data = ds.samples[:, ds.a.bogus_features[0]]
# choose bogus feature, which
# should have close to normal distribution
# Lets test ad-hoc rv_semifrozen
floc = rv_semifrozen(scipy.stats.norm, loc=0).fit(data)
self.assertTrue(floc[0] == 0)
fscale = rv_semifrozen(scipy.stats.norm, scale=1.0).fit(data)
self.assertTrue(fscale[1] == 1)
flocscale = rv_semifrozen(scipy.stats.norm, loc=0, scale=1.0).fit(data)
self.assertTrue(flocscale[1] == 1 and flocscale[0] == 0)
full = scipy.stats.norm.fit(data)
for res in [floc, fscale, flocscale, full]:
self.assertTrue(len(res) == 2)
data_mean = np.mean(data)
for loc in [None, data_mean]:
for test in ['p-roc', 'kstest']:
# some really basic testing
matched = match_distribution(
data=data,
distributions = ['scipy',
('norm',
{'name': 'norm_fixed',
'loc': 0.2,
'scale': 0.3})],
test=test, loc=loc, p=0.05)
# at least norm should be in there
names = [m[2] for m in matched]
if test == 'p-roc':
if cfg.getboolean('tests', 'labile', default='yes'):
# we can guarantee that only for norm_fixed
self.assertTrue('norm' in names)
self.assertTrue('norm_fixed' in names)
inorm = names.index('norm_fixed')
# and it should be at least in the first
# 30 best matching ;-)
self.assertTrue(inorm <= 30)
# Test plotting only once
if loc is None and externals.exists("pylab plottable"):
import pylab as pl
from mvpa2.clfs.stats import plot_distribution_matches
fig = pl.figure()
plot_distribution_matches(data, matched, legend=1, nbest=5)
#pl.show()
pl.close(fig)
#kwargs = {'permutations':10, 'tail':'any'}
permutator = AttributePermutator('targets', count=30)
nulldist_sweep = [
MCNullDist(permutator, tail='any'),
MCNullDist(permutator, tail='right')
]
if externals.exists('scipy'):
from mvpa2.support.stats import scipy
from scipy.stats import f_oneway
from mvpa2.clfs.stats import rv_semifrozen
nulldist_sweep += [
MCNullDist(permutator, scipy.stats.norm, tail='any'),
MCNullDist(permutator, scipy.stats.norm, tail='right'),
MCNullDist(permutator,
rv_semifrozen(scipy.stats.norm, loc=0),
tail='right'),
MCNullDist(permutator, scipy.stats.expon, tail='right'),
FixedNullDist(scipy.stats.norm(0, 10.0), tail='any'),
FixedNullDist(scipy.stats.norm(0, 10.0), tail='right'),
scipy.stats.norm(0, 0.1)
]
class StatsTests(unittest.TestCase):
"""Unittests for various statistics"""
@sweepargs(null=nulldist_sweep[1:])
def test_null_dist_prob(self, null):
"""Testing null dist probability"""
if not isinstance(null, NullDist):
return
# Prepare few distributions to test
#kwargs = {'permutations':10, 'tail':'any'}
permutator = AttributePermutator('targets', count=30)
nulldist_sweep = [ MCNullDist(permutator, tail='any'),
MCNullDist(permutator, tail='right')]
if externals.exists('scipy'):
from mvpa2.support.stats import scipy
from scipy.stats import f_oneway
from mvpa2.clfs.stats import rv_semifrozen
nulldist_sweep += [ MCNullDist(permutator, scipy.stats.norm,
tail='any'),
MCNullDist(permutator, scipy.stats.norm,
tail='right'),
MCNullDist(permutator,
rv_semifrozen(scipy.stats.norm, loc=0),
tail='right'),
MCNullDist(permutator, scipy.stats.expon,
tail='right'),
FixedNullDist(scipy.stats.norm(0, 10.0), tail='any'),
FixedNullDist(scipy.stats.norm(0, 10.0), tail='right'),
scipy.stats.norm(0, 0.1)
]
class StatsTests(unittest.TestCase):
"""Unittests for various statistics"""
@sweepargs(null=nulldist_sweep[1:])
def test_null_dist_prob(self, null):
"""Testing null dist probability"""
from mvpa2.measures.corrcoef import pearson_correlation
# Prepare few distributions to test
# kwargs = {'permutations':10, 'tail':'any'}
permutator = AttributePermutator("targets", count=30)
nulldist_sweep = [MCNullDist(permutator, tail="any"), MCNullDist(permutator, tail="right")]
if externals.exists("scipy"):
from mvpa2.support.scipy.stats import scipy
from scipy.stats import f_oneway
from mvpa2.clfs.stats import rv_semifrozen
nulldist_sweep += [
MCNullDist(permutator, scipy.stats.norm, tail="any"),
MCNullDist(permutator, scipy.stats.norm, tail="right"),
MCNullDist(permutator, rv_semifrozen(scipy.stats.norm, loc=0), tail="right"),
MCNullDist(permutator, scipy.stats.expon, tail="right"),
FixedNullDist(scipy.stats.norm(0, 10.0), tail="any"),
FixedNullDist(scipy.stats.norm(0, 10.0), tail="right"),
scipy.stats.norm(0, 0.1),
]
class StatsTests(unittest.TestCase):
"""Unittests for various statistics"""
@sweepargs(null=nulldist_sweep[1:])
def test_null_dist_prob(self, null):
"""Testing null dist probability"""
if not isinstance(null, NullDist):
return
