from statsmodels.compat.python import lrange, lmap, iterkeys, iteritems
import numpy as np
from scipy import stats
from statsmodels.iolib.table import SimpleTable
from statsmodels.tools.decorators import nottest
def _kurtosis(a):
'''wrapper for scipy.stats.kurtosis that returns nan instead of raising Error
missing options
'''
try:
res = stats.kurtosis(a)
except ValueError:
res = np.nan
return res
def _skew(a):
'''wrapper for scipy.stats.skew that returns nan instead of raising Error
missing options
'''
try:
res = stats.skew(a)
except ValueError:
res = np.nan
return res
_sign_test_doc = '''
Signs test.
Parameters
----------
samp : array-like
1d array. The sample for which you want to perform the signs
test.
mu0 : float
See Notes for the definition of the sign test. mu0 is 0 by
default, but it is common to set it to the median.
Returns
---------
M, p-value
Notes
-----
The signs test returns
M = (N(+) - N(-))/2
where N(+) is the number of values above `mu0`, N(-) is the number of
values below. Values equal to `mu0` are discarded.
The p-value for M is calculated using the binomial distrubution
and can be intrepreted the same as for a t-test. The test-statistic
is distributed Binom(min(N(+), N(-)), n_trials, .5) where n_trials
equals N(+) + N(-).
See Also
---------
scipy.stats.wilcoxon
'''
[docs]@nottest
def sign_test(samp, mu0=0):
samp = np.asarray(samp)
pos = np.sum(samp > mu0)
neg = np.sum(samp < mu0)
M = (pos-neg)/2.
p = stats.binom_test(min(pos,neg), pos+neg, .5)
return M, p
sign_test.__doc__ = _sign_test_doc
class Describe(object):
'''
Calculates descriptive statistics for data.
Defaults to a basic set of statistics, "all" can be specified, or a list
can be given.
Parameters
----------
dataset : array-like
2D dataset for descriptive statistics.
'''
def __init__(self, dataset):
self.dataset = dataset
#better if this is initially a list to define order, or use an
# ordered dict. First position is the function
# Second position is the tuple/list of column names/numbers
# third is are the results in order of the columns
self.univariate = dict(
obs = [len, None, None],
mean = [np.mean, None, None],
std = [np.std, None, None],
min = [np.min, None, None],
max = [np.max, None, None],
ptp = [np.ptp, None, None],
var = [np.var, None, None],
mode_val = [self._mode_val, None, None],
mode_bin = [self._mode_bin, None, None],
median = [np.median, None, None],
skew = [stats.skew, None, None],
uss = [lambda x: np.sum(np.asarray(x)**2, axis=0), None, None],
kurtosis = [stats.kurtosis, None, None],
percentiles = [self._percentiles, None, None],
#BUG: not single value
#sign_test_M = [self.sign_test_m, None, None],
#sign_test_P = [self.sign_test_p, None, None]
)
#TODO: Basic stats for strings
#self.strings = dict(
#unique = [np.unique, None, None],
#number_uniq = [len(
#most = [
#least = [
#TODO: Multivariate
#self.multivariate = dict(
#corrcoef(x[, y, rowvar, bias]),
#cov(m[, y, rowvar, bias]),
#histogram2d(x, y[, bins, range, normed, weights])
#)
self._arraytype = None
self._columns_list = None
def _percentiles(self,x):
p = [stats.scoreatpercentile(x,per) for per in
(1,5,10,25,50,75,90,95,99)]
return p
def _mode_val(self,x):
return stats.mode(x)[0][0]
def _mode_bin(self,x):
return stats.mode(x)[1][0]
def _array_typer(self):
"""if not a sctructured array"""
if not(self.dataset.dtype.names):
"""homogeneous dtype array"""
self._arraytype = 'homog'
elif self.dataset.dtype.names:
"""structured or rec array"""
self._arraytype = 'sctruct'
else:
assert self._arraytype == 'sctruct' or self._arraytype == 'homog'
def _is_dtype_like(self, col):
"""
Check whether self.dataset.[col][0] behaves like a string, numbern
unknown. `numpy.lib._iotools._is_string_like`
"""
def string_like():
#TODO: not sure what the result is if the first item is some type of
# missing value
try:
self.dataset[col][0] + ''
except (TypeError, ValueError):
return False
return True
def number_like():
try:
self.dataset[col][0] + 1.0
except (TypeError, ValueError):
return False
return True
if number_like()==True and string_like()==False:
return 'number'
elif number_like()==False and string_like()==True:
return 'string'
else:
assert (number_like()==True or string_like()==True), '\
Not sure of dtype'+str(self.dataset[col][0])
#@property
def summary(self, stats='basic', columns='all', orientation='auto'):
"""
Return a summary of descriptive statistics.
Parameters
-----------
stats: list or str
The desired statistics, Accepts 'basic' or 'all' or a list.
'basic' = ('obs', 'mean', 'std', 'min', 'max')
'all' = ('obs', 'mean', 'std', 'min', 'max', 'ptp', 'var',
'mode', 'meadian', 'skew', 'uss', 'kurtosis',
'percentiles')
columns : list or str
The columns/variables to report the statistics, default is 'all'
If an object with named columns is given, you may specify the
column names. For example
"""
#NOTE
# standard array: Specifiy column numbers (NEED TO TEST)
# percentiles currently broken
# mode requires mode_val and mode_bin separately
if self._arraytype == None:
self._array_typer()
if stats == 'basic':
stats = ('obs', 'mean', 'std', 'min', 'max')
elif stats == 'all':
#stats = self.univariate.keys()
#dict doesn't keep an order, use full list instead
stats = ['obs', 'mean', 'std', 'min', 'max', 'ptp', 'var',
'mode_val', 'mode_bin', 'median', 'uss', 'skew',
'kurtosis', 'percentiles']
else:
for astat in stats:
pass
#assert astat in self.univariate
#hack around percentiles multiple output
#bad naming
import scipy.stats
#BUG: the following has all per the same per=99
##perdict = dict(('perc_%2d'%per, [lambda x:
# scipy.stats.scoreatpercentile(x, per), None, None])
## for per in (1,5,10,25,50,75,90,95,99))
def _fun(per):
return lambda x: scipy.stats.scoreatpercentile(x, per)
perdict = dict(('perc_%02d'%per, [_fun(per), None, None])
for per in (1,5,10,25,50,75,90,95,99))
if 'percentiles' in stats:
self.univariate.update(perdict)
idx = stats.index('percentiles')
stats[idx:idx+1] = sorted(iterkeys(perdict))
#JP: this doesn't allow a change in sequence, sequence in stats is
#ignored
#this is just an if condition
if any([aitem[1] for aitem in iteritems(self.univariate) if aitem[0] in
stats]):
if columns == 'all':
self._columns_list = []
if self._arraytype == 'sctruct':
self._columns_list = self.dataset.dtype.names
#self._columns_list = [col for col in
# self.dataset.dtype.names if
#(self._is_dtype_like(col)=='number')]
else:
self._columns_list = lrange(self.dataset.shape[1])
else:
self._columns_list = columns
if self._arraytype == 'sctruct':
for col in self._columns_list:
assert (col in self.dataset.dtype.names)
else:
assert self._is_dtype_like(self.dataset) == 'number'
columstypes = self.dataset.dtype
#TODO: do we need to make sure they dtype is float64 ?
for astat in stats:
calc = self.univariate[astat]
if self._arraytype == 'sctruct':
calc[1] = self._columns_list
calc[2] = [calc[0](self.dataset[col]) for col in
self._columns_list if (self._is_dtype_like(col) ==
'number')]
#calc[2].append([len(np.unique(self.dataset[col])) for col
#in self._columns_list if
#self._is_dtype_like(col)=='string']
else:
calc[1] = ['Col '+str(col) for col in self._columns_list]
calc[2] = [calc[0](self.dataset[:,col]) for col in
self._columns_list]
return self.print_summary(stats, orientation=orientation)
else:
return self.print_summary(stats, orientation=orientation)
def print_summary(self, stats, orientation='auto'):
#TODO: need to specify a table formating for the numbers, using defualt
title = 'Summary Statistics'
header = stats
stubs = self.univariate['obs'][1]
data = [[self.univariate[astat][2][col] for astat in stats] for col in
range(len(self.univariate['obs'][2]))]
if (orientation == 'varcols') or \
(orientation == 'auto' and len(stubs) < len(header)):
#swap rows and columns
data = lmap(lambda *row: list(row), *data)
header, stubs = stubs, header
part_fmt = dict(data_fmts = ["%#8.4g"]*(len(header)-1))
table = SimpleTable(data,
header,
stubs,
title=title,
txt_fmt = part_fmt)
return table
def sign_test(self, samp, mu0=0):
return sign_test(samp, mu0)
sign_test.__doc__ = _sign_test_doc
#TODO: There must be a better way but formating the stats of a fuction that
# returns 2 values is a problem.
#def sign_test_m(samp,mu0=0):
#return self.sign_test(samp,mu0)[0]
#def sign_test_p(samp,mu0=0):
#return self.sign_test(samp,mu0)[1]
if __name__ == "__main__":
#unittest.main()
t1 = Describe(data4)
#print(t1.summary(stats='all'))
noperc = ['obs', 'mean', 'std', 'min', 'max', 'ptp', #'mode', #'var',
'median', 'skew', 'uss', 'kurtosis']
#TODO: mode var raise exception,
#TODO: percentile writes list in cell (?), huge wide format
print(t1.summary(stats=noperc))
print(t1.summary())
print(t1.summary( orientation='varcols'))
print(t1.summary(stats=['mean', 'median', 'min', 'max'], orientation=('varcols')))
print(t1.summary(stats='all'))
data1 = np.array([(1,2,'a','aa'),
(2,3,'b','bb'),
(2,4,'b','cc')],
dtype = [('alpha',float), ('beta', int),
('gamma', '|S1'), ('delta', '|S2')])
data2 = np.array([(1,2),
(2,3),
(2,4)],
dtype = [('alpha',float), ('beta', float)])
data3 = np.array([[1,2,4,4],
[2,3,3,3],
[2,4,4,3]], dtype=float)
data4 = np.array([[1,2,3,4,5,6],
[6,5,4,3,2,1],
[9,9,9,9,9,9]])
class TestSimpleTable(object):
#from statsmodels.iolib.table import SimpleTable, default_txt_fmt
def test_basic_1(self):
print('test_basic_1')
t1 = Describe(data1)
print(t1.summary())
def test_basic_2(self):
print('test_basic_2')
t2 = Describe(data2)
print(t2.summary())
def test_basic_3(self):
print('test_basic_3')
t1 = Describe(data3)
print(t1.summary())
def test_basic_4(self):
print('test_basic_4')
t1 = Describe(data4)
print(t1.summary())
def test_basic_1a(self):
print('test_basic_1a')
t1 = Describe(data1)
print(t1.summary(stats='basic', columns=['alpha']))
def test_basic_1b(self):
print('test_basic_1b')
t1 = Describe(data1)
print(t1.summary(stats='basic', columns='all'))
def test_basic_2a(self):
print('test_basic_2a')
t2 = Describe(data2)
print(t2.summary(stats='all'))
def test_basic_3(aself):
t1 = Describe(data3)
print(t1.summary(stats='all'))
def test_basic_4a(self):
t1 = Describe(data4)
print(t1.summary(stats='all'))
