def confidence_interval_std(std, num, confidence=0.95):
""" calculates the confidence interval of the standard deviation given a
standard deviation and a number of observations, assuming a normal
distribution """
c = stats.chi(num - 1).ppf(0.5 + 0.5 * confidence)
lower_bound = np.sqrt(num - 1) * std / c
c = stats.chi(num - 1).ppf(0.5 - 0.5 * confidence)
upper_bound = np.sqrt(num - 1) * std / c
return 0.5 * (upper_bound - lower_bound)
def confidence_interval_std(std, num, confidence=0.95):
""" calculates the confidence interval of the standard deviation given a
standard deviation and a number of observations, assuming a normal
distribution """
c = stats.chi(num - 1).ppf(0.5 + 0.5*confidence)
lower_bound = np.sqrt(num - 1)*std/c
c = stats.chi(num - 1).ppf(0.5 - 0.5*confidence)
upper_bound = np.sqrt(num - 1)*std/c
return 0.5*(upper_bound - lower_bound)
def test_crossmatch_cartesian_gaussian_distribution(cartesian_gaussian,
contours, n_coordinates):
"""Test on a Cartesian Gaussian distribution.
This distribution has closed-form expressions for the following outputs:
* contour_vols
* probdensity_vol
* searched_prob_vol
* searched_vol
"""
skymap = cartesian_gaussian_to_skymap(6, cartesian_gaussian.mean,
cartesian_gaussian.cov)
if n_coordinates is None:
coordinates = None
else:
coordinates_xyz = cartesian_gaussian.rvs(size=n_coordinates)
coordinates = SkyCoord(*coordinates_xyz.T * u.Mpc,
representation_type=CartesianRepresentation)
result = crossmatch(skymap, contours=contours, coordinates=coordinates)
standard_vol = 4 / 3 * np.pi * np.sqrt(
np.linalg.det(cartesian_gaussian.cov))
expected = standard_vol * stats.chi(3).ppf(contours)**3
np.testing.assert_allclose(result.contour_vols, expected, rtol=2e-3)
if coordinates is None:
assert np.isnan(result.probdensity_vol)
assert np.isnan(result.searched_prob_vol)
assert np.isnan(result.searched_vol)
elif np.size(coordinates) == 0:
assert np.size(result.probdensity_vol) == 0
assert np.size(result.searched_prob_vol) == 0
assert np.size(result.searched_vol) == 0
else:
expected = cartesian_gaussian.pdf(coordinates_xyz)
np.testing.assert_allclose(result.probdensity_vol, expected, rtol=4e-2)
d = coordinates_xyz - cartesian_gaussian.mean
r = np.sqrt(
np.sum(((d @ np.linalg.inv(cartesian_gaussian.cov)) * d), axis=-1))
expected = stats.chi(3).cdf(r)
np.testing.assert_allclose(result.searched_prob_vol,
expected,
atol=1e-2)
expected = standard_vol * r**3
np.testing.assert_allclose(result.searched_vol, expected, rtol=6e-2)
def compute(matrixname, chrNum):
hash12 = pickle.load(open("hash12", 'rb'))
sums1 = pickle.load(open("sums1", 'rb'))
sums2 = pickle.load(open("sums2", 'rb'))
p = []
sumtime = 0
#takes longer each iteration, ask Dr. Ay
for x in hash12:
if x not in sums1 or x not in sums2:
continue
startt = time.time()
for y in hash12[x]:
chi2, pval, dof, exp = chi([[sums1[x], sums2[x]],
[hash12[x][y][0], hash12[x][y][1]]])
p.append(pval)
endt = time.time()
#print ("Index\t%s\ttime\t%f\tnumberOfTests\t%d" % (x,endt - startt,len(hash12[x])))
sumtime += (endt - startt)
print("Computing chromsome %s took %s" % (chrNum, sumtime))
return plothist(p, len(p), matrixname, chrNum)
def __init__(self, dofs):
self.dofs = dofs
if self.dofs is not None:
if self.dofs == 1:
self.bounds = np.array([1e-15, np.inf])
else:
self.bounds = np.array([0.0, np.inf])
if self.dofs >= 1:
mean, var, skew, kurt = chi.stats(dofs, moments='mvsk')
self.parent = chi(dofs)
self.mean = mean
self.variance = var
self.skewness = skew
self.kurtosis = kurt
self.x_range_for_pdf = np.linspace(0.0, 10.0*self.mean,RECURRENCE_PDF_SAMPLES)
self.parent = chi(self.dofs)
def threshold_for_N(max_error, samples, desired_std): # TODO each threshold for X and Y should be seperate, otherwise we do mean of 2 std and we might have little and big std
# the threshold for std for getting the sigma smaller than desired_std with the given max error
# the error might be less than max_error, because if we set threshold and we never reach it, we will never get wrong...
# even if we set initial det to be small, after multiply in A it might be large and we will reach the threshold
threshold = chi(samples).ppf(max_error) * (desired_std) / np.sqrt(samples)
print('for max error of %g, with desired std of %g and %d samples, threshold is %g' % (max_error, desired_std, samples, threshold))
return threshold
def chiScoreCandidate(self, a, antFreq, conFreq):
if a < 0.00001:
return 0,5
b = antFreq - a
c = conFreq - a
d = self.N - antFreq - c
return chi(np.array([[a,b],[c,d]]))[0:2]
def chi_square_error(df, loc, scale):
distribution = chi(df=df, loc=loc, scale=scale)
square_errors = [
np.power(mean - distribution.mean(), 2.0),
np.power(lejp - distribution.ppf(0.9), 2.0),
np.power(uejp - distribution.ppf(0.975), 2.0)
]
return square_errors
def summarize(self):
"""
Summarize data
"""
list = self.countsym(self.root)
obs = list[0][0]+list[1][0]
exp = max(list[0][0],list[1][0])*2
print ("Number of observed species: ", obs)
print ("Number of extinct species: ", exp-obs)
print ("% extinct: ", (exp-obs)/(exp)*100)
print ("chi: ", chi(f_obs = obs, f_exp = exp, ddof = -(obs-1)))
def stark_intervals(y,
K,
alpha,
h,
options_dict={'maxiter': 500},
method='slsqp'):
"""
Starks chi-sq intervals.
NOTE:
- data and K matrix are assumed to be Cholesky transformed
Parameters:
y (np arr) : m element array Cholesky trans observations
K (np arr) : mxn smearing matrix
alpha (float) : interval level
h (np arr) : n element functional on the parameters
options_dict (dict) : optimizer options
method (str) : optimizer method for scipy.optimize
Returns:
tuple -- lower/upper bound
"""
# dimensions of problem
m, n = K.shape
# find the chi-sq critical value
chisq_q = stats.chi(df=m).ppf(1 - alpha)
# define constraint
constr_stark = [{
'type': 'ineq',
'fun': lambda x: chisq_q - np.linalg.norm(y - K @ x)
}]
# find the bounds for full rank
stark_lb = minimize(fun=lambda x: np.dot(h, x),
x0=np.zeros(n),
constraints=constr_stark,
bounds=Bounds(lb=np.zeros(n), ub=np.ones(n) * np.inf),
method='slsqp',
options=options_dict)
stark_ub = minimize(fun=lambda x: -np.dot(h, x),
x0=np.zeros(n),
constraints=constr_stark,
bounds=Bounds(lb=np.zeros(n), ub=np.ones(n) * np.inf),
method='slsqp',
options=options_dict)
assert stark_lb['success']
assert stark_ub['success']
return stark_lb['fun'], -stark_ub['fun']
def chi2fun(flux1,flux2,lamb,lim1,lim2):
''' Method for selecting and fiting region with chi-squared
Parameters
----------
flux1: numpy.ndarray
array with fluxes for interpoleted observed spectra
flux2: numpy.ndarray
array for synthetic spectra
lamb: numpy.ndarray
array with wavelenghs to run chi2 method
lim1: float
inferior limit for chi2 method
lim2: float
superior limit for chi2 method f
Returns
-------
O_chi : numpy.ndarray
value of chi2 and p value
Comments: It's possible look at the each region by each chi2 analyse in each abundance ran
using the command at the terminal: python chi2.py plot
The word plot will allow to show this.
'''
# Seleting wavelenths for chi squared adjust
aux = lim(lamb,lim1,lim2)
# Adjusting and renormalyzing the spectra
O_chi = chi(norm(flux1[aux]),norm(flux2[1][aux]),ddof=9,axis=0)
# Plot each region for Abundance
if 'plot' in sys.argv:
plt.scatter(aux,norm(flux1[aux]),marker='o')
plt.scatter(aux,norm(flux2[1][aux]),marker='^',color='g')
plt.legend(("Observed","synthetic"),loc="lower left")
plt.plot([min(aux),max(aux)],[1,1],'--k')
plt.plot([min(aux),max(aux)],[1,1],'--k')
plt.show()
# Return the chi2 coeficient and the limits of each region
return O_chi[0]
def __init__(self, dofs):
if dofs is None:
self.dofs = 1
else:
self.dofs = dofs
if self.dofs < 0:
raise ValueError('Invalid parameter in chi distribution: dofs must be positive.')
if self.dofs == 1:
self.bounds = np.array([1e-15, np.inf])
else:
self.bounds = np.array([0.0, np.inf])
mean, var, skew, kurt = chi.stats(dofs, moments='mvsk')
self.mean = mean
self.variance = var
self.skewness = skew
self.kurtosis = kurt
self.x_range_for_pdf = np.linspace(0.0, 10.0*self.mean,RECURRENCE_PDF_SAMPLES)
self.parent = chi(self.dofs)
def test_chi(self):
from scipy.stats import chi
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1, 1)
df = 78
mean, var, skew, kurt = chi.stats(df, moments='mvsk')
x = np.linspace(chi.ppf(0.01, df), chi.ppf(0.99, df), 100)
ax.plot(x, chi.pdf(x, df), 'r-', lw=5, alpha=0.6, label='chi pdf')
rv = chi(df)
ax.plot(x, rv.pdf(x), 'k-', lw=2, label='frozen pdf')
vals = chi.ppf([0.001, 0.5, 0.999], df)
np.allclose([0.001, 0.5, 0.999], chi.cdf(vals, df))
r = chi.rvs(df, size=1000)
ax.hist(r, density=True, histtype='stepfilled', alpha=0.2)
ax.legend(loc='best', frameon=False)
self.assertEqual(str(ax), "AxesSubplot(0.125,0.11;0.775x0.77)")
def compute(matrixname, chrNum):
hash12 = pickle.load(open("hash12",'rb'))
sums1 = pickle.load(open("sums1",'rb'))
sums2 = pickle.load(open("sums2",'rb'))
p = []
sumtime = 0
#takes longer each iteration, ask Dr. Ay
for x in hash12:
if x not in sums1 or x not in sums2:
continue
startt = time.time()
for y in hash12[x]:
chi2, pval, dof, exp = chi([[sums1[x],sums2[x]],[hash12[x][y][0],hash12[x][y][1]]])
p.append(pval)
endt = time.time()
#print ("Index\t%s\ttime\t%f\tnumberOfTests\t%d" % (x,endt - startt,len(hash12[x])))
sumtime += (endt-startt)
print ("Computing chromsome %s took %s" % (chrNum, sumtime))
return plothist(p, len(p), matrixname, chrNum)
def build_gauges():
"""Creates gauge object for each observation point's data and appends each to a list.
Returns
-------
gauges : (list) of Gauge objects
"""
gauges = list()
# Pulu Ai
name = 'Pulu Ai'
dists = dict()
dists['height'] = stats.norm(loc=3, scale=0.8)
gauge = Gauge(name, dists)
gauge.lat = [-4.5175]
gauge.lon = [129.775]
gauges.append(gauge)
# Ambon
name = 'Ambon'
dists = dict()
dists['height'] = stats.norm(loc=1.8, scale=0.4)
gauge = Gauge(name, dists)
gauge.lat = [-3.691]
gauge.lon = [128.178]
gauges.append(gauge)
# Banda Neira
name = 'Banda Neira'
dists = dict()
dists['arrival'] = stats.skewnorm(a=2, loc=15, scale=5)
dists['height'] = stats.norm(loc=6.5, scale=1.5)
dists['inundation'] = stats.norm(loc=185, scale=65)
gauge = Gauge(name, dists)
gauge.lat = [-4.5248]
gauge.lon = [129.8965]
gauge.beta = 4.253277987952933
gauge.n = 0.06
gauges.append(gauge)
# Buru
name = 'Buru'
dists = dict()
dists['height'] = stats.chi(df=1.01, loc=0.5, scale=1.5)
gauge = Gauge(name, dists)
gauge.lat = [-3.3815]
gauge.lon = [127.113]
gauges.append(gauge)
# Hulaliu
name = 'Hulaliu'
dists = dict()
dists['height'] = stats.chi(df=1.01, loc=0.5, scale=2.0)
gauge = Gauge(name, dists)
gauge.lat = [-3.543]
gauge.lon = [128.557]
gauges.append(gauge)
# Saparua
name = 'Saparua'
dists = dict()
dists['arrival'] = stats.norm(loc=45, scale=5)
dists['height'] = stats.norm(loc=5, scale=1)
dists['inundation'] = stats.norm(loc=125, scale=40)
gauge = Gauge(name, dists)
gauge.lat = [-3.576]
gauge.lon = [128.657]
gauge.beta = 1.1067189507222546
gauge.n = 0.06
gauges.append(gauge)
# Kulur
name = 'Kulur'
dists = dict()
dists['height'] = stats.norm(loc=3, scale=1)
gauge = Gauge(name, dists)
gauge.lat = [-3.501]
gauge.lon = [128.562]
gauges.append(gauge)
# Ameth
name = 'Ameth'
dists = dict()
dists['height'] = stats.norm(loc=3, scale=1)
gauge = Gauge(name, dists)
gauge.lat = [-3.6455]
gauge.lon = [128.807]
gauges.append(gauge)
# Amahai
name = 'Amahai'
dists = dict()
dists['height'] = stats.norm(loc=3.5, scale=1)
gauge = Gauge(name, dists)
gauge.lat = [-3.338]
gauge.lon = [128.921]
gauges.append(gauge)
return gauges
def test_Rayleigh_to_Chi(self):
X = RV(Rayleigh())
sims = X.sim(Nsim)
cdf = stats.chi(df=2).cdf
pval = stats.kstest(sims, cdf).pvalue
self.assertTrue(pval > .01)
33062195.426077582)
income_model_dict['exponweib'] = st.exponweib(-3.5157658448986489,
0.44492833350419714,
-15427.454196748848,
2440.0278856175246)
drivingdistance_model_dict = ct.OrderedDict()
drivingdistance_model_dict['nakagami'] = st.nakagami(0.11928581143831021,
14.999999999999996,
41.404620910360876)
drivingdistance_model_dict['ncx2'] = st.ncx2(0.30254190304723211,
1.1286538320791935,
14.999999999999998,
8.7361471573932192)
drivingdistance_model_dict['chi'] = st.chi(0.47882729877571095,
14.999999999999996,
44.218301183844645)
drivingdistance_model_dict['recipinvgauss'] = st.recipinvgauss(
2447246.0546641815, 14.999999999994969, 31.072009722580802)
drivingdistance_model_dict['f'] = st.f(0.85798489720127036, 4.1904554804436929,
14.99998319939356, 21.366492843433996)
drivingduration_model_dict = ct.OrderedDict()
drivingduration_model_dict['betaprime'] = st.betaprime(2.576282082814398,
9.7247974165209996,
9.1193851632305201,
261.3457987967214)
drivingduration_model_dict['exponweib'] = st.exponweib(2.6443841639764942,
0.89242254172118096,
10.603640861374947,
40.28556311444698)
y2 = rv2.cdf(x)
y3 = rv3.cdf(x)
# plot the pdf
plt.clf()
plt.plot(x, y1, lw=3, label='scale=5')
plt.plot(x, y2, lw=3, label='scale=3')
plt.plot(x, y3, lw=3, label='scale=7')
plt.xlabel('X', fontsize=20)
plt.ylabel('PDF', fontsize=15)
plt.legend()
plt.savefig('/home/tomer/articles/python/tex/images/norm_cdf.png')
# generate instance cauchy, chi, exponential, uniform
rv1 = st.cauchy(loc=0, scale=5)
rv2 = st.chi(2, loc=0, scale=8)
rv3 = st.expon(loc=0, scale=7)
rv4 = st.uniform(loc=0, scale=20)
# estimate pdf at some points
y1 = rv1.pdf(x)
y2 = rv2.pdf(x)
y3 = rv3.pdf(x)
y4 = rv4.pdf(x)
# plot the pdf
plt.clf()
plt.plot(x, y1, lw=3, label='Cauchy')
plt.plot(x, y2, lw=3, label='Chi')
plt.plot(x, y3, lw=3, label='Exponential')
plt.plot(x, y4, lw=3, label='Uniform')
df = 78 mean, var, skew, kurt = chi.stats(df, moments='mvsk') # Display the probability density function (``pdf``): x = np.linspace(chi.ppf(0.01, df), chi.ppf(0.99, df), 100) ax.plot(x, chi.pdf(x, df), 'r-', lw=5, alpha=0.6, label='chi pdf') # Alternatively, the distribution object can be called (as a function) # to fix the shape, location and scale parameters. This returns a "frozen" # RV object holding the given parameters fixed. # Freeze the distribution and display the frozen ``pdf``: rv = chi(df) ax.plot(x, rv.pdf(x), 'k-', lw=2, label='frozen pdf') # Check accuracy of ``cdf`` and ``ppf``: vals = chi.ppf([0.001, 0.5, 0.999], df) np.allclose([0.001, 0.5, 0.999], chi.cdf(vals, df)) # True # Generate random numbers: r = chi.rvs(df, size=1000) # And compare the histogram: ax.hist(r, normed=True, histtype='stepfilled', alpha=0.2)
import distcan as dc import numpy as np from numpy.testing import assert_allclose import scipy as sp import scipy.stats as st # Get some random places to check pdf np.random.seed(1234) x = np.random.rand(10) # Create chi distributions chi_dc = dc.univariate.Chi(5) chi_sp = st.chi(5) # Check chi cdfs/pdfs against each other chidc_cdf = chi_dc.cdf(x) chisp_cdf = chi_sp.cdf(x) assert_allclose(chidc_cdf, chisp_cdf) # Create chi2 distributions chi2_dc = dc.univariate.Chisq(5) chi2_sp = st.chi2(5) # Check chi2 cdfs/pdfs against each other chi2dc_cdf = chi2_dc.cdf(x) chi2sp_cdf = chi2_sp.cdf(x) assert_allclose(chi2dc_cdf, chi2sp_cdf) # Create Uniform un_dc = dc.univariate.Uniform(0., 7.5)
def __init__(self, k):
self.k = k
# set dist before calling super's __init__
self.dist = st.chi(df=k)
super(Chi, self).__init__()
def __init__(self, name, longitude, latitude, distance,
kind, arrival_params, height_params, inundation_params, beta, n, city_name):
self.name = name
self.city_name = city_name
self.longitude = longitude
self.latitude = latitude
self.distance = distance
self.kind = kind
self.arrival_params = arrival_params
self.height_params = height_params
self.beta = beta
self.n = n
self.inundation_params = inundation_params
if name is not None: # Allows for None initialized object
# Kind[0] is for Wave Arrival Times
# kind[1] is for Wave Height
# kind[2] is for Inundation
if kind[0] == 'norm':
mean = arrival_params[0]
std = arrival_params[1]
self.arrival_dist = stats.norm(mean, std)
elif kind[0] == 'chi2':
k = arrival_params[0]
loc = arrival_params[1]
scale = arrival_params[2]
self.arrival_dist = stats.chi2(k, loc=loc, scale=scale)
elif kind[0] == 'chi':
k = arrival_params[0]
loc = arrival_params[1]
scale = arrival_params[2]
self.arrival_dist = stats.chi(k, loc=loc, scale=scale)
elif kind[0] == 'skewnorm':
skew_param = arrival_params[0]
mean = arrival_params[1]
std = arrival_params[2]
self.arrival_dist = stats.skewnorm(skew_param, mean, std)
if kind[1] == 'norm':
mean = height_params[0]
std = height_params[1]
self.height_dist = stats.norm(mean, std)
elif kind[1] == 'chi2':
k = height_params[0]
loc = height_params[1]
scale = height_params[2]
self.height_dist = stats.chi2(k, loc=loc, scale=scale)
elif kind[1] == 'chi':
k = height_params[0]
loc = height_params[1]
scale = height_params[2]
self.height_dist = stats.chi(k, loc=loc, scale=scale)
elif kind[1] == 'skewnorm':
skew_param = height_params[0]
mean = height_params[1]
std = height_params[2]
self.height_dist = stats.skewnorm(skew_param, mean, std)
if kind[2] == 'norm':
mean = inundation_params[0]
std = inundation_params[1]
self.inundation_dist = stats.norm(mean, std)
elif kind[2] == 'chi2':
k = inundation_params[0]
loc = inundation_params[1]
scale = inundation_params[2]
self.inundation_dist = stats.chi2(k, loc=loc, scale=scale)
elif kind[2] == 'chi':
k = inundation_params[0]
loc = inundation_params[1]
scale = inundation_params[2]
self.inundation_dist = stats.chi(k, loc=loc, scale=scale)
elif kind[2] == 'skewnorm':
skew_param = inundation_params[0]
mean = inundation_params[1]
std = inundation_params[2]
self.inundation_dist = stats.skewnorm(skew_param, mean, std)
def build_gauges():
gauges = list()
# Pulu Ai
name = 'Pulu Ai'
dists = dict()
dists['height'] = stats.norm(loc=3, scale=0.2)
gauge = Gauge(name, dists)
gauge.lat = -4.5166
gauge.lon = 129.775
gauges.append(gauge)
# Ambon
name = 'Ambon'
dists = dict()
dists['height'] = stats.norm(loc=1.8, scale=0.1)
gauge = Gauge(name, dists)
gauge.lat = -3.691
gauge.lon = 128.178
gauges.append(gauge)
# Banda Neira
name = 'Banda Neira'
dists = dict()
dists['arrival'] = stats.skewnorm(a=2, loc=15, scale=5)
dists['height'] = stats.norm(loc=6.5, scale=1)
dists['inundation'] = stats.skewnorm(a=3, loc=231, scale=85)
gauge = Gauge(name, dists)
gauge.lat = -4.5248
gauge.lon = 129.896
gauge.beta = 4.253277987952933
gauge.n = 0.03
gauges.append(gauge)
# Buru
name = 'Buru'
dists = dict()
dists['height'] = stats.chi(df=1.01, loc=1.0, scale=1.0)
gauge = Gauge(name, dists)
gauge.lat = -3.3815
gauge.lon = 127.115
gauges.append(gauge)
# Saparua
name = 'Saparua'
dists = dict()
dists['arrival'] = stats.norm(loc=45, scale=5)
dists['height'] = stats.norm(loc=5, scale=.75)
dists['inundation'] = stats.norm(loc=120, scale=10)
gauge = Gauge(name, dists)
gauge.lat = -3.576
gauge.lon = 128.657
gauge.beta = 1.1067189507222546
gauge.n = 0.03
gauges.append(gauge)
# Kulur
name = 'Kulur'
dists = dict()
dists['height'] = stats.norm(loc=2.5, scale=0.7)
gauge = Gauge(name, dists)
gauge.lat = -3.501
gauge.lon = 128.562
gauges.append(gauge)
# Ameth
name = 'Ameth'
dists = dict()
dists['height'] = stats.norm(loc=3, scale=1)
gauge = Gauge(name, dists)
gauge.lat = -3.6455
gauge.lon = 128.807
gauges.append(gauge)
# Amahai
name = 'Amahai'
dists = dict()
dists['height'] = stats.norm(loc=3.5, scale=1)
gauge = Gauge(name, dists)
gauge.lat = -3.338
gauge.lon = 128.921
gauges.append(gauge)
return gauges
def all_dists():
# dists param were taken from scipy.stats official
# documentaion examples
# Total - 89
return {
"alpha":
stats.alpha(a=3.57, loc=0.0, scale=1.0),
"anglit":
stats.anglit(loc=0.0, scale=1.0),
"arcsine":
stats.arcsine(loc=0.0, scale=1.0),
"beta":
stats.beta(a=2.31, b=0.627, loc=0.0, scale=1.0),
"betaprime":
stats.betaprime(a=5, b=6, loc=0.0, scale=1.0),
"bradford":
stats.bradford(c=0.299, loc=0.0, scale=1.0),
"burr":
stats.burr(c=10.5, d=4.3, loc=0.0, scale=1.0),
"cauchy":
stats.cauchy(loc=0.0, scale=1.0),
"chi":
stats.chi(df=78, loc=0.0, scale=1.0),
"chi2":
stats.chi2(df=55, loc=0.0, scale=1.0),
"cosine":
stats.cosine(loc=0.0, scale=1.0),
"dgamma":
stats.dgamma(a=1.1, loc=0.0, scale=1.0),
"dweibull":
stats.dweibull(c=2.07, loc=0.0, scale=1.0),
"erlang":
stats.erlang(a=2, loc=0.0, scale=1.0),
"expon":
stats.expon(loc=0.0, scale=1.0),
"exponnorm":
stats.exponnorm(K=1.5, loc=0.0, scale=1.0),
"exponweib":
stats.exponweib(a=2.89, c=1.95, loc=0.0, scale=1.0),
"exponpow":
stats.exponpow(b=2.7, loc=0.0, scale=1.0),
"f":
stats.f(dfn=29, dfd=18, loc=0.0, scale=1.0),
"fatiguelife":
stats.fatiguelife(c=29, loc=0.0, scale=1.0),
"fisk":
stats.fisk(c=3.09, loc=0.0, scale=1.0),
"foldcauchy":
stats.foldcauchy(c=4.72, loc=0.0, scale=1.0),
"foldnorm":
stats.foldnorm(c=1.95, loc=0.0, scale=1.0),
# "frechet_r": stats.frechet_r(c=1.89, loc=0.0, scale=1.0),
# "frechet_l": stats.frechet_l(c=3.63, loc=0.0, scale=1.0),
"genlogistic":
stats.genlogistic(c=0.412, loc=0.0, scale=1.0),
"genpareto":
stats.genpareto(c=0.1, loc=0.0, scale=1.0),
"gennorm":
stats.gennorm(beta=1.3, loc=0.0, scale=1.0),
"genexpon":
stats.genexpon(a=9.13, b=16.2, c=3.28, loc=0.0, scale=1.0),
"genextreme":
stats.genextreme(c=-0.1, loc=0.0, scale=1.0),
"gausshyper":
stats.gausshyper(a=13.8, b=3.12, c=2.51, z=5.18, loc=0.0, scale=1.0),
"gamma":
stats.gamma(a=1.99, loc=0.0, scale=1.0),
"gengamma":
stats.gengamma(a=4.42, c=-3.12, loc=0.0, scale=1.0),
"genhalflogistic":
stats.genhalflogistic(c=0.773, loc=0.0, scale=1.0),
"gilbrat":
stats.gilbrat(loc=0.0, scale=1.0),
"gompertz":
stats.gompertz(c=0.947, loc=0.0, scale=1.0),
"gumbel_r":
stats.gumbel_r(loc=0.0, scale=1.0),
"gumbel_l":
stats.gumbel_l(loc=0.0, scale=1.0),
"halfcauchy":
stats.halfcauchy(loc=0.0, scale=1.0),
"halflogistic":
stats.halflogistic(loc=0.0, scale=1.0),
"halfnorm":
stats.halfnorm(loc=0.0, scale=1.0),
"halfgennorm":
stats.halfgennorm(beta=0.675, loc=0.0, scale=1.0),
"hypsecant":
stats.hypsecant(loc=0.0, scale=1.0),
"invgamma":
stats.invgamma(a=4.07, loc=0.0, scale=1.0),
"invgauss":
stats.invgauss(mu=0.145, loc=0.0, scale=1.0),
"invweibull":
stats.invweibull(c=10.6, loc=0.0, scale=1.0),
"johnsonsb":
stats.johnsonsb(a=4.32, b=3.18, loc=0.0, scale=1.0),
"johnsonsu":
stats.johnsonsu(a=2.55, b=2.25, loc=0.0, scale=1.0),
"ksone":
stats.ksone(n=1e03, loc=0.0, scale=1.0),
"kstwobign":
stats.kstwobign(loc=0.0, scale=1.0),
"laplace":
stats.laplace(loc=0.0, scale=1.0),
"levy":
stats.levy(loc=0.0, scale=1.0),
"levy_l":
stats.levy_l(loc=0.0, scale=1.0),
"levy_stable":
stats.levy_stable(alpha=0.357, beta=-0.675, loc=0.0, scale=1.0),
"logistic":
stats.logistic(loc=0.0, scale=1.0),
"loggamma":
stats.loggamma(c=0.414, loc=0.0, scale=1.0),
"loglaplace":
stats.loglaplace(c=3.25, loc=0.0, scale=1.0),
"lognorm":
stats.lognorm(s=0.954, loc=0.0, scale=1.0),
"lomax":
stats.lomax(c=1.88, loc=0.0, scale=1.0),
"maxwell":
stats.maxwell(loc=0.0, scale=1.0),
"mielke":
stats.mielke(k=10.4, s=3.6, loc=0.0, scale=1.0),
"nakagami":
stats.nakagami(nu=4.97, loc=0.0, scale=1.0),
"ncx2":
stats.ncx2(df=21, nc=1.06, loc=0.0, scale=1.0),
"ncf":
stats.ncf(dfn=27, dfd=27, nc=0.416, loc=0.0, scale=1.0),
"nct":
stats.nct(df=14, nc=0.24, loc=0.0, scale=1.0),
"norm":
stats.norm(loc=0.0, scale=1.0),
"pareto":
stats.pareto(b=2.62, loc=0.0, scale=1.0),
"pearson3":
stats.pearson3(skew=0.1, loc=0.0, scale=1.0),
"powerlaw":
stats.powerlaw(a=1.66, loc=0.0, scale=1.0),
"powerlognorm":
stats.powerlognorm(c=2.14, s=0.446, loc=0.0, scale=1.0),
"powernorm":
stats.powernorm(c=4.45, loc=0.0, scale=1.0),
"rdist":
stats.rdist(c=0.9, loc=0.0, scale=1.0),
"reciprocal":
stats.reciprocal(a=0.00623, b=1.01, loc=0.0, scale=1.0),
"rayleigh":
stats.rayleigh(loc=0.0, scale=1.0),
"rice":
stats.rice(b=0.775, loc=0.0, scale=1.0),
"recipinvgauss":
stats.recipinvgauss(mu=0.63, loc=0.0, scale=1.0),
"semicircular":
stats.semicircular(loc=0.0, scale=1.0),
"t":
stats.t(df=2.74, loc=0.0, scale=1.0),
"triang":
stats.triang(c=0.158, loc=0.0, scale=1.0),
"truncexpon":
stats.truncexpon(b=4.69, loc=0.0, scale=1.0),
"truncnorm":
stats.truncnorm(a=0.1, b=2, loc=0.0, scale=1.0),
"tukeylambda":
stats.tukeylambda(lam=3.13, loc=0.0, scale=1.0),
"uniform":
stats.uniform(loc=0.0, scale=1.0),
"vonmises":
stats.vonmises(kappa=3.99, loc=0.0, scale=1.0),
"vonmises_line":
stats.vonmises_line(kappa=3.99, loc=0.0, scale=1.0),
"wald":
stats.wald(loc=0.0, scale=1.0),
"weibull_min":
stats.weibull_min(c=1.79, loc=0.0, scale=1.0),
"weibull_max":
stats.weibull_max(c=2.87, loc=0.0, scale=1.0),
"wrapcauchy":
stats.wrapcauchy(c=0.0311, loc=0.0, scale=1.0),
}
import pandas as pd,numpy as np
from scipy.stats import chi,chi2
import plotly as py
import cufflinks
k=20
res=pd.DataFrame()
for std in [1,1.5,2,2.5,3]:
df=pd.DataFrame(index=np.linspace(0, 28, 1000))
df['chi_%03d_std_%g'%(k,std)]=chi(k).pdf(df.index.values)
'''now we fix x axis:'''
df.index=std*df.index.values/np.sqrt(k) # k-1 for sampled std with fixing bias and k for sampled std as is
res=pd.concat([res,df[df>1e-3].dropna()],axis=0)
fig=res.iplot(asFigure=True)
py.offline.plot(fig)
def nat_to_scipy_distribution(self, q: ChiNP) -> Any:
return ss.chi((q.k_over_two_minus_one + 1.0) * 2.0)
y3 = rv3.cdf(x)
# plot the pdf
plt.clf()
plt.plot(x, y1, lw=3, label='scale=5')
plt.plot(x, y2, lw=3, label='scale=3')
plt.plot(x, y3, lw=3, label='scale=7')
plt.xlabel('X', fontsize=20)
plt.ylabel('PDF', fontsize=15)
plt.legend()
plt.savefig('/home/tomer/articles/python/tex/images/norm_cdf.png')
# generate instance cauchy, chi, exponential, uniform
rv1 = st.cauchy(loc=0, scale=5)
rv2 = st.chi(2, loc=0, scale=8)
rv3 = st.expon(loc=0, scale=7)
rv4 = st.uniform(loc=0, scale=20)
# estimate pdf at some points
y1 = rv1.pdf(x)
y2 = rv2.pdf(x)
y3 = rv3.pdf(x)
y4 = rv4.pdf(x)
# plot the pdf
plt.clf()
plt.plot(x, y1, lw=3, label='Cauchy')
plt.plot(x, y2, lw=3, label='Chi')
plt.plot(x, y3, lw=3, label='Exponential')
plt.plot(x, y4, lw=3, label='Uniform')
#%% Plots
dist_gamma = gamma(a=best_params_gamma[0],
loc=best_params_gamma[1],
scale=best_params_gamma[2])
dist_lognorm = lognorm(s=best_params_log[0],
loc=best_params_log[1],
scale=best_params_log[2])
dist_pareto = pareto(b=best_params_pareto[0],
loc=best_params_pareto[1],
scale=best_params_pareto[2])
dist_chi = chi(df=best_params_chi[0],
loc=best_params_chi[1],
scale=best_params_chi[2])
lognorm_mu = np.log(best_params_log[2])
lognorm_sigma = best_params_log[0]
gamma_alpha = best_params_gamma[0]
gamma_beta = 1 / best_params_gamma[2]
pareto_b = best_params_pareto[0]
chi_df = best_params_chi[0]
x = np.linspace(0, 1, num=500)
plt.plot(x, dist_gamma.ppf(x), color='red', label='gamma')
def _scipy(self, loc=0.0, scale=1.0):
return ss.chi(df=self.df, loc=loc, scale=scale)
best_dist = getattr(st, best_fit_name)
print(best_fit_name, best_fit_params, best_dist)
# Make PDF with best params
cdf = make_pdf(best_dist, best_fit_params)
# Display
plt.figure(figsize=(12, 8))
# ax = cdf.plot(lw=2, label='PDF', legend=True)
# data.plot(kind='hist', bins=50, normed=True, alpha=0.5, label='Data', legend=True, ax=ax)
x = np.linspace(0, 25, 100)
plt.plot(days, cdf_die)
plt.plot(best_dist.cdf(days, *best_fit_params))
f = lambda x, mu, sigma: st.chi(mu, loc=0, scale=sigma).cdf(x)
mu, sigma = curve_fit(f, days, cdf_die)[0]
# plt.plot(days, cdf_die)
# plt.plot(days, cdf_die)
plt.plot(x, st.chi(mu, loc=0, scale=sigma).cdf(x), 'k')
# param_names = (best_dist.shapes + ', loc, scale').split(', ') if best_dist.shapes else ['loc', 'scale']
# param_str = ', '.join(['{}={:0.2f}'.format(k, v) for k, v in zip(param_names, best_fit_params)])
# dist_str = '{}({})'.format(best_fit_name, param_str)
# ax.set_title(u'El Niño sea temp. with best fit distribution \n' + dist_str)
# ax.set_xlabel(u'Temp. (°C)')
# ax.set_ylabel('Frequency')