def reg(x, y):
"""Conduct OLS regression on y = beta * x
Return betas and p_values from t-test of betas
"""
try:
dim_x = x.shape
constant = numpy.ones(dim_x[0])
x = numpy.append(constant.T, x.T)
x = x.reshape(dim_x[1] + 1, dim_x[0]).T
beta = numpy.dot(numpy.dot(numpy.linalg.inv(numpy.dot(x.T, x)),x.T),y)
epsilon = y - numpy.dot(x, beta.T)
var_cov = numpy.dot(numpy.dot(epsilon.T, epsilon),numpy.linalg.inv(numpy.dot(x.T, x))) / \
(dim_x[0] - dim_x[1])
std_err = numpy.diagonal(var_cov) ** 0.5
t_stat = beta / std_err
p_values = list()
for i in t_stat:
if t.cdf(i,dim_x[0]-dim_x[1]-1)>0.5:
p_values.append(2*(1-t.cdf(i,dim_x[0]-dim_x[1]-1)))
else:
p_values.append(2*t.cdf(i,dim_x[0]-dim_x[1]-1))
except:
dim_x = x.shape
beta = numpy.zeros(dim_x[1] + 1)
p_values = numpy.zeros(dim_x[1] + 1)
print("Error: " + str(sys.exc_info()[1]) + " occurs when conducting OLS regression")
return beta, p_values
def t_to_z(mr, dof): data = mr.get_data() # Select just the nonzero voxels nonzero = data[data!=0] # We will store our results here Z = np.zeros(len(nonzero)) # Select values less than or == 0, and greater than zero c = np.zeros(len(nonzero)) k1 = (nonzero <= c) k2 = (nonzero > c) # Subset the data into two sets t1 = nonzero[k1] t2 = nonzero[k2] # Calculate p values for <=0 p_values_t1 = t.cdf(t1, df = dof) z_values_t1 = norm.ppf(p_values_t1) # Calculate p values for > 0 p_values_t2 = t.cdf(-t2, df = dof) z_values_t2 = -norm.ppf(p_values_t2) Z[k1] = z_values_t1 Z[k2] = z_values_t2 # Create new nifti empty_nii = np.zeros(mr.shape) empty_nii[mr.get_data()!=0] = Z Z_nii_fixed = nib.nifti1.Nifti1Image(empty_nii,affine=mr.get_affine(),header=mr.get_header()) return Z_nii_fixed
def TtoZ(t_stat_map,output_nii,dof):
'''TtoZ:
for details see
https://github.com/vsoch/TtoZ
Also provided for command line.
t_stat_map:
file path to t stat image
output_nii:
output nifti file
dof:
degrees of freedom (typically number subjects - 2)
'''
print("Converting map %s to Z-Scores..." %(t_stat_map))
mr = nibabel.load(t_stat_map)
data = mr.get_data()
# Select just the nonzero voxels
nonzero = data[data!=0]
# We will store our results here
Z = np.zeros(len(nonzero))
# Select values less than or == 0, and greater than zero
c = np.zeros(len(nonzero))
k1 = (nonzero <= c)
k2 = (nonzero > c)
# Subset the data into two sets
t1 = nonzero[k1]
t2 = nonzero[k2]
# Calculate p values for <=0
p_values_t1 = t.cdf(t1, df = dof)
z_values_t1 = norm.ppf(p_values_t1)
# Calculate p values for > 0
p_values_t2 = t.cdf(-t2, df = dof)
z_values_t2 = -norm.ppf(p_values_t2)
Z[k1] = z_values_t1
Z[k2] = z_values_t2
# Write new image to file
empty_nii = np.zeros(mr.shape)
empty_nii[mr.get_data()!=0] = Z
Z_nii_fixed = nibabel.nifti1.Nifti1Image(empty_nii,
affine=mr.get_affine(),
header=mr.get_header())
nibabel.save(Z_nii_fixed,output_nii)
def t_uneqvar(list_1, list_2, **kwargs):
""" Performs a t-test without the equal variance
assumption of Student's t. For example, see:
Ruxton, G. D. (2006).
The unequal variance t-test is an alternative to
Student's t-test and the Mann-Whitney U test
Behavioral Ecology, 17(4), 688–690.
Arguments:
list_1, list_2: list of values from the first and final condition, respectively
Returns: a dict containing keys:
'p': the p-value resulting from a two-tailed test for change
note two-tailed p-values are preferred to avoid numerical issues
associated with highly significant p-values
'dir': the direction
't': the t statistic
'df': the calculated degrees of freedom
"""
from scipy.stats import t
from numpy import std, mean
from math import sqrt
two_tailed = test_kwarg('two_tailed', kwargs, [True, False])
the_return_dict = {}
var_1 = (std(list_1, ddof = 1))**2
var_2 = (std(list_2, ddof = 1))**2
the_u = var_2 / var_1
n_1 = len(list_1) * 1.
n_2 = len(list_2) * 1.
df = (1./n_1 + the_u/n_2)**2/(1/(n_1**2*(n_1-1)) + the_u**2/(n_2**2*(n_2-1)))
# Use 1 - 2 here before calculating p so more positive changes corresponse to smaller p
t_val = (mean(list_1) - mean(list_2)) / sqrt((var_1 / n_1) + (var_2 / n_2))
# One-sided p
the_p = t.cdf(t_val, df)
t_val = -1. * t_val
if two_tailed:
if t_val > 0:
the_p = 2. * the_p
the_dir = '+'
else:
# It is numerically preferable to avoid
# y = 2 * (1 - x) in case x is close to zero
the_p = 2. * t.cdf(t_val, df)
the_dir = '-'
return_dict = {'t': t_val, 'p': the_p, 'df': df, 'dir': the_dir}
return return_dict
def show_bootstrap_statistics(clf, X, y, features):
num_features = len(features)
coefs = []
for i in range(num_features):
coefs.append([])
for _ in range(BOOTSTRAP_ITERATIONS):
X_sample, y_sample = resample(X, y)
clf.fit(X_sample, y_sample)
for i, c in enumerate(get_normalized_coefs(clf)):
coefs[i].append(c)
poi_index = features.index('POI')
building_index = features.index('Building')
coefs[building_index] = coefs[poi_index]
intervals = []
print()
print('***** Bootstrap statistics *****')
print('{:<20}{:<20}{:<10}{:<10}'.format('Feature', '95% interval', 't-value', 'Pr(>|t|)'))
print()
for i, cs in enumerate(coefs):
values = np.array(cs)
lo = np.percentile(values, 2.5)
hi = np.percentile(values, 97.5)
interval = '({:.3f}, {:.3f})'.format(lo, hi)
tv = np.mean(values) / np.std(values)
pr = (1.0 - t.cdf(x=abs(tv), df=len(values))) * 0.5
stv = '{:.3f}'.format(tv)
spr = '{:.3f}'.format(pr)
print('{:<20}{:<20}{:<10}{:<10}'.format(features[i], interval, stv, spr))
def neuropowertable(request):
# Get the template/step status
sid = get_session_id(request)
template = "neuropower/neuropowertable.html"
steps = get_neuropower_steps(template,sid)
context = {"steps":steps}
if not ParameterModel.objects.filter(SID=sid):
# Should not be able to reach this condition
context["text"] = "No data found. Go to 'Input' and fill out the form."
return render(request,template,context)
else:
sid = request.session.session_key #why are we getting session id again?
parsdata = ParameterModel.objects.filter(SID=sid)[::-1][0]
SPM = nib.load(parsdata.location).get_data()
if parsdata.ZorT == 'T':
SPM = -norm.ppf(t.cdf(-SPM,df=float(parsdata.DoF)))
cluster.cluster(SPM,parsdata.ExcZ,parsdata.peaktable)
peaks = pd.read_csv(parsdata.peaktable,sep="\t")
if len(peaks) < 30:
context["text"] = "There are too few peaks for a good estimation. Either the ROI is too small or the screening threshold is too high."
else:
pvalues = np.exp(-float(parsdata.ExcZ)*(np.array(peaks.peak)-float(parsdata.ExcZ)))
pvalues = [max(10**(-6),p) for p in pvalues]
peaks['pval'] = pvalues
peakform = PeakTableForm()
form = peakform.save(commit=False)
form.SID = sid
form.data = peaks
form.save()
context["peaks"] = peaks.to_html(classes=["table table-striped"])
return render(request,template,context)
def GeneratePDF(Data, method = 'Robust_Student_t', lower_threshold = 0.15, upper_threshold = 0.85):
'''Generate the pdf estimate of the data
Input: /Data/ data to estimate pdf on
/method/ Method of estimation.
Available methods: 'Robust_Student_t'; 'KDE'; 'Normal'
/lower_threshold/ in percentage
/upper_threshold/ in percentage
Output: /pdf/ fitted pdf
/cdf/ fitted cdf
'''
x = np.linspace(min(Data), max(Data), 100)
if method == 'Robust_Student_t':
nu, mu, sigma = uvtfit(Data)
pdf = t.pdf(x, nu, mu, sigma)
cdf = t.cdf(x, nu, mu, sigma)
lower = t.ppf(lower_threshold, nu, mu, sigma)
upper = t.ppf(upper_threshold, nu, mu, sigma)
elif method == 'Normal':
mu, sigma = norm.fit(Data)
pdf = norm.pdf(x, mu, sigma)
cdf = norm.cdf(x, mu, sigma)
lower = norm.ppf(lower_threshold, mu, sigma)
upper = norm.ppf(upper_threshold, mu, sigma)
elif method == 'KDE':
kernal = gaussian_kde(Data)
pdf = kernal.evaluate(x)
cdf = np.array([kernal.integrate_box(x[0], x[i+1]) for i in range(len(x)-1)])
lower = np.percentile(cdf, lower_threshold*100)
upper = np.percentile(cdf, upper_threshold*100)
return x, pdf, cdf, lower, upper
def compute_zscore(self):
#get background and peri rates
bg_rates = np.array([t.bg_rate for t in self.trials])
peri_rates = np.array([t.peri_rate for t in self.trials])
bg_counts = np.array([t.bg_count for t in self.trials])
peri_counts = np.array([t.peri_count for t in self.trials])
rate_diff = peri_rates - bg_rates
count_diff = peri_counts - bg_counts
if peri_counts.sum() + bg_counts.sum() < len(self.trials):
pval = 0.5 #kludge
z = 0.0
tstat = 0.0
else:
rate_diff_std = rate_diff.std(ddof=1)
count_diff_std = count_diff.std(ddof=1)
if rate_diff_std == 0.0:
print 'Very strange that this happenend, rate_diff_std=%0.3f, count_diff_std=%0.3f, stim_num=%d' % (rate_diff_std, count_diff_std, self.stim_number)
rate_diff_std = 1.0
z = rate_diff.mean() / rate_diff_std
tstat = z*np.sqrt(len(bg_rates))
pval = (1.0 - tdist.cdf(np.abs(tstat), len(bg_rates)-1))*2 #two-tailed t-test pvalue
self.zscore = z
self.tstat = tstat
self.pval = pval
def t_stat(X, c, beta, MRSS, df):
"""
parameters
----------
X: 2D array (n_trs * number of regressors)
design matrix.
c: a contrast vector.
betas: 2D array (number of regressors x n_vols)
estimated betas for linear model.
MRSS: 1D array of length n_volx
Mean residual sum of squares.
df: int
n - rank of X.
Returns
______
t: a vector of length n_vols
t statistics for each voxel.
p: a vector of length n_vols
p values for each voxel.
"""
X = np.asarray(X)
c = np.atleast_2d(c).T
# calculate bottom half of t statistic
SE = np.sqrt(MRSS * c.T.dot(npl.pinv(X.T.dot(X)).dot(c)))
t = c.T.dot(beta) / SE
# Get p value for t value using cumulative density dunction
# (CDF) of t distribution
ltp = t_dist.cdf(t, df) # lower tail p
p = 1 - ltp # upper tail p
return t, p
def pcor(X,Y,Z):
"""
computes the correlation amtrix of X and Y conditioning on Z
"""
if X.ndim==1: X = X[:,SP.newaxis]
if Y.ndim==1: Y = Y[:,SP.newaxis]
if Z is None: return STATS.pearsonr(X,Y)
if Z.ndim==1: Z = Z[:,SP.newaxis]
nSamples = X.shape[0]
betaX, _, _, _ = LA.lstsq(Z,X)
betaY, _, _, _ = LA.lstsq(Z,Y)
Xres = X - SP.dot(Z,betaX)
Yres = Y - SP.dot(Z,betaY)
corr_cond = SP.corrcoef(Xres[:,0],Yres[:,0])[0,1]
dz = Z.shape[1] # dimension of conditioning variable
df = max(nSamples - dz - 2,0) # degrees of freedom
with warnings.catch_warnings():
warnings.filterwarnings("ignore")
tstat = corr_cond / SP.sqrt(1.0 - corr_cond ** 2) # calculate t statistic
tstat = math.sqrt(df) * tstat
pv_cond = 2 * t.cdf(-abs(tstat), df, loc=0, scale=1) # calculate p value
return corr_cond,pv_cond
def t_stat(data, X_matrix):
"""
Return the estimated betas, t-values, degrees of freedom, and p-values for the glm_multi regression
Parameters
----------
data_4d: numpy array of 4 dimensions
The image data of one subject, one run
X_matrix: numpy array
The design matrix for glm_multi
Note that the fourth dimension of `data_4d` (time or the number
of volumes) must be the same as the number of rows that X has.
Returns
-------
beta: estimated beta values
t: t-values of the betas
df: degrees of freedom
p: p-values corresponding to the t-values and degrees of freedom
"""
beta = glm_beta(data, X_matrix)
# Calculate the parameters - b hat
beta = np.reshape(beta, (-1, beta.shape[-1])).T
fitted = X_matrix.dot(beta)
# Residual error
y = np.reshape(data, (-1, data.shape[-1]))
errors = y.T - fitted
# Residual sum of squares
RSS = (errors**2).sum(axis=0)
df = X_matrix.shape[0] - npl.matrix_rank(X_matrix)
# Mean residual sum of squares
MRSS = RSS / df
# calculate bottom half of t statistic
Cov_beta=npl.pinv(X_matrix.T.dot(X_matrix))
SE =np.zeros(beta.shape)
for i in range(X_matrix.shape[-1]):
c = np.zeros(X_matrix.shape[-1])
c[i]=1
c = np.atleast_2d(c).T
SE[i,:]= np.sqrt(MRSS* c.T.dot(npl.pinv(X_matrix.T.dot(X_matrix)).dot(c)))
zeros = np.where(SE==0)
SE[zeros] = 1
t = beta / SE
t[:,zeros] =0
# Get p value for t value using CDF of t didstribution
ltp = t_dist.cdf(abs(t), df)
p = 1 - ltp # upper tail
return beta.T, t, df, p
def corrParallel(X,Y=None,df=None):
"""
computes the mxk correlation matrix between the mxn matrix X and the kxn matrix Z
"""
if Y is None:
return corrParallelSym(X,df=df)
assert X.shape[1]==Y.shape[1], 'ouch, samples do not match'
nSamples = X.shape[1]
Xstd = X.T
Xstd-= Xstd.mean(0)
Xstd/= Xstd.std(0)
Ystd = Y.T
Ystd-= Ystd.mean(0)
Ystd/= Ystd.std(0)
corr = SP.dot(Xstd.T,Ystd)/nSamples
if df is None:
df = max(nSamples - 2,0) # degrees of freedom
with warnings.catch_warnings():
warnings.filterwarnings("ignore")
tstat = corr / SP.sqrt(1.0 - corr ** 2) # calculate t statistic
tstat = math.sqrt(df) * tstat
pv = 2 * t.cdf(-abs(tstat), df, loc=0, scale=1) # calculate p value
return corr,pv
def t_fun():
# accumulate from -infinity to 3.077
res = t.cdf(3.0777, df=1)
print(res)
# probability of middle
a, b = t.interval(0.95, 1)
print(a, b)
def _t(M, Rho, nu):
N = Rho.shape[0]
mu = np.zeros(N) # zero mean
x = mvt.multivariate_t_rvs(mu,Rho,nu,M) # generate T RV's
U = t.cdf(x, nu)
return U
def sample_procedure(dist1, dist2):
non_bon = 0
bon = 0
for i in xrange(trials):
flag = True
for _ in xrange(repeats):
# First sample
sample1 = np.random.choice(dist1, (sample_size, ))
mean1 = np.mean(sample1)
std1 = np.std(sample1)
# Second sample
sample2 = np.random.choice(dist2, (sample_size, ))
mean2 = np.mean(sample2)
std2 = np.std(sample2)
# T test
result = t_test(mean1, mean2, std1, std2, sample_size, sample_size)
p_value = (1 - t.cdf(result, sample_size - 1)) * 2
if p_value < alpha and flag:
non_bon += 1
flag = False
if p_value < bonferroni:
bon += 1
break
print "Time of reject in alpha: ", non_bon / trials
print "Time of reject in bonferroni: ", bon / trials
def t_test2(data1,data2):
"""
Compute t test for two samples with significantly different variances (use f_test_var) to test if they have same mean
H0: samples have same means (p-value close to one).
Parameters
----------
data1: n,1 - dim array with data
data2: n,1 - dim array with data
Returns
-------
p-value of t test, the t value itself and the degrees of freedom
Notes
-----
See 3rd Edition of Numerical recipes chapter 14.2.1, p.728
"""
N1, N2 = len(data1), len(data2)
mean1, mean2 = np.mean(data1), np.mean(data2)
var1, var2= np.var(data1,ddof = 1), np.var(data2,ddof = 1)
T = (mean1 - mean2) / np.sqrt(var1/N1 + var2/N2) # Eq. 14.2.3
df = (var1/N1 + var2/N2)**2. / ( (var1/N1)**2./(N1 - 1) + (var2/N2)**2./(N2 - 1))
return t.cdf(T, df), T, df
def t_test1(data1,data2):
"""
Compute t test for two samples with same variance to test if they have same mean
H0: samples have same means (p-value close to one).
Parameters
----------
data1: n,1 - dim array with data
data2: n,1 - dim array with data
Returns
-------
p-value of t test, the t value itself and the degrees of freedom
Notes
-----
See 3rd Edition of Numerical recipes chapter 14.2.1, p.727
"""
if not isinstance(data1,np.ndarray):
data1 = np.array(data1)
if not isinstance(data2,np.ndarray):
data2 = np.array(data2)
N1, N2 = len(data1), len(data2)
mean1, mean2 = np.mean(data1), np.mean(data2)
# Eq. 14.2.1
sD = np.sqrt( (np.sum( (data1 - np.ones(N1) * mean1) ** 2.) + np.sum( (data2 - np.ones(N2) * mean2) ** 2.)) / (N1 + N2 - 2.) * (1./N1 + 1./N2))
T = (mean1 - mean2) / sD
return t.cdf(T, N1 + N2 - 2),T,N1 + N2 - 2
def calc_cdf(mu_null, n, mean, stddev): one_sample_t = ( mean - mu_null)/ (stddev/math.sqrt(n)) if n > 50: cdf_val = normcdf(one_sample_t,0. , 1.) else: cdf_val = t.cdf(one_sample_t, n - 1) return cdf_val
def tdist(var, year, x, eu=None):
s,f = seznam_vzorec(var, year, eu=eu)
n = len(s)
x = abs(x)
# print "=TDIST(%s, %s, 2)" % (x, n-2)
result = ( 1-t.cdf(x, n-2) ) * 2
return result
def solve_t(t_value=None, f=None, p=None):
max_1_none(t_value, f, p)
if t_value == None:
return t(f, p)
elif f == None:
raise NotImplemented("Not implemented yet - sorry")
elif p == None:
return sympify(sci_t.cdf(float(t_value), float(f)))
def corrsig(N, c=None, p=.95):
# if c exists, this returns the cutoff
import numpy as np
from scipy.stats import t
if not c is None:
return t.cdf(c/np.sqrt((1-c**2)/(N-2)), N-2)
else:
print "functionality not implemented yet, please query a correlation"
return
def log_principal_anomaly(x, N, Q, S):
assert N > 3, "N must be more than 3, is %r" % N
mean = float(S) / N
val = mean - abs(mean - x)
scale = sqrt(max(0, (float(N) * Q - pow(S, 2))) / ((N + 1) * (N - 3)))
if scale == 0:
raise ("Scale is 0!", N, Q, S)
t_cdf = t.cdf(val, N - 1, loc=mean, scale=scale)
return -log(2 * t_cdf)
def simulateCopula(simulations=10, type=str('g'), rho=float, lamda=tuple, tDof=4, basketSize=5, useGPU=False):
result = []
"""
$\tau = F^{-1}(u) = -\frac{log(1-u)}{\lambda}$
"""
print 'simulating t distribution' if type == 't' else 'simulating gaussian dist'
for z in xrange(0, simulations):
# for the t distribution we use the same method but
# sample from the chisquared distribution
# if GPU is enabled, hand over to GPU to provide random number sample
if useGPU and type == 'g':
z1, z2, z3, z4, z5 = rng.getPseudoRandomNumbers_Standard_cuda(basketSize)
else:
z1, z2, z3, z4, z5 = random.chisquare(tDof, size=basketSize) if type == 't' else random.normal(size=5)
# z1, z2, z3, z4, z5 = chi2.rvs(1, size=5) if type == 't' else random.normal(size=5)
x1 = z1
# using factorised copula procedure
# $A_i = w_iZ + \sqrt{1-w{^2}{_i}\Epsilon_i $
x2, x3, x4, x5 = [z1 * rho + sqrt(1 - square(rho)) * zn for zn in [z2, z3, z4, z5]]
# converting to normal variables from t or normal distribution successfully
# via cdf of relevant distribution
if type == 't':
u1, u2, u3, u4, u5 = [t.cdf(x, 1) for x in [x1, x2, x3, x4, x5]]
else:
u1, u2, u3, u4, u5 = [norm.cdf(x) for x in [x1, x2, x3, x4, x5]]
u = [u1, u2, u3, u4, u5]
# $\tau_i = -\frac{-log(1-u)}{\lambda_i} $
tau1, tau2, tau3, tau4, tau5 = [-log(1 - u) / lamda[index] for index, u in enumerate(u)]
result.append({'z1': z1,
'z2': z2,
'z3': z3,
'z4': z4,
'z5': z5,
'x1': x1,
'x2': x2,
'x3': x3,
'x4': x4,
'x5': x5,
'u1': u1,
'u2': u2,
'u3': u3,
'u4': u4,
'u5': u5,
'tau1': tau1,
'tau2': tau2,
'tau3': tau3,
'tau4': tau4,
'tau5': tau5,
})
return DataFrame(result)
def main():
parser = argparse.ArgumentParser(
description="Convert a whole brain T score map to a Z score map without loss of precision for strongly positive and negative values.")
parser.add_argument("t_stat_map", help="T-score statistical map in the form of a 3D NIFTI file (.nii or .nii.gz).", type=nifti_file)
parser.add_argument("dof", help="Degrees of freedom (eg. for a two-sample T-test: number of subjects in group - 2)",type=int)
parser.add_argument("--output_nii", help="The name for the output Z-Score Map.",type=str,default="z_stat_map.nii")
args = parser.parse_args()
print "Converting map %s to Z-Scores..." %(args.t_stat_map)
mr = nib.load(args.t_stat_map)
data = mr.get_data()
# Select just the nonzero voxels
nonzero = data[data!=0]
# We will store our results here
Z = np.zeros(len(nonzero))
# Select values less than or == 0, and greater than zero
c = np.zeros(len(nonzero))
k1 = (nonzero <= c)
k2 = (nonzero > c)
# Subset the data into two sets
t1 = nonzero[k1]
t2 = nonzero[k2]
# Calculate p values for <=0
p_values_t1 = t.cdf(t1, df = args.dof)
z_values_t1 = norm.ppf(p_values_t1)
# Calculate p values for > 0
p_values_t2 = t.cdf(-t2, df = args.dof)
z_values_t2 = -norm.ppf(p_values_t2)
Z[k1] = z_values_t1
Z[k2] = z_values_t2
# Write new image to file
empty_nii = np.zeros(mr.shape)
empty_nii[mr.get_data()!=0] = Z
Z_nii_fixed = nib.nifti1.Nifti1Image(empty_nii,affine=mr.get_affine(),header=mr.get_header())
nib.save(Z_nii_fixed,args.output_nii)
def pVal(mu1,mu2,s1,s2,n1,n2): se = np.sqrt(s1*s1/n1+s2*s2/n2) df = (s1**2/n1 + s2**2/n2)**2 / ( ((s1**2 / n1)**2 / (n1 - 1)) + ((s2**2 / n2)**2 / (n2 - 1))) tVal = (mu1 - mu2)/se return (1 - t.cdf(tVal,df)) #[email protected]:ryu577/base.git
def SimulateUniforms(self):
"""docstring for Simulate"""
mean = [0.0] * self.size
cov = self.copula_covariance
s = chi2.rvs(self.dof)
Z = multivariate_normal(mean, cov)
X = [math.sqrt(self.dof)/math.sqrt(s) * z for z in Z]
Y = [t.cdf(x, self.dof) for x in X]
return Y
def comparison_test(arr1, arr2, name1, name2, tail=1, bonf=1):
stats = _stats(arr1, arr2)
p_value = 1 - t.cdf(t_test(*stats), min(len(arr1), len(arr2)) - 1)
if tail == 2: #In case for two tail test
p_value *= 2
alpha = ALPHA / bonf
print "The p-value between {0} and {1} is {2:.5f} and it {3} the null hypothesis".format(
name1, name2, p_value,
"reject" if p_value < alpha else "does not reject")
print "Actual Alpha is", format(alpha, '.4f')
if p_value < alpha:
print "The effect size is {0:.5f}".format(cohen_d(*stats))
def sig_test(r, n, twotailed = True): import numpy as np from scipy.stats import t as tdist df = n - 2 #Create t-statistic #Use absolute value to be able to deal with negative scores t = np.abs(r * np.sqrt(df/(1-r**2))) p = (1 - tdist.cdf(t,df)) if twotailed: p = p * 2 return p
def cdf(self, arg):
"""Cumulative density function (CDF).
Parameters
----------
arg : array
Grid of point to evaluate CDF at
Returns
-------
array
CDF values. Same shape as the input.
"""
a = self.__const_a()
b = self.__const_b()
y = (b*arg+a)/(1+np.sign(arg+a/b)*self.lam) * (1-2/self.eta)**(-.5)
cond = arg < -a/b
return cond * (1-self.lam) * t.cdf(y, self.eta) \
+ ~cond * (-self.lam + (1+self.lam) * t.cdf(y, self.eta))
def naiveTopt(icm,cutoff=.05): #like topt but doesn't correct for tail direction
""" Returns cluster by fitting t-test and returning residues above cutoff """
param = t.fit(icm,loc=np.median(icm))
x = np.linspace(-1,1,200)
cdf = t.cdf(x,param[0],loc=param[1], scale=param[2])
minx = np.max(x[np.nonzero(cdf<cutoff)])
# deal with direction of tail:
cursect = np.array([i for i in range(icm.size) if icm[i]<minx])
return cursect
def __init__(self,x,y):
self.x = x
self.y = y
(self.n,self.r) = x.shape
xx = np.dot(x.T,x)
xy = np.dot(x.T,y)
self.xxi = np.linalg.inv(xx)
self.b = np.linalg.solve(xx,xy).reshape(-1,1)
e = y - np.dot(x,self.b)
self.resid = e
self.vb = self.genvariance(e)
self.se = np.sqrt(np.diagonal(self.vb)).reshape(-1,1)
self.tstat = np.divide(self.b,self.se)
self.pval = 2*t.cdf(-np.abs(self.tstat),df=self.n-self.r)
self.rsq = 1-e.var()/y.var()
self.adjrsq = 1-(1-self.rsq)*(self.n-1)/(self.n-self.r)
self.logl = -self.n/2*(np.log(2*np.pi*e.var())+1)
self.aic = 2*self.r-2*self.logl
self.bic = np.log(self.n)*self.r-2*self.logl
nulllike = -self.n/2*(np.log(2*np.pi*y.var())+1)
self.deviance = 2*(self.logl-nulllike)
def two_sample_Welch_t_test(data1, data2, scale_estimator=lambda x: np.std(x)):
"""
--Independent two-sample test--
Assuming Gaussian distributions and UNequal variances and unequal sample sizes.
Hypothesis H0: mu_1 == mu__2
scale_estimator is a function that estimates the square root of the variance (~st.dev.)
"""
sample_mean1 = np.mean(data1)
sample_mean2 = np.mean(data2)
n1 = len(data1)
n2 = len(data2)
s1 = scale_estimator(data1)
s2 = scale_estimator(data2)
s_delta = np.sqrt((s1**2) / n1 + (s2**2) / n2)
t_statistic = (sample_mean1 - sample_mean2) / s_delta
degrees_of_freedom = s_delta**4 / (
(s1**2 / n1)**2 / (n1 - 1) + (s2**2 / n2)**2 /
(n2 - 1)) # Welch–Satterthwaite equation
p_value = (1 - t.cdf(abs(t_statistic), degrees_of_freedom)
) * 2 # Look up from Student's t-distribution
return p_value, t_statistic, degrees_of_freedom
def student_test(data1, data2):
print("Student test of Ex = Ey")
n, m = len(data1), len(data2)
criteria = t.cdf((1 - alfa) / 2, len(data1) + len(data2) - 2)
# test = ttest_ind(data1, data2)
test = ((np.mean(data1) - np.mean(data2)) * math.sqrt(n * m *(n + m - 2))) \
/ (math.sqrt((n + m) * (n * np.var(data1) + m * np.var(data2))))
if test > criteria:
print(f"Ho отвергается т.к значение > {criteria}")
print("Ex != Ey")
else:
print(f"Ho подтверждается т.к значение < {criteria}")
print("Ex = Ey")
print()
return criteria, test
def independent_ttest(data1, data2, alpha):
# calculate means
mean1, mean2 = mean(data1), mean(data2)
print(mean1)
print(mean2)
mean1_glob = mean1
mean2_glob = mean2
# calculate standard errors
se1, se2 = sem(data1), sem(data2)
# standard error on the difference between the samples
sed = sqrt(se1**2.0 + se2**2.0)
# calculate the t statistic
t_stat = (mean1 - mean2) / sed
# degrees of freedom
df = len(data1) + len(data2) - 2
# calculate the critical value
cv = t.ppf(1.0 - alpha, df)
# calculate the p-value
p = (1.0 - t.cdf(abs(t_stat), df)) * 2.0
# return everything
return t_stat, df, cv, p
def simple_linear_reg(y, x):
"""一元线性回归"""
assert len(x) == len(y)
n = len(x)
assert n > 1
mean_x = mean(x)
mean_y = mean(y)
beta1 = covariance(x, y) / variance(x)
beta0 = mean_y - beta1 * mean_x
y_hat = [beta0 + beta1 * e for e in x]
ss_residual = sum((e1 - e2)**2 for e1, e2 in zip(y, y_hat))
se_model = sqrt(ss_residual / (n - 2))
t_value = beta1 / (se_model / sqrt((n - 1) * variance(x)))
p = 2 * (1 - t.cdf(abs(t_value), n - 2))
return beta0, beta1, t_value, n - 2, p
def bharath_Ttest1s(sMean,sd,pMean,n,alpha=0.05):
tstatistics=(sMean-pMean)/(sd/np.sqrt(n))
if tstatistics>0:
tstatistics=-tstatistics
print("\nT Statistics:",tstatistics)
tcritical=[t.ppf(q=alpha/2,df=n-1),-t.ppf(q=alpha/2,df=n-1)]
print("T critical Values are :",tcritical)
if tstatistics<tcritical[0] or tstatistics>tcritical[1]:
print("Reject the Null Hypothesis")
else:
print("Fail to reject the Null Hypothesis")
pvalue=2*t.cdf(tstatistics,df=n-1)
print("\nPvalue value is:",pvalue)
if pvalue < 0.05:
print("Reject the Null Hypothesis")
else:
print("Fails to reject the Null Hypothesis")
print("\n")
def data_process_3():
data = [3, -3, 3, 12, 15, -16, 17, 19, 23, -24, 32]
# Problem 2 Question 1
# confidence interval
c1 = 0.95
samp_size = len(data)
avg = np.mean(data)
sd = np.std(data, ddof=1)
stand_err = sd / np.sqrt(samp_size)
t_c = t.ppf(1 - (1 - c1) / 2, df=samp_size - 1)
intervals = (avg - (t_c * sd) / np.sqrt(samp_size), avg + (t_c * sd) / np.sqrt(samp_size))
# Problem 2 Question 2
c2 = 0.9
t_c_2 = t.ppf(1 - (1 - c2) / 2, df=samp_size - 1)
intervals2 = (avg - (t_c_2 * sd) / np.sqrt(samp_size), avg + (t_c_2 * sd) / np.sqrt(samp_size))
# Problem 2 Question 3
new_sd = 16.836
new_std_err = new_sd / np.sqrt(samp_size)
z_c = norm.ppf(1 - (1 - c1) / 2)
intervals3 = (avg - (z_c * new_sd) / np.sqrt(samp_size), avg + (z_c * new_sd) / np.sqrt(samp_size))
# Problem 2 Question 4
# solve for t_c when lower interval endpoint is zero (mu = 0)
t_c_new = avg / (sd / np.sqrt(samp_size))
# find p value
p_val = 2 * t.cdf(-abs(t_c_new), df=samp_size - 1)
new_c = 1 - p_val
intervals4 = (avg - (t_c_new * sd) / np.sqrt(samp_size), avg + (t_c_new * sd) / np.sqrt(samp_size))
return (samp_size, avg, sd, stand_err, t_c, intervals), (t_c_2, intervals2), (avg, new_std_err, z_c, intervals3), (
t_c_new, p_val, new_c, intervals4)
def student_t(t_input: Tuple[str, float],
radius: float,
size: float,
ignore: bool) -> float:
"""
Function to calculate the false positive fraction for a given sigma level (Mawet et al. 2014).
Parameters
----------
t_input : tuple(str, float)
Tuple with the input type ('sigma' or 'fpf') and the input value.
radius : float
Aperture radius (pix).
size : float
Separation of the aperture center (pix).
ignore : bool
Ignore neighboring apertures of the point source to exclude the self-subtraction lobes.
Returns
-------
float
False positive fraction (FPF).
"""
num_ap = int(math.pi*radius/size)
if ignore:
num_ap -= 2
# Note that the number of degrees of freedom is given by nu = n-1 with n the number of samples.
# The number of samples is equal to the number of apertures minus 1 (i.e. the planet aperture).
# See Section 3 of Mawet et al. (2014) for more details on the Student's t distribution.
if t_input[0] == 'sigma':
t_result = 1. - t.cdf(t_input[1], num_ap-2, loc=0., scale=1.)
elif t_input[0] == 'fpf':
t_result = t.ppf(1. - t_input[1], num_ap-2, loc=0., scale=1.)
return t_result
def test_two_sample_welch_test(self):
sal_a = self.data.loc[self.data['discipline'] == 'A']['salary']
sal_b = self.data.loc[self.data['discipline'] == 'B']['salary']
ttest = tTest(y1=sal_a, y2=sal_b)
test_summary = ttest.test_summary
assert_almost_equal(test_summary['Sample 1 Mean'], np.mean(sal_a))
assert_almost_equal(test_summary['Sample 2 Mean'], np.mean(sal_b))
assert_almost_equal(test_summary['t-statistic'], -3.1386989278486013)
assert_almost_equal(test_summary['degrees of freedom'],
377.89897288941387)
assert_almost_equal(
test_summary['p-value'],
t.cdf(test_summary['t-statistic'],
test_summary['degrees of freedom']) * 2)
assert test_summary['alternative'] == 'two-sided'
assert test_summary['test description'] == "Two-Sample Welch's t-test"
ttest_group = tTest(group=self.data['discipline'],
y1=self.data['salary'])
test_group_summary = ttest_group.test_summary
assert_almost_equal(test_summary['Sample 1 Mean'],
test_group_summary['Sample 1 Mean'])
assert_almost_equal(test_summary['Sample 2 Mean'],
test_group_summary['Sample 2 Mean'])
assert_almost_equal(test_summary['p-value'],
test_group_summary['p-value'])
assert_almost_equal(test_summary['degrees of freedom'],
test_group_summary['degrees of freedom'], 5)
assert_almost_equal(test_summary['t-statistic'],
test_group_summary['t-statistic'])
assert test_group_summary['alternative'] == 'two-sided'
assert test_group_summary[
'test description'] == "Two-Sample Welch's t-test"
def dependent_corr(self, xy, xz, yz, n, twotailed=False, method='steiger'):
"""
Calculates the statistic significance between two dependent correlation coefficients
@param xy: correlation coefficient between x and y
@param xz: correlation coefficient between x and z
@param yz: correlation coefficient between y and z
@param n: number of elements in x, y and z
@param twotailed: whether to calculate a one or two tailed test, only works for 'steiger' method
@param conf_level: confidence level, only works for 'zou' method
@param method: defines the method uses, 'steiger' or 'zou'
@return: t and p-val
"""
if method == 'steiger':
d = xy - xz
determin = 1 - xy * xy - xz * xz - yz * yz + 2 * xy * xz * yz
av = (xy + xz) / 2
cube = (1 - yz) * (1 - yz) * (1 - yz)
t2 = d * np.sqrt(
(n - 1) * (1 + yz) / (((2 * (n - 1) /
(n - 3)) * determin + av * av * cube)))
p = 1 - t.cdf(abs(t2), n - 3)
if twotailed:
p *= 2
return t2, p
elif method == 'zou':
L1 = self.rz_ci(xy, n)[0]
U1 = self.rz_ci(xy, n)[1]
L2 = self.rz_ci(xz, n)[0]
U2 = self.rz_ci(xz, n)[1]
rho_r12_r13 = self.rho_rxy_rxz(xy, xz, yz)
lower = xy - xz - pow((pow((xy - L1), 2) + pow(
(U2 - xz), 2) - 2 * rho_r12_r13 * (xy - L1) * (U2 - xz)), 0.5)
upper = xy - xz + pow((pow((U1 - xy), 2) + pow(
(xz - L2), 2) - 2 * rho_r12_r13 * (U1 - xy) * (xz - L2)), 0.5)
return lower, upper
else:
raise Exception('Wrong method!')
def dependent_corr(xy, xz, yz, n, twotailed=False, conf_level=None, method='steiger'):
"""
Calculates the statistic significance between two dependent correlation coefficients
@param xy: correlation coefficient between x and y
@param xz: correlation coefficient between x and z
@param yz: correlation coefficient between y and z
@param n: number of elements in x, y and z
@param twotailed: whether to calculate a one or two tailed test, only works for 'steiger' method
@param conf_level: confidence level, only works for 'zou' method
@param method: defines the method uses, 'steiger' or 'zou'
@return: t and p-val
"""
if method == 'steiger':
d = xy - xz
determin = 1 - xy ** 2 - xz ** 2 - yz ** 2 + 2 * xy * xz * yz
av = (xy + xz)/2
cube = (1 - yz) * (1 - yz) * (1 - yz)
e = (n - 1) * (1 + yz)/(((2 * (n - 1)/(n - 3)) * determin + (av ** 2) * cube))
if e < 0:
return np.nan, np.nan
t2 = d * np.sqrt(e)
p = 1 - t.cdf(abs(t2), n - 2)
if twotailed:
p *= 2
" p is the probability of the null hypothesis"
return t2, p
elif method == 'zou':
if conf_level==None:
conf_level=0.95
L1 = rz_ci(xy, n, conf_level=conf_level)[0]
U1 = rz_ci(xy, n, conf_level=conf_level)[1]
L2 = rz_ci(xz, n, conf_level=conf_level)[0]
U2 = rz_ci(xz, n, conf_level=conf_level)[1]
rho_r12_r13 = rho_rxy_rxz(xy, xz, yz)
lower = xy - xz - pow((pow((xy - L1), 2) + pow((U2 - xz), 2) - 2 * rho_r12_r13 * (xy - L1) * (U2 - xz)), 0.5)
upper = xy - xz + pow((pow((U1 - xy), 2) + pow((xz - L2), 2) - 2 * rho_r12_r13 * (U1 - xy) * (xz - L2)), 0.5)
return lower, upper
else:
raise Exception('Wrong method!')
def DiscretizeNormalizeParam(tau, k_, model, par):
# This function discretizes the one-step normalized pdf when the
# distribution is parametrically specified
# INPUTS
# tau :[scalar] projection horizon
# k_ :[scalar] coarseness level
# model :[string] specifies the distribution: shiftedLN,.TStudent t.T,Uniform
# par :[struct] model parameters
# OUTPUTS
# xi :[1 x k_] centers of the bins
# f :[1 x k_] discretized pdf of invariant
## Code
# grid
a = -norm.ppf(10**(-15),0,sqrt(tau))
h = 2*a/k_
xi = arange(-a+h,a+h,h)
# discretized initial pdf (standardized)
if model=='shiftedLN':
m, s,_ = ShiftedLNMoments(par)
csi = par.c
mu = par.mu
sig = sqrt(par.sig2)
if sign(par.skew)==1:
M = (m-csi)/s
f = 1/h*(lognorm.cdf(xi+h/2+M,sig,scale=exp(mu-log(s)))-lognorm.cdf(xi-h/2+M,sig,scale=exp(mu-log(s))))
f[k_] = 1/h*(lognorm.cdf(-a+h/2+M,sig,scale=exp(mu-log(s)))-lognorm.cdf(-a+M,sig,scale=exp(mu-log(s))) +\
lognorm.cdf(a+M,sig,scale=exp(mu-log(s)))-lognorm.cdf(a-h/2+M,sig,scale=exp(mu-log(s))))
elif sign(par.skew)==-1:
M = (m+csi)/s
f = 1/h*(lognorm.cdf(-(xi-h/2+M),sig,scale=exp(mu-log(s)))-lognorm.cdf(-(xi+h/2+M),sig,scale=exp(mu-log(s))))
f[k_-1] = 1/h*(lognorm.cdf(-(-a+M),sig,scale=exp(mu-log(s)))-lognorm.cdf(-(-a+h/2+M),sig,scale=exp(mu-log(s))) +\
lognorm.cdf(-(a-h/2+M),sig,scale=exp(mu-log(s)))-lognorm.cdf(-(a+M),sig,scale=exp(mu-log(s))))
elif model=='Student t':
nu = par
f = 1/h*(t.cdf(xi+h/2,nu)-t.cdf(xi-h/2,nu))
f[k_-1] = 1/h*(t.cdf(-a+h/2,nu)-t.cdf(-a,nu) + t.cdf(a,nu)-t.cdf(a-h/2,nu))
elif model=='Uniform':
mu = par.mu
sigma = par.sigma
f = zeros(k_)
f[(xi>=-mu/sigma)&(xi<=(1-mu)/sigma)] = sigma
return xi, f
def independent_t_test(self, data1, data2, alpha):
'''Reference:
BrownLee, Jason, 2019, 'How to Code the Student's t-Test from Scratch in Python', MachineLeanring Mastery, retrieved from: https://machinelearningmastery.com/how-to-code-the-students-t-test-from-scratch-in-python/
'''
rejected = False
tReject = False
pReject = False
# calculate means
mean1, mean2 = np.mean(data1), np.mean(data2)
# calculate standard errors
se1, se2 = sem(data1), sem(data2)
# standard error on the difference between the samples
sed = np.sqrt(se1**2.0 + se2**2.0)
# calculate the t statistic
t_stat = (mean1 - mean2) / sed
# degrees of freedom
df = len(data1) + len(data2) - 2
# calculate the critical value
cv = t.ppf(1.0 - alpha, df)
# calculate the p-value
p = (1.0 - t.cdf(abs(t_stat), df)) * 2.0
# return everything
print('t=%.3f, df=%d, cv=%.3f, p=%.3f' % (t_stat, df, cv, p))
# interpret via critical value
if abs(t_stat) <= cv:
print('Accept null hypothesis that the means are equal.')
else:
print('Reject the null hypothesis that the means are equal.')
tReject = True
# interpret via p-value
if p > alpha:
print('Accept null hypothesis that the means are equal.')
else:
print('Reject the null hypothesis that the means are equal.')
pReject = True
rejected = tReject and pReject
#return t_stat, df, cv, p
return rejected
def independent_ttest(data1,data2,alpha):
from scipy.stats import sem
from scipy.stats import t
from numpy import mean
from math import sqrt
# calcualte means
mean1,mean2 = mean(data1),mean(data2)
# caculate standard errors
se1, se2 = sem(data1),sem(data2)
# standard error on the difference between the samples
sed = sqrt(se1**2.0 + se2**2.0)
# calculate the t statistic
t_stat = (mean1 - mean2) / sed
# degrees of freedom
df = len(data1)+len(data2) - 2
# calculate the critical value
cv = t.ppf(1.0 - alpha, df)
# calculate the p-value
p = (1.0 - t.cdf(abs(t_stat), df)) * 2.0
# return results
return t_stat, df, cv, p
def paired_t_test(y1_score, y2_score, alpha):
"""
成对t检验
:param y1_score: y1
:param y2_score: y2
:param alpha: α
:return: t_stat, df, cv, pv
"""
k = len(y1_score)
d = [y1_score[i] - y2_score[i] for i in range(k)]
d = np.array(d)
# d_ 均值
d_ = np.mean(d)
# s 标准差
s = np.std(d)
# calculate the t statistic
t_stat = abs(k**0.5 * d_ / s)
# degrees of freedom
df = k - 1
cv = t.ppf(1.0 - alpha, df)
pv = (1.0 - t.cdf(t_stat, df)) * 2.0
return t_stat, df, cv, pv
def compute_conf_interval(alpha,
x,
samp_mean,
samp_mean_dev,
var=None,
df=None,
central=True):
if central:
low_val = (1 - alpha) / 2
upp_val = (1 + alpha) / 2
else:
low_val = 1 - alpha
upp_val = alpha
if var is not None:
cdf_arr = norm.cdf(x, samp_mean, samp_mean_dev)
else:
x = (samp_mean - x) / (samp_mean_dev)
x = x[::-1]
cdf_arr = t.cdf(x, df)
low_int = x[cdf_arr < low_val][-1]
upp_int = x[cdf_arr > upp_val][0]
if central:
if var is not None:
print("Alpha: ", alpha, "; Central CI (Gauss): ",
np.round((low_int, upp_int), 2))
else:
print(
"Alpha: ", alpha, "; Central CI (tStudent): ",
np.round((samp_mean + low_int * samp_mean_dev,
samp_mean + upp_int * samp_mean_dev), 2))
else:
if var is not None:
print("Alpha: ", alpha, "; Lower CI (Gauss): ", round(low_int, 2))
print("Alpha: ", alpha, "; Upper CI (Gauss): ", round(upp_int, 2))
else:
print("Alpha: ", alpha, "; Lower CI: ",
round(samp_mean + low_int * samp_mean_dev, 2))
print("Alpha: ", alpha, "; Upper CI: ",
round(samp_mean + upp_int * samp_mean_dev, 2))
def fit_model(y, x, covars=None):
"""
y is n X 1 - phenotype
x is n X 1 - site under test
covars (optional) is n X p
Returns three arrays of (1+p+m) X 1 - coefficients, t-statistic and p-values:
the first is the coefficients array where coefficients[0] if the coef of the intercept
coefficients[-1] if the coef of the site under test (the m from input x)
coefficients[1],..., coefficients[p+1] the coefficient of the covariates
the second array holds the f-statistics - again index 0 if for the intercept, index -1 for site under test and 1 to p+1 for covars
the third array holds the p-values - again index 0 if for the intercept, index -1 for site under test and 1 to p+1 for covars
to sum up - in order to get thecoeffs, p-values and the t-statistic of the site under test (input x) extract coefficients[-1], t-statistic[-1] and p-values[-1]
"""
if x.ndim == 1:
x = x.reshape(-1, 1) # make sure dim is (n,1) and not(n,)
if y.ndim == 1:
y = y.reshape(-1, 1)
X = x
if covars is not None:
X = column_stack((covars, X))
regr = linear_model.LinearRegression(False)
n = X.shape[0] # number of sites
X = np.concatenate((np.ones((n, 1)), X), axis=1)
mdl = regr.fit(X, y)
sse = np.sum(
(mdl.predict(X) - y)**2, axis=0) / float(X.shape[0] - X.shape[1])
se = np.array([
np.sqrt(np.diagonal(sse[i] * np.linalg.inv(np.dot(X.T, X))))
for i in range(sse.shape[0])
])
Ts = mdl.coef_ / se
p = 2 * (1 - t.cdf(np.abs(Ts), y.shape[0] - X.shape[1]))
return mdl.coef_.reshape(-1), Ts.reshape(-1), p.reshape(
-1) #coefficients, t-statistic and p-values
def independent_ttest(data1, data2, alpha):
# calculate means
mean1, mean2 = data1.mean(), data2.mean()
# Standard deviation
std1, std2 = data1.std(), data2.std()
# Standard errors
n1, n2 = len(df_columns), len(df_columns2)
print('n1: ' + str(n1))
print('n2: ' + str(n2))
se1, se2 = std1 / math.sqrt(n1), std2 / math.sqrt(n2)
# standard error on the difference between the samples
sed = math.sqrt(se1**2.0 + se2**2.0)
# calculate the t statistic
t_stat = (mean1 - mean2) / sed
# degrees of freedom
df = len(data1) + len(data2) - 2
# calculate the critical value
cv = t.ppf(1.0 - alpha, df)
# calculate the p-value
p = (1.0 - t.cdf(abs(t_stat), df)) * 2.0
# return everything
return t_stat, df, cv, p
def tExpectedImprovement(self, tau, mean, std, nu=3.0):
"""
Expected Improvement acquisition function. Only to be used with `tStudentProcess` surrogate.
Parameters
----------
tau: float
Best observed function evaluation.
mean: float
Point mean of the posterior process.
std: float
Point std of the posterior process.
Returns
-------
float
Expected improvement.
"""
gamma = (mean - tau - self.eps) / (std + self.eps)
return gamma * std * t.cdf(gamma, df=nu) + std * (1 + (gamma**2 - 1) /
(nu - 1)) * t.pdf(
gamma, df=nu)
def h_ratio_fit(response, contrast) -> Tuple[int, OptimizeResult]:
if isinstance(response[0], np.ndarray):
y, sd = response
else:
y = np.nanmean(response, axis=0)
sd = np.nanstd(response, axis=0)
initial_values = np.array([2.0 * y[-1], 0.25, 4.0])
bounds = ((0, None), (0, 1), (1.0, 10.0))
fit = minimize(h_ratio_ml,
initial_values,
args=(contrast, y, sd),
method="SLSQP",
bounds=bounds)
fit.evaluate = lambda a: h_ratio(fit.x, a)
fit.df = len(y) - len(initial_values)
jac = fit.jac.reshape(1, -1)
fit.var = np.diag(pinv(jac.T.dot(jac)))
fit.parameter_names = ['r_max', 'c_50', 'n']
fit.compare = lambda x: (1 - t.cdf(
np.abs(fit.x - x.x) / np.sqrt(fit.var / fit.df + x.var / x.df), fit.df
+ x.df)) * 2
return fit
def neuropowertable(request):
# Get the template/step status
sid = get_session_id(request)
template = "neuropower/neuropowertable.html"
context = {}
# Initiate peak table
peakform = PeakTableForm()
form = peakform.save(commit=False)
form.SID = sid
# Load model data
parsdata = ParameterModel.objects.filter(SID=sid)[::-1][0]
# Compute peaks
SPM = nib.load(parsdata.location).get_data()
MASK = nib.load(parsdata.masklocation).get_data()
if parsdata.ZorT == 'T':
SPM = -norm.ppf(t.cdf(-SPM, df=float(parsdata.DoF)))
peaks = cluster.cluster(SPM, float(parsdata.ExcZ), MASK)
if len(peaks) < 30:
context[
"text"] = "There are too few peaks for a good estimation. Either the ROI is too small or the screening threshold is too high."
form.err = context["text"]
else:
pvalues = np.exp(-float(parsdata.ExcZ) *
(np.array(peaks.peak) - float(parsdata.ExcZ)))
pvalues = [max(10**(-6), p) for p in pvalues]
peaks['pval'] = pvalues
form.data = peaks
context["peaks"] = peaks.to_html(classes=["table table-striped"])
form.save()
# Get step status
context["steps"] = get_neuropower_steps(template, sid)
return render(request, template, context)
def calculateFairness(communities, predictions):
comm_count = {0: 0, 1: 0}
predicted_count = {0: 0, 1: 0}
for comm in predictions:
comm_code = int(comm)
if (communities[comm_code]['ethnicity'] == 0) or (communities[comm_code]['ethnicity'] == 1):
comm_count[1] += 1
predicted_count[1] += predictions[comm]
else:
comm_count[0] += 1
predicted_count[0] += predictions[comm]
df = comm_count[0]+comm_count[1]-2
if (predicted_count[0] == 0) and (predicted_count[1] == 0):
return 1
means = {0: predicted_count[0]/comm_count[0], 1: predicted_count[1]/comm_count[1]}
variances = {0: 0, 1: 0}
for comm in predictions:
comm_code = int(comm)
if (communities[comm_code]['ethnicity'] == 0) or (communities[comm_code]['ethnicity'] == 1):
variances[1] += (predictions[comm]-means[1])**2
else:
variances[0] += (predictions[comm]-means[0])**2
variances = {0: variances[0]/(comm_count[0]-1), 1: variances[1]/(comm_count[1]-1)}
sigma = ((((comm_count[0]-1)*(variances[0]**2))+((comm_count[1]-1)*(variances[1]**2)))/(comm_count[0]+comm_count[1]-2))**0.5
t_stat = (means[0]-means[1])/(sigma*(((1/comm_count[0])+(1/comm_count[1]))**0.5))
fairness = (1 - t.cdf(abs(t_stat), df)) * 2
fairness = fairness*100
return fairness
def corr_dep_ttest(data1, data2, len_train_set, len_test_set, alpha):
# Implementation of Corrected resampled t -test statistic
# based on https://gist.github.com/jensdebruijn/13e8eeda85eb8644ac2a4ac4c3b8e732
# confidenz level 1 - alpha
# alpha = 0.05
n = len(data1)
differences = [(data1[i] - data2[i]) for i in range(n)]
if np.sum(differences) == 0:
return np.nan, np.nan, np.nan, np.nan
sd = stdev(differences)
divisor = 1 / n * sum(differences)
test_training_ratio = len_test_set / len_train_set
denominator = sqrt(1 / n + test_training_ratio) * sd
t_stat = divisor / denominator
# degrees of freedom
df = n - 1
# calculate the critical value
cv = t.ppf(1.0 - alpha, df)
# calculate the p-value
p = (1.0 - t.cdf(abs(t_stat), df)) * 2.0
# return everything
return t_stat, df, cv, p
def test_tstudent(self):
from scipy.stats import t
import matplotlib.pyplot as plt
fig, ax = plt.subplots(1, 1)
df = 2.74
mean, var, skew, kurt = t.stats(df, moments='mvsk')
x = np.linspace(t.ppf(0.01, df), t.ppf(0.99, df), 100)
ax.plot(x, t.pdf(x, df), 'r-', lw=5, alpha=0.6, label='t pdf')
rv = t(df)
ax.plot(x, rv.pdf(x), 'k-', lw=2, label='frozen pdf')
vals = t.ppf([0.001, 0.5, 0.999], df)
np.allclose([0.001, 0.5, 0.999], t.cdf(vals, df))
r = t.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 one_sample_t(X, SigLevel):
from scipy.stats import t
import numpy as np
nume = np.mean(X, axis=2)
Xvar = np.var(X, axis=2)
denume = np.sqrt(Xvar / X.shape[2])
XT = np.divide(nume, denume)
PvalST = np.zeros(XT.shape)
for ii in range(XT.shape[0]):
for jj in range(XT.shape[1]):
temp = 1-t.cdf(XT[ii,jj], X.shape[2] - 1)
if temp > 0.5 :
PvalST[ii, jj] = 1 - temp
else:
PvalST[ii, jj] = temp
SigST = 1.0 * (PvalST < SigLevel/2)
nSigS = np.sum(SigST, axis=0)
nSigT = np.sum(SigST, axis=1)
statOut = {'T':XT,'Pval':PvalST,'Sig':SigST,'nSigS':nSigS,'nSigT':nSigT}
return statOut #[XT, PvalST, SigST, nSig, nSigT]
def compute_diff_mean(base_case, new_case):
"""
This function computes the mean difference and applies t-test to compute
the p value.
@Input:
base_case: base case data set
new_case: new case data set
@Output:
diff: mean difference
p_value: p value of the t-test
"""
#compute the number of observations for both cases
n_base = len(base_case)
n_new = len(new_case)
#compute the average
average_base = np.mean(base_case.iloc[:,0])
average_new = np.mean(new_case.iloc[:,0])
#compute the standard deviation
var_base = np.var(base_case.iloc[:,0])
var_new = np.var(new_case.iloc[:,0])
#compute the difference of deaths
diff = average_new - average_base
#compute t-score
t_score = np.absolute(diff)/np.sqrt(var_base/n_base+var_new/n_new)
#compute degrees of freedom
#df = ((var_base/n_base + var_new/n_new)**2)/(((var_base/n_base)**2)/(n_base-1) + ((var_new/n_new)**2)/(n_new-1))
#compute the p-value
p_value = t.cdf(t_score, min(n_base-1, n_new-1))
#return result
return diff, 2*(1-p_value)
def show_bootstrap_statistics(clf, X, y, features):
num_features = len(features)
coefs = []
for i in range(num_features):
coefs.append([])
for _ in range(BOOTSTRAP_ITERATIONS):
X_sample, y_sample = resample(X, y)
clf.fit(X_sample, y_sample)
for i, c in enumerate(get_normalized_coefs(clf)):
coefs[i].append(c)
subpoi_index = features.index('SUBPOI')
poi_index = features.index('COMPLEX_POI')
building_index = features.index('Building')
coefs[building_index] = coefs[subpoi_index]
coefs[poi_index] = coefs[subpoi_index]
intervals = []
print()
print('***** Bootstrap statistics *****')
print('{:<20}{:<20}{:<10}{:<10}'.format('Feature', '95% interval',
't-value', 'Pr(>|t|)'))
print()
for i, cs in enumerate(coefs):
values = np.array(cs)
lo = np.percentile(values, 2.5)
hi = np.percentile(values, 97.5)
interval = '({:.3f}, {:.3f})'.format(lo, hi)
tv = np.mean(values) / np.std(values)
pr = (1.0 - t.cdf(x=abs(tv), df=len(values))) * 0.5
stv = '{:.3f}'.format(tv)
spr = '{:.3f}'.format(pr)
print('{:<20}{:<20}{:<10}{:<10}'.format(features[i], interval, stv,
spr))
def compute_waitlist_death_diff(base_case, new_case):
"""
This function computes the difference of deaths between the base case and
another case. It appleis t-test to compute p-value.
@Input:
@base_case: base case death data set
@new_case: new case deathd data set
@Output:
@diff: death difference
@p_value: p value of the test
"""
#count the number of observations in each case
n_base = len(base_case)
n_new = len(new_case)
#compute the average number of deaths
average_base = np.mean(base_case)
average_new = np.mean(new_case)
#compute the variance of deaths
var_base = np.var(base_case)
var_new = np.var(new_case)
#compute the difference of deaths
diff = average_new - average_base
#compute the t score
t_score = np.absolute(diff)/np.sqrt(var_base/n_base+var_new/n_new)
#compute degrees of freedom
#df = ((var_base/n_base + var_new/n_new)**2)/(((var_base/n_base)**2)/(n_base-1) + ((var_new/n_new)**2)/(n_new-1))
#compute p_value
p_value = t.cdf(t_score, min(n_base-1, n_new-1))
#return results
return diff, 2*(1-p_value)
def whelchs_t(a_mu, a_var, b_mu, b_var, a_n, b_n):
"""
:param np.ndarray a_mu:
:param np.ndarray a_var:
:param np.ndarray b_mu:
:param np.ndarray b_var:
:param int a_n:
:param int b_n:
:return float, float: statistic and p-value
"""
df = whelch_satterthwaite_df(a_var, b_var, a_n, b_n)
numerator = a_mu - b_mu # (samples, genes)
denominator = np.sqrt(a_var + b_var) # (samples, genes)
statistic = numerator / denominator # (samples, genes)
# statistic has NaNs where there are no observations of a or b (DivideByZeroError)
statistic[np.isnan(statistic)] = 0
median_statistic = np.median(np.abs(statistic), axis=0)
p = (1 - t.cdf(median_statistic, df)) * 2 # p-value
ci_95 = np.percentile(np.abs(statistic), [2.5, 97.5], axis=0).T
return median_statistic, p, ci_95
def dependent_ttest(data1, data2, alpha): # calculate means mean1, mean2 = mean(data1), mean(data2) # number of paired samples n = len(data1) # sum squared difference between observations d1 = sum([(data1[i]-data2[i])**2 for i in range(n)]) # sum difference between observations d2 = sum([data1[i]-data2[i] for i in range(n)]) # standard deviation of the difference between means sd = sqrt((d1 - (d2**2 / n)) / (n - 1)) # standard error of the difference between the means sed = sd / sqrt(n) # calculate the t statistic t_stat = (mean1 - mean2) / sed # degrees of freedom df = n - 1 # calculate the critical value cv = t.ppf(1.0 - alpha, df) # calculate the p-value p = (1.0 - t.cdf(abs(t_stat), df)) * 2.0 # return everything return t_stat, df, cv, p
