def FPvalue( *args): df_btwn, df_within = __degree_of_freedom_( *args) mss_btwn = __ss_between_( *args) / float( df_btwn) mss_within = __ss_within_( *args) / float( df_within) F = mss_btwn / mss_within P = special.fdtrc( df_btwn, df_within, F) return( F, P)
def welch_anova_np(args, var_equal=False):
"""
args : array like of array likes
A list of groups (lists of floats) which should be compared.
var_equal : boolean
The groups share a common variance.
"""
# Define Welch's ANOVA, which is robust against unequal variances
# see https://statisticsbyjim.com/anova/welchs-anova-compared-to-classic-one-way-anova/
# https://stackoverflow.com/questions/50964427/welchs-anova-in-python
# https://github.com/scipy/scipy/issues/11122
args = [np.asarray(arg, dtype=float) for arg in args]
k = len(args)
ni = np.array([len(arg) for arg in args])
mi = np.array([np.mean(arg) for arg in args])
vi = np.array([np.var(arg, ddof=1) for arg in args])
wi = ni / vi
tmp = np.sum((1 - wi / np.sum(wi))**2 / (ni - 1))
tmp /= (k**2 - 1)
dfbn = k - 1
dfwn = 1 / (3 * tmp)
m = np.sum(mi * wi) / np.sum(wi)
f = np.sum(wi * (mi - m)**2) / (dfbn * (1 + 2 * (dfbn - 1) * tmp))
prob = fdtrc(dfbn, dfwn, f)
return stats.stats.F_onewayResult(f, prob)
def FPvalue(*args):
df_btwn, df_within = __degree_of_freedom_(*args)
mss_btwn = __ss_between_(*args) / float(df_btwn)
mss_within = __ss_within_(*args) / float(df_within)
F = mss_btwn / mss_within
P = special.fdtrc(df_btwn, df_within, F)
return (F, P)
def f_oneway(*args):
n_classes = len(args)
args = [as_float_array(a) for a in args]
n_samples_per_class = np.array([a.shape[0] for a in args])
n_samples = np.sum(n_samples_per_class)
ss_alldata = sum(safe_sqr(a).sum(axis=0) for a in args)
sums_args = [np.asarray(a.sum(axis=0)) for a in args]
square_of_sums_alldata = sum(sums_args)**2
square_of_sums_args = [s**2 for s in sums_args]
sstot = ss_alldata - square_of_sums_alldata / float(n_samples)
ssbn = 0.
for k, _ in enumerate(args):
ssbn += square_of_sums_args[k] / n_samples_per_class[k]
ssbn -= square_of_sums_alldata / float(n_samples)
sswn = sstot - ssbn
dfbn = n_classes - 1
dfwn = n_samples - n_classes
msb = ssbn / float(dfbn)
msw = sswn / float(dfwn)
constant_features_idx = np.where(msw == 0.)[0]
if (np.nonzero(msb)[0].size != msb.size and constant_features_idx.size):
warnings.warn("Features %s are constant." % constant_features_idx,
UserWarning)
f = msb / msw
# flatten matrix to vector in sparse case
f = np.asarray(f).ravel()
prob = special.fdtrc(dfbn, dfwn, f)
return f, prob
def FTest(chi2_1, dof_1, chi2_2, dof_2):
"""
Run F-test.
Compute an F-test to see if a model with extra parameters is
significant compared to a simpler model. The input values are the
(non-reduced) chi^2 values and the numbers of DOF for '1' the
original model and '2' for the new model (with more fit params).
The probability is computed exactly like Sherpa's F-test routine
(in Ciao) and is also described in the Wikipedia article on the
F-test: http://en.wikipedia.org/wiki/F-test
The returned value is the probability that the improvement in
chi2 is due to chance (i.e. a low probability means that the
new fit is quantitatively better, while a value near 1 means
that the new model should likely be rejected).
Parameters
-----------
chi2_1 : Float
Chi-squared value of model with fewer parameters
dof_1 : Int
Degrees of freedom of model with fewer parameters
chi2_2 : Float
Chi-squared value of model with more parameters
dof_2 : Int
Degrees of freedom of model with more parameters
Returns
--------
ft : Float
F-test significance value for the model with the larger number of
components over the other.
"""
delta_chi2 = chi2_1 - chi2_2
if delta_chi2 > 0 and dof_1 != dof_2:
delta_dof = dof_1 - dof_2
new_redchi2 = chi2_2 / dof_2
F = np.float64((delta_chi2 / delta_dof) /
new_redchi2) # fdtr doesn't like float128
ft = fdtrc(delta_dof, dof_2, F)
else:
if delta_chi2 <= 0:
log.warning(
"Chi^2 for Model 2 is larger than Chi^2 for Model 1, cannot preform F-test."
)
elif dof_1 == dof_2:
log.warning(
"Models have equal degrees of freedom, cannot preform F-test.")
ft = False
return ft
def anova(arr):
def _square_of_sums(a):
s = np.sum(a, 0)
if not np.isscalar(s):
return s.astype(float) * s
else:
return float(s) * s
def _sum_of_squares(a):
return np.sum(a * a, 0)
# # If all inputs equivalent return 0, not nan as default behaviour
# if sum([(np.asarray(arr[0]) == x).all() for x in arr[1:]]) == len(arr)-1:
# return 0
args = [np.asarray(arg, dtype=float) for arg in arr]
# ANOVA on N groups, each in its own array
num_groups = len(args)
alldata = np.concatenate(args)
bign = len(alldata)
# Determine the mean of the data, and subtract that from all inputs to a
# variance (via sum_of_sq / sq_of_sum) calculation. Variance is invariance
# to a shift in location, and centering all data around zero vastly
# improves numerical stability.
offset = alldata.mean()
alldata -= offset
sstot = _sum_of_squares(alldata) - (_square_of_sums(alldata) / float(bign))
ssbn = 0
for a in args:
ssbn += _square_of_sums(a - offset) / float(len(a))
# Naming: variables ending in bn/b are for "between treatments", wn/w are
# for "within treatments"
ssbn -= (_square_of_sums(alldata) / float(bign))
sswn = sstot - ssbn
dfbn = num_groups - 1
dfwn = bign - num_groups
msb = ssbn / float(dfbn)
msw = sswn / float(dfwn)
f = msb / msw
if f < 0: # correct rounding errors :/
f = 0
prob = special.fdtrc(dfbn, dfwn, f) # equivalent to stats.f.sf
return prob
def compute_F_statistic_and_pvalue(*args):
"""
Return F statistic an p-value
"""
# Compute degrees of freedom
df_btwn, df_within = __degree_of_freedom_(*args)
# Compute sums of squares
mss_btwn = __ss_between_(*args) / float(df_btwn)
mss_within = __ss_within_(*args) / float(df_within)
# F statistic
F = mss_btwn / mss_within
pvalue = special.fdtrc(df_btwn, df_within, F)
return (F, pvalue, df_btwn, df_within)
def _f_oneway_lower(lifted):
"""Performs a 1-way ANOVA.
Parameters
----------
lifted : FOnewayData
The result of `to_monoid`.
Returns
-------
F-value : float
The computed F-value of the test.
p-value : float
The associated p-value from the F-distribution.
"""
classes = lifted.classes
n_samples_per_class = lifted.n_samples_per_class
n_samples = lifted.n_samples
ss_alldata = lifted.ss_alldata
sums_samples = lifted.sums_samples
sums_alldata = lifted.sums_alldata
n_classes = len(classes)
square_of_sums_alldata = sums_alldata ** 2
square_of_sums_args = {k: s ** 2 for k, s in sums_samples.items()}
sstot = ss_alldata - square_of_sums_alldata / float(n_samples)
ssbn = 0.0
for k in n_samples_per_class:
ssbn += square_of_sums_args[k] / n_samples_per_class[k]
ssbn -= square_of_sums_alldata / float(n_samples)
sswn = sstot - ssbn
dfbn = n_classes - 1
dfwn = n_samples - n_classes
msb = ssbn / float(dfbn)
msw = sswn / float(dfwn)
# constant_features_idx = np.where(msw == 0.0)[0]
# if (np.nonzero(msb)[0].size != msb.size and constant_features_idx.size):
# warnings.warn("Features %s are constant." % constant_features_idx,
# UserWarning)
f = msb / msw
# flatten matrix to vector in sparse case
f = np.asarray(f).ravel()
prob = special.fdtrc(dfbn, dfwn, f)
return f, prob
def linRegstats(x, y, conf):
if size(shape(x)) == 1:
p = 2
n = len(x) # Sample size
else:
p, n = shape(x) # (samples size, # of parameters)
p = p + 1 # add one for intercept
dof = n - p # Degrees of freedom
nov = p - 1 # number of variables
ym = mean(y) # Mean of log recovery
X = vstack((ones(n), x)).T # observed x-variable matrix
XTX = dot(X.T, X)
iXTX = inv(XTX)
bhat = dot(dot(iXTX, X.T), y)
yhat = dot(X, bhat) # Linear fit line
SSE = sum((y - yhat)**2) # Sum of Squared Errors
SST = sum((y - ym)**2) # Sum of Squared Total
SSR = sum((yhat - ym)**2) # Sum of Squared Residuals (SSR = SST - SSE)
R2 = SSR / SST # R^2 Statistic (rval**2)
MSE = SSE / dof # Mean Squared Error (MSE)
MSR = SSR / nov # Mean Squared Residual (MSR)
F = MSR / MSE # F-Statistic
F_p = fdtrc(nov, dof, F) # F-Stat. p-value
# variance of beta estimates :
VARb = MSE * iXTX # diag(VARb) == varB
varB = diag(VARb) # variance of beta hat
seb = sqrt(varB) # vector of standard errors for beta hat
## variance of y estimates :
#VARy = MSE * dot(dot(X, iXTX), X.T)
#varY = diag(VARy) # variance of y hat
#sey = sqrt(varY) # standard errors for yhat
# calculate t-statistic :
t_b = bhat / seb
#t_y = yhat / sey
# calculate p-values :
pval = t.sf(abs(t_b), dof) * 2
tbonf = t.ppf((1 + conf) / 2.0, dof) # uncorrected t*-value
ci_b = [
bhat - tbonf * seb, # Confidence intervals for betas
bhat + tbonf * seb
] # in 2 columns (lower,upper)
#ci_y = [yhat - tbonf*sey, # Confidence intervals for estimates
# yhat + tbonf*sey] # in 2 columns (lower,upper)
resid = y - yhat
#vara = { 'SSR' : SSR,
# 'SSE' : SSE,
# 'SST' : SST,
# 'df' : (nov, dof, n-1),
# 'MSR' : MSR,
# 'MSE' : MSE,
# 'F' : F,
# 'F_pval': F_p,
# 'varY' : varY,
# 'varB' : varB,
# 'SEB' : seb,
# 'SEY' : sey,
# 'tbonf' : tbonf,
# 't_beta': t_b,
# 't_y' : t_y,
# 'pval' : pval,
# 'CIB' : array(ci_b),
# 'CIY' : array(ci_y),
# 'bhat' : bhat,
# 'yhat' : yhat,
# 'R2' : R2,
# 'resid' : resid}
vara = {
'SSR': SSR,
'SSE': SSE,
'SST': SST,
'df': (nov, dof, n - 1),
'MSR': MSR,
'MSE': MSE,
'F': F,
'F_pval': F_p,
'varB': varB,
'SEB': seb,
'tbonf': tbonf,
't_beta': t_b,
'pval': pval,
'CIB': array(ci_b),
'bhat': bhat,
'yhat': yhat,
'R2': R2,
'resid': resid
}
return vara
def glm(x,y,w=1.0):
p,n = shape(x) # sample size
p += 1 # add one for intercept
dof = n - p # degrees of freedom
sig = var(y) # variance
mu = (y + mean(y))/2.0 # initial mean estimate
eta = log(mu) # initial predictor
X = vstack((ones(n), x)).T # observed x-variable matrix
# Newton-Raphson :
converged = False
rtol = 1e-12
dtol = 1e-12
lmbda = 1.0
nIter = 0
deviance = 1
D = 1
ahat = zeros(p) # initial parameters
rel_res = zeros(p) # initial relative residual
maxIter = 100
rel_a = []
dev_a = []
while not converged and nIter < maxIter:
W = diags(w*mu**2/sig, 0) # compute weights
z = eta + (y - mu)/mu # adjusted dependent variable
WX = W.dot(X)
XTWX = dot(X.T, WX)
iXTWX = inv(XTWX)
Wz = W.dot(z)
ahat_n = dot(iXTWX, dot(X.T, Wz))
eta = dot(X, ahat_n) # compute estimates
mu = exp(eta) # linear predictor
# calculate residual :
rel_res = norm(ahat - ahat_n, inf)
rel_a.append(rel_res)
ahat = ahat_n
D_n = sum((y - mu)**2)
deviance = abs(D_n - D)
D = D_n
dev_a.append(deviance)
if rel_res < rtol or deviance < dtol: converged = True
nIter += 1
string = "Newton iteration %d: d (abs) = %.2e, (tol = %.2e) r (rel) = %.2e (tol = %.2e)"
print string % (nIter, deviance, dtol, rel_res, rtol)
# calculate statistics :
varA = diag(iXTWX) # variance of alpha hat
sea = sqrt(varA) # vector of standard errors for alpha hat
t_a = ahat / sea
pval = t.sf(abs(t_a), dof) * 2
conf = 0.95 # 95% confidence interval
tbonf = t.ppf((1 - conf/p), dof) # bonferroni corrected t-value
ci = tbonf*sea # confidence interval for ahat
resid = (y - mu) # 'working' residual
RSS = sum((y - mu)**2) # residual sum of squares
TSS = sum((y - mean(y))**2) # total sum of squares
R2 = (TSS-RSS)/TSS # R2
F = (TSS-RSS)/(p-1) * (n-p)/RSS # F-statistic
F_p = fdtrc(p-1, dof, F) # F-Stat. p-value
# log-likelihood :
L = sum((y*mu - mu**2/2)/(2*sig) - y**2/(2*sig) - 0.5*log(2*pi*sig))
AIC = (-2*L + 2*p)/n # AIC statistic
# estimated error variance :
sighat = 1/(n-p) * RSS
vara = { 'ahat' : ahat,
'yhat' : mu,
'sea' : sea,
'ci' : ci,
'dof' : dof,
'resid' : resid,
'rel_a' : rel_a,
'dev_a' : dev_a,
'R2' : R2,
'F' : F,
'AIC' : AIC,
'sighat': sighat}
return vara
def anovan(x, y, factor_names, conf, interaction=False):
ym = mean(y)
SST = sum((y - ym)**2)
# find the indexes to each of the groups within each treatment :
# n-way analysis
if type(x) == list:
tmt_names = []
tmt_idxs = []
tmt_means = []
tmt_lens = []
X = [] # design matrix
na = float(shape(x)[1]) # Sample size
X.append(ones(na)) # tack on intercept
for x_i in x:
types = unique(x_i)
tmt_names.append(types)
ii = []
means = []
lens = []
for t in types:
i = where(x_i == t)[0]
x_c = zeros(na)
x_c[i] = 1.0
ii.append(i)
lens.append(len(i))
means.append(mean(y[i]))
X.append(x_c)
X = X[:-1] # remove the redundant information
tmt_idxs.append(array(ii))
tmt_means.append(array(means))
tmt_lens.append(array(lens))
tmt_names = array(tmt_names)
tmt_idxs = array(tmt_idxs)
tmt_means = array(tmt_means)
tmt_lens = array(tmt_lens)
# sum of squares between cells :
SSB = 0
a = len(tmt_idxs[0])
b = len(tmt_idxs[1])
dfT = len(y) - 1
dfA = a - 1
dfB = b - 1
dfAB = dfA * dfB
dfE = len(y) - a * b
cell_means = []
for l1 in tmt_idxs[0]:
c_m = []
for l2 in tmt_idxs[1]:
ii = intersect1d(l1, l2)
if ii.size != 0:
c_m.append(mean(y[ii]))
SSB += len(y[ii]) * (mean(y[ii]) - ym)**2
cell_means.append(array(c_m))
cell_means = array(cell_means)
# one-way analysis
else:
na = float(len(x))
tmt_names = unique(x)
X = [] # design matrix
X.append(ones(na)) # tack on intercept
for t in tmt_names:
ii = where(x == t)[0]
# form a column of the design matrix :
x_c = zeros(na)
x_c[ii] = 1.0
# append to the lists :
X.append(x_c)
X = X[:-1] # ensure non-singular matrix
# add rows for interaction terms :
if interaction and type(x) == list:
k = 0
for t in tmt_names[:-1]:
k += len(t)
for i, x1 in enumerate(X[1:k]):
for x2 in X[k:]:
X.append(x1 * x2)
X = array(X).T # design matrix is done
# calculate statistics :
SS = array([])
inter_names = []
for il, nl, name, mul in zip(tmt_idxs, tmt_lens, factor_names, tmt_means):
SS = append(SS, sum( nl*(mul - ym)**2))
inter_names.append(name)
if interaction:
inter_names.append(inter_names[0] + ' x ' + inter_names[1])
SS = append(SS, SSB - SS[0] - SS[1])
# fit the data to the model :
muhat = dot( dot( inv(dot(X.T, X)), X.T), y)
yhat = dot(X, muhat)
resid = y - yhat
SSE = SST - sum(SS)
# calculate mean-squares :
MSA = SS[0] / dfA
MSB = SS[1] / dfB
MSE = SSE / dfE
# calculate F-statistics :
FA = MSA / MSE
FB = MSB / MSE
# calculate p-values:
pA = fdtrc(dfA, dfE, FA)
pB = fdtrc(dfB, dfE, FB)
if interaction :
MSAB = SS[2] / dfAB
FAB = MSAB / MSE
pAB = fdtrc(dfAB, dfE, FAB)
vara = {'tmt_names' : tmt_names,
'tmt_means' : tmt_means,
'tmt_lens' : tmt_lens,
'tmt_idxs' : tmt_idxs,
'cell_means': cell_means,
'SST' : SST,
'SSB' : SSB,
'SSE' : SSE,
'SS' : SS,
'MSA' : MSA,
'MSB' : MSB,
'MSAB' : MSAB,
'MSE' : MSE,
'FA' : FA,
'FB' : FB,
'FAB' : FAB,
'dfA' : dfA,
'dfB' : dfB,
'dfAB' : dfAB,
'dfE' : dfE,
'dfT' : dfT,
'pA' : pA,
'pB' : pB,
'pAB' : pAB,
'i_names' : inter_names,
'muhat' : muhat,
'yhat' : yhat,
'resid' : resid}
else :
vara = {'tmt_names' : tmt_names,
'tmt_means' : tmt_means,
'tmt_lens' : tmt_lens,
'tmt_idxs' : tmt_idxs,
'cell_means': cell_means,
'SST' : SST,
'SSB' : SSB,
'SSE' : SSE,
'SS' : SS,
'MSA' : MSA,
'MSB' : MSB,
'MSE' : MSE,
'FA' : FA,
'FB' : FB,
'dfA' : dfA,
'dfB' : dfB,
'dfE' : dfE,
'dfT' : dfT,
'pA' : pA,
'pB' : pB,
'i_names' : inter_names,
'muhat' : muhat,
'yhat' : yhat,
'resid' : resid}
return vara
def nonlinRegstats(x, y, f, beta0, conf):
def residual(beta, x, y, f):
err = y - f(x, beta)
return err
out = leastsq(residual, beta0, args=(x,y,f), full_output=True)
bhat = out[0]
J = out[1]
nfo = out[2]
fjac = nfo['fjac']
ipvt = nfo['ipvt']
msg = out[3]
ier = out[4]
n = float(len(x)) # Sample size
p = float(len(beta0)) # number of parameters
dof = max(0, n - p) # Degrees of freedom
nov = p - 1 # number of variables
xm = mean(x) # Mean of time values
ym = mean(y) # Mean of log recovery
yhat = f(x, bhat) # non-linear fit line
SSE = sum((y - yhat)**2) # Sum of Squared Errors
SST = sum((y - ym )**2) # Sum of Squared Total
SSR = sum((yhat - ym )**2) # Sum of Squared Residuals (SSR = SST - SSE)
R2 = SSR / SST # R^2 Statistic (rval**2)
MSE = SSE / dof # Mean Squared Error (MSE)
MSR = SSR / nov # Mean Squared Residual (MSR)
F = MSR / MSE # F-Statistic
F_p = fdtrc(nov, dof, F) # F-Stat. p-value
# covariance matrix:
covB = MSE * J
# Vector of standard errors for beta hat (seb) and yhat (sey)
seb = sqrt(diag(covB))
sey = sqrt(MSE * (1.0/n + (x - xm)**2 / sum((x - xm)**2) ) )
tbonf = t.ppf((1+conf)/2.0, dof) # uncorrected t*-value
# calculate t-statistic :
t_b = bhat / seb
t_y = yhat / sey
# calculate p-values :
pval = t.sf(abs(t_b), dof) * 2
# Confidence intervals
ci_b = [bhat - tbonf*seb,
bhat + tbonf*seb]
ci_y = [yhat - tbonf*sey,
yhat + tbonf*sey]
resid = y - yhat
vara = { 'SSR' : SSR,
'SSE' : SSE,
'SST' : SST,
'df' : (nov, dof, n-1),
'MSR' : MSR,
'MSE' : MSE,
'F' : F,
'F_p' : F_p,
'SEB' : seb,
'SEY' : sey,
't_beta': t_b,
't_y' : t_y,
'pval' : pval,
't' : tbonf,
'CIB' : array(ci_b),
'CIY' : array(ci_y),
'bhat' : bhat,
'yhat' : yhat,
'R2' : R2,
'covB' : covB,
'J' : J,
'fjac' : fjac,
'resid' : resid}
return vara
def linRegstats(x, y, conf):
if size(shape(x)) == 1:
p = 2
n = float(len(x)) # Sample size
else:
p,n = shape(x) # (samples size, # of parameters)
n = float(n)
p = p + 1 # add one for intercept
dof = n - p # Degrees of freedom
nov = p - 1 # number of variables
ym = mean(y) # Mean of log recovery
X = vstack((ones(n), x)).T # observed x-variable matrix
bhat = dot( dot( inv(dot(X.T, X)), X.T), y)
yhat = dot(X, bhat) # Linear fit line
SSE = sum((y - yhat)**2) # Sum of Squared Errors
SST = sum((y - ym )**2) # Sum of Squared Total
SSR = sum((yhat - ym )**2) # Sum of Squared Residuals (SSR = SST - SSE)
R2 = SSR / SST # R^2 Statistic (rval**2)
MSE = SSE / dof # Mean Squared Error (MSE)
MSR = SSR / nov # Mean Squared Residual (MSR)
F = MSR / MSE # F-Statistic
F_p = fdtrc(nov, dof, F) # F-Stat. p-value
# variance of beta estimates :
VARb = MSE * inv(dot(X.T, X)) # diag(VARb) == varB
varB = diag(VARb) # variance of beta hat
seb = sqrt(varB) # vector of standard errors for beta hat
# variance of y estimates :
VARy = MSE * dot(dot(X, inv(dot(X.T, X))), X.T)
varY = diag(VARy) # variance of y hat
sey = sqrt(varY) # standard errors for yhat
# calculate t-statistic :
t_b = bhat / seb
t_y = yhat / sey
# calculate p-values :
pval = t.sf(abs(t_b), dof) * 2
tbonf = t.ppf((1+conf)/2.0, dof) # uncorrected t*-value
ci_b = [bhat - tbonf*seb, # Confidence intervals for betas
bhat + tbonf*seb] # in 2 columns (lower,upper)
ci_y = [yhat - tbonf*sey, # Confidence intervals for betas
yhat + tbonf*sey] # in 2 columns (lower,upper)
resid = y - yhat
vara = { 'SSR' : SSR,
'SSE' : SSE,
'SST' : SST,
'df' : (nov, dof, n-1),
'MSR' : MSR,
'MSE' : MSE,
'F' : F,
'F_pval': F_p,
'varY' : varY,
'varB' : varB,
'SEB' : seb,
'SEY' : sey,
'tbonf' : tbonf,
't_beta': t_b,
't_y' : t_y,
'pval' : pval,
'CIB' : array(ci_b),
'CIY' : array(ci_y),
'bhat' : bhat,
'yhat' : yhat,
'R2' : R2,
'resid' : resid}
return vara
def durbin(*args):
# taken verbatim from scipy.stats._support.abut
def _abut(source, *args):
source = np.asarray(source)
if len(source.shape) == 1:
width = 1
source = np.resize(source, [source.shape[0], width])
else:
width = source.shape[1]
for addon in args:
if len(addon.shape) == 1:
width = 1
addon = np.resize(addon, [source.shape[0], width])
else:
width = source.shape[1]
if len(addon) < len(source):
addon = np.resize(addon, [source.shape[0], addon.shape[1]])
elif len(addon) > len(source):
source = np.resize(source, [addon.shape[0], source.shape[1]])
source = np.concatenate((source, addon), 1)
return source
# also taken from scipy.stats, but ignores everything under 0.
def _rankposdata(a):
a = np.ravel(a)
b = np.argsort(a)
a = a[b]
n = len(a)
dupcount = 0
oldrank = -1
sumranks = 0
newarray = np.zeros(n, float)
for i in range(n):
if a[i] <= 0.:
newarray[b[i]] = 0.
continue
oldrank += 1
sumranks += oldrank
dupcount += 1
if i == n - 1 or a[i] != a[i + 1]:
averrank = float(sumranks) / float(dupcount) + 1
for j in range(i - dupcount + 1, i + 1):
newarray[b[j]] = averrank
sumranks = 0
dupcount = 0
return newarray
b = len(args)
if b < 3:
raise ValueError('Less than 3 levels. Durbin test is not appropriate')
k = len(args[0])
for i in range(1, b):
if len(args[i]) != k:
raise ValueError('Unequal N in durbin. Aborting.')
data = _abut(*args)
data = data.astype(float)
A = 0.
t = data.shape[1]
R = np.zeros(t, float)
rs = np.zeros(t, int)
for i in range(len(data)):
data[i] = _rankposdata(data[i])
for j in range(len(data[i])):
A += pow(data[i, j], 2.)
R[j] += data[i, j]
if data[i, j] > 0.:
rs[j] += 1
r = np.mean(rs)
t = float(t)
b = float(b)
k = float(k)
C = b * k * pow(k + 1, 2) / 4
T1 = (t - 1) * sum([pow(x, 2) - r * C for x in R]) / (A - C)
T2 = (T1 / (t - 1)) / ((b * k - b - T1) / (b * k - b - t + 1))
print(data)
print(R)
print("r = %g, t = %g, b = %g, k = %g, C = %g, A = %g, T1 = %g" % (r, t, b, k, C, A, T1))
return T2, fdtrc(k - 1, b * k - b - t + 1, T2)
def grpStats(x, y, alpha, interaction=False):
grp = unique(x)
sig = std(y)
t = float(len(grp))
na = float(len(y))
ymt = mean(y)
idx = [] # index list corresponding to group
yms = [] # mean of groups
ss = [] # standard deviations of groups
nums = [] # number of elements in group
sems = [] # standard errors of groups
X = [] # design matrix
X.append(ones(na)) # tack on intercept
for g in grp:
ii = where(x == g)[0]
# form a column of the design matrix :
x_c = zeros(na)
x_c[ii] = 1.0
# collect necessary statistics :
n = float(len(ii))
ym = mean(y[ii])
s = std(y[ii])
sem = s / sqrt(n)
# append to the lists :
X.append(x_c)
idx.append(ii)
yms.append(ym)
ss.append(s)
nums.append(n)
sems.append(sem)
X = array(X[:-1]).T # remove the redundant information
idx = array(idx)
yms = array(yms)
ss = array(ss)
nums = array(nums)
sems = array(sems)
pair = []
pair_mean = []
hsd_ci = []
# sort from largest to smallest
srt = argsort(yms)[::-1]
grp_s = grp[srt]
yms_s = yms[srt]
num_s = nums[srt]
# calculate the Tukey confidence intervals :
for i,(g1, ym1, n1) in enumerate(zip(grp_s, yms_s, num_s)):
for g2, ym2, n2 in zip(grp_s[i+1:][::-1],
yms_s[i+1:][::-1],
num_s[i+1:][::-1]):
p_m = ym1 - ym2
c = qsturng(alpha, t, na - t) / sqrt(2) * sig * sqrt(1/n1 + 1/n2)
pair_mean.append(p_m)
pair.append(g1 + ' - ' + g2)
hsd_ci.append(c)
srt = argsort(pair_mean)
pair = array(pair)[srt]
pair_mean = array(pair_mean)[srt]
hsd_ci = array(hsd_ci)[srt]
# calculate more statistics :
SSB = sum( nums * (yms - ymt)**2 )
SSW = sum((nums - 1) * ss**2)
MSW = SSW / (na - t)
MSB = SSB / (t - 1)
f = MSB / MSW
p = fdtrc((t - 1), (na - t), f)
# fit the data to the model :
muhat = dot( dot( inv(dot(X.T, X)), X.T), y)
yhat = dot(X, muhat)
resid = y - yhat
vara = {'grp_means' : yms,
'grp_SDs' : ss,
'grp_SEMs' : sems,
'grp_names' : grp,
'grp_lens' : nums,
'grp_dof' : t - 1,
'dof' : na - t,
'F' : f,
'MSW' : MSW,
'MSB' : MSB,
'alpha' : alpha,
'pval' : p,
'pairs' : pair,
'pair_means' : pair_mean,
'HSD_CIs' : hsd_ci,
'muhat' : muhat,
'yhat' : yhat,
'resid' : resid}
return vara
def f_oneway(*args):
"""Performs a 1-way ANOVA.
The one-way ANOVA tests the null hypothesis that 2 or more groups have
the same population mean. The test is applied to samples from two or
more groups, possibly with differing sizes.
Read more in the :ref:`User Guide <univariate_feature_selection>`.
Parameters
----------
*args : array_like, sparse matrices
sample1, sample2... The sample measurements should be given as
arguments.
Returns
-------
F-value : float
The computed F-value of the test.
p-value : float
The associated p-value from the F-distribution.
Notes
-----
The ANOVA test has important assumptions that must be satisfied in order
for the associated p-value to be valid.
1. The samples are independent
2. Each sample is from a normally distributed population
3. The population standard deviations of the groups are all equal. This
property is known as homoscedasticity.
If these assumptions are not true for a given set of data, it may still be
possible to use the Kruskal-Wallis H-test (`scipy.stats.kruskal`_) although
with some loss of power.
The algorithm is from Heiman[2], pp.394-7.
See ``scipy.stats.f_oneway`` that should give the same results while
being less efficient.
References
----------
.. [1] Lowry, Richard. "Concepts and Applications of Inferential
Statistics". Chapter 14.
http://faculty.vassar.edu/lowry/ch14pt1.html
.. [2] Heiman, G.W. Research Methods in Statistics. 2002.
"""
n_classes = len(args)
args = [as_float_array(a) for a in args]
n_samples_per_class = np.array([a.shape[0] for a in args])
n_samples = np.sum(n_samples_per_class)
ss_alldata = sum(safe_sqr(a).sum(axis=0) for a in args)
sums_args = [np.asarray(a.sum(axis=0)) for a in args]
square_of_sums_alldata = sum(sums_args)**2
square_of_sums_args = [s**2 for s in sums_args]
sstot = ss_alldata - square_of_sums_alldata / float(n_samples)
ssbn = 0.
for k, _ in enumerate(args):
ssbn += square_of_sums_args[k] / n_samples_per_class[k]
ssbn -= square_of_sums_alldata / float(n_samples)
sswn = sstot - ssbn
dfbn = n_classes - 1
dfwn = n_samples - n_classes
msb = ssbn / float(dfbn)
msw = sswn / float(dfwn)
constant_features_idx = np.where(msw == 0.)[0]
if (np.nonzero(msb)[0].size != msb.size and constant_features_idx.size):
warnings.warn("Features %s are constant." % constant_features_idx,
UserWarning)
f = msb / msw
# flatten matrix to vector in sparse case
f = np.asarray(f).ravel()
prob = special.fdtrc(dfbn, dfwn, f)
return f, prob
def h2o_f_oneway(*args):
"""Performs a 1-way ANOVA.
The one-way ANOVA tests the null hypothesis that 2 or more groups have
the same population mean. The test is applied to samples from two or
more groups, possibly with differing sizes.
Parameters
----------
sample1, sample2, ... : array_like, H2OFrames, shape=(n_classes,)
The sample measurements should be given as varargs (*args).
A slice of the original input frame for each class in the
target feature.
Returns
-------
f : float
The computed F-value of the test.
prob : float
The associated p-value from the F-distribution.
Notes
-----
The ANOVA test has important assumptions that must be satisfied in order
for the associated p-value to be valid.
1. The samples are independent
2. Each sample is from a normally distributed population
3. The population standard deviations of the groups are all equal. This
property is known as homoscedasticity.
If these assumptions are not true for a given set of data, it may still be
possible to use the Kruskal-Wallis H-test (``scipy.stats.kruskal``) although
with some loss of power.
The algorithm is from Heiman[2], pp.394-7.
See ``scipy.stats.f_oneway`` and ``sklearn.feature_selection.f_oneway``.
References
----------
.. [1] Lowry, Richard. "Concepts and Applications of Inferential
Statistics". Chapter 14.
http://faculty.vassar.edu/lowry/ch14pt1.html
.. [2] Heiman, G.W. Research Methods in Statistics. 2002.
"""
n_classes = len(args)
# sklearn converts everything to float here. Rather than do so,
# we will test for total numericism and fail out if it's not 100%
# numeric.
if not all([all([X.isnumeric() for X in args])]):
raise ValueError("All features must be entirely numeric for F-test")
n_samples_per_class = [X.shape[0] for X in args]
n_samples = np.sum(n_samples_per_class)
# compute the sum of squared values in each column, and then compute the column
# sums of all of those intermittent rows rbound together
ss_alldata = rbind_all(*[X.apply(lambda x: (x * x).sum())
for X in args]).apply(lambda x: x.sum())
# compute the sum of each column for each X in args, then rbind them all
# and sum them up, finally squaring them. Tantamount to the squared sum
# of each complete column. Note that we need to add a tiny fraction to ensure
# all are real numbers for the rbind...
sum_args = [X.apply(lambda x: x.sum() + 1e-12).asnumeric()
for X in args] # col sums
square_of_sums_alldata = rbind_all(*sum_args).apply(lambda x: x.sum())
square_of_sums_alldata *= square_of_sums_alldata
square_of_sums_args = [s * s for s in sum_args]
sstot = ss_alldata - square_of_sums_alldata / float(n_samples)
ssbn = None # h2o frame
for k, _ in enumerate(args):
tmp = square_of_sums_args[k] / n_samples_per_class[k]
ssbn = tmp if ssbn is None else (ssbn + tmp)
ssbn -= square_of_sums_alldata / float(n_samples)
sswn = sstot - ssbn
dfbn = n_classes - 1
dfwn = n_samples - n_classes
msb = ssbn / float(dfbn)
msw = sswn / float(dfwn)
constant_feature_idx = (msw == 0)
constant_feature_sum = constant_feature_idx.sum() # sum of ones
nonzero_size = (msb != 0).sum()
if nonzero_size != msb.shape[1] and constant_feature_sum:
warnings.warn(
"Features %s are constant." %
np.arange(msw.shape[1])[constant_feature_idx], UserWarning)
f = (msb / msw)
# convert to numpy ndarray for special
f = f.as_data_frame(use_pandas=True).iloc[0].values
# compute prob
prob = special.fdtrc(dfbn, dfwn, f)
return f, prob
def durbin(*args):
# taken verbatim from scipy.stats._support.abut
def _abut(source, *args):
source = np.asarray(source)
if len(source.shape) == 1:
width = 1
source = np.resize(source, [source.shape[0], width])
else:
width = source.shape[1]
for addon in args:
if len(addon.shape) == 1:
width = 1
addon = np.resize(addon, [source.shape[0], width])
else:
width = source.shape[1]
if len(addon) < len(source):
addon = np.resize(addon, [source.shape[0], addon.shape[1]])
elif len(addon) > len(source):
source = np.resize(source,
[addon.shape[0], source.shape[1]])
source = np.concatenate((source, addon), 1)
return source
# also taken from scipy.stats, but ignores everything under 0.
def _rankposdata(a):
a = np.ravel(a)
b = np.argsort(a)
a = a[b]
n = len(a)
dupcount = 0
oldrank = -1
sumranks = 0
newarray = np.zeros(n, float)
for i in range(n):
if a[i] <= 0.:
newarray[b[i]] = 0.
continue
oldrank += 1
sumranks += oldrank
dupcount += 1
if i == n - 1 or a[i] != a[i + 1]:
averrank = float(sumranks) / float(dupcount) + 1
for j in range(i - dupcount + 1, i + 1):
newarray[b[j]] = averrank
sumranks = 0
dupcount = 0
return newarray
b = len(args)
if b < 3:
raise ValueError(
'Less than 3 levels. Durbin test is not appropriate')
k = len(args[0])
for i in range(1, b):
if len(args[i]) != k:
raise ValueError('Unequal N in durbin. Aborting.')
data = _abut(*args)
data = data.astype(float)
A = 0.
t = data.shape[1]
R = np.zeros(t, float)
rs = np.zeros(t, int)
for i in range(len(data)):
data[i] = _rankposdata(data[i])
for j in range(len(data[i])):
A += pow(data[i, j], 2.)
R[j] += data[i, j]
if data[i, j] > 0.:
rs[j] += 1
r = np.mean(rs)
t = float(t)
b = float(b)
k = float(k)
C = b * k * pow(k + 1, 2) / 4
T1 = (t - 1) * sum([pow(x, 2) - r * C for x in R]) / (A - C)
T2 = (T1 / (t - 1)) / ((b * k - b - T1) / (b * k - b - t + 1))
print(data)
print(R)
print("r = %g, t = %g, b = %g, k = %g, C = %g, A = %g, T1 = %g" %
(r, t, b, k, C, A, T1))
return T2, fdtrc(k - 1, b * k - b - t + 1, T2)
def glm(x,y,w=1.0):
p,n = shape(x) # sample size
p += 1 # add one for intercept
dof = n - p # degrees of freedom
sig = var(y) # variance
mu = (y + mean(y))/2.0 # initial mean estimate
eta = log(mu) # initial predictor
X = vstack((ones(n), x)).T # observed x-variable matrix
# Newton-Raphson :
converged = False
rtol = 1e-15
dtol = 1e-15
lmbda = 1.0
nIter = 0
deviance = 1
D = 1
ahat = zeros(p) # initial parameters
rel_res = zeros(p) # initial relative residual
maxIter = 65
rel_a = []
dev_a = []
while not converged and nIter < maxIter:
W = diags(w*mu**2/sig, 0) # compute weights
z = eta + (y - mu)/mu # adjusted dependent variable
WX = W.dot(X)
XTWX = dot(X.T, WX)
iXTWX = inv(XTWX)
Wz = W.dot(z)
ahat_n = dot(iXTWX, dot(X.T, Wz))
eta = dot(X, ahat_n) # compute estimates
mu = exp(eta) # linear predictor
# calculate residual :
rel_res = norm(ahat - ahat_n, inf)
rel_a.append(rel_res)
ahat = ahat_n
D_n = sum((y - mu)**2)
deviance = abs(D_n - D)
D = D_n
dev_a.append(deviance)
if rel_res < rtol or deviance < dtol: converged = True
nIter += 1
string = "Newton iteration %d: d (abs) = %.2e, (tol = %.2e) r (rel) = %.2e (tol = %.2e)"
print string % (nIter, deviance, dtol, rel_res, rtol)
# calculate statistics :
varA = diag(iXTWX) # variance of alpha hat
sea = sqrt(varA) # vector of standard errors for alpha hat
t_a = ahat / sea
pval = t.sf(abs(t_a), dof) * 2
conf = 0.95 # 95% confidence interval
tbonf = t.ppf((1 - conf/p), dof) # bonferroni corrected t-value
ci = tbonf*sea # confidence interval for ahat
resid = (y - mu) # 'working' residual
RSS = sum((y - mu)**2) # residual sum of squares
TSS = sum((y - mean(y))**2) # total sum of squares
R2 = (TSS-RSS)/TSS # R2
F = (TSS-RSS)/(p-1) * (n-p)/RSS # F-statistic
F_p = fdtrc(p-1, dof, F) # F-Stat. p-value
# log-likelihood :
L = sum((y*mu - mu**2/2)/(2*sig) - y**2/(2*sig) - 0.5*log(2*pi*sig))
AIC = (-2*L + 2*p)/n # AIC statistic
# estimated error variance :
sighat = 1/(n-p) * RSS
vara = { 'ahat' : ahat,
'yhat' : mu,
'sea' : sea,
'ci' : ci,
'dof' : dof,
'resid' : resid,
'rel_a' : rel_a,
'dev_a' : dev_a,
'R2' : R2,
'F' : F,
'AIC' : AIC,
'sighat': sighat}
return vara
def h2o_f_oneway(*args):
"""Performs a 1-way ANOVA.
The one-way ANOVA tests the null hypothesis that 2 or more groups have
the same population mean. The test is applied to samples from two or
more groups, possibly with differing sizes.
Parameters
----------
sample1, sample2, ... : array_like, H2OFrames, shape=(n_classes,)
The sample measurements should be given as varargs (*args).
A slice of the original input frame for each class in the
target feature.
Returns
-------
f : float
The computed F-value of the test.
prob : float
The associated p-value from the F-distribution.
Notes
-----
The ANOVA test has important assumptions that must be satisfied in order
for the associated p-value to be valid.
1. The samples are independent
2. Each sample is from a normally distributed population
3. The population standard deviations of the groups are all equal. This
property is known as homoscedasticity.
If these assumptions are not true for a given set of data, it may still be
possible to use the Kruskal-Wallis H-test (``scipy.stats.kruskal``) although
with some loss of power.
The algorithm is from Heiman[2], pp.394-7.
See ``scipy.stats.f_oneway`` and ``sklearn.feature_selection.f_oneway``.
References
----------
.. [1] Lowry, Richard. "Concepts and Applications of Inferential
Statistics". Chapter 14.
http://faculty.vassar.edu/lowry/ch14pt1.html
.. [2] Heiman, G.W. Research Methods in Statistics. 2002.
"""
n_classes = len(args)
# sklearn converts everything to float here. Rather than do so,
# we will test for total numericism and fail out if it's not 100%
# numeric.
if not all([all([X.isnumeric() for X in args])]):
raise ValueError("All features must be entirely numeric for F-test")
n_samples_per_class = [X.shape[0] for X in args]
n_samples = np.sum(n_samples_per_class)
# compute the sum of squared values in each column, and then compute the column
# sums of all of those intermittent rows rbound together
ss_alldata = rbind_all(*[X.apply(lambda x: (x*x).sum()) for X in args]).apply(lambda x: x.sum())
# compute the sum of each column for each X in args, then rbind them all
# and sum them up, finally squaring them. Tantamount to the squared sum
# of each complete column. Note that we need to add a tiny fraction to ensure
# all are real numbers for the rbind...
sum_args = [X.apply(lambda x: x.sum() + 1e-12).asnumeric() for X in args] # col sums
square_of_sums_alldata = rbind_all(*sum_args).apply(lambda x: x.sum())
square_of_sums_alldata *= square_of_sums_alldata
square_of_sums_args = [s*s for s in sum_args]
sstot = ss_alldata - square_of_sums_alldata / float(n_samples)
ssbn = None # h2o frame
for k, _ in enumerate(args):
tmp = square_of_sums_args[k] / n_samples_per_class[k]
ssbn = tmp if ssbn is None else (ssbn + tmp)
ssbn -= square_of_sums_alldata / float(n_samples)
sswn = sstot - ssbn
dfbn = n_classes - 1
dfwn = n_samples - n_classes
msb = ssbn / float(dfbn)
msw = sswn / float(dfwn)
constant_feature_idx = (msw == 0)
constant_feature_sum = constant_feature_idx.sum() # sum of ones
nonzero_size = (msb != 0).sum()
if nonzero_size != msb.shape[1] and constant_feature_sum:
warnings.warn("Features %s are constant." % np.arange(msw.shape[1])[constant_feature_idx], UserWarning)
f = (msb / msw)
# convert to numpy ndarray for special
f = f.as_data_frame(use_pandas=True).iloc[0].values
# compute prob
prob = special.fdtrc(dfbn, dfwn, f)
return f, prob
def f_oneway(*args):
"""Performs a 1-way ANOVA.
The one-way ANOVA tests the null hypothesis that 2 or more groups have
the same population mean. The test is applied to samples from two or
more groups, possibly with differing sizes.
Read more in the :ref:`User Guide <univariate_feature_selection>`.
Parameters
----------
sample1, sample2, ... : array_like, sparse matrices
The sample measurements should be given as arguments.
Returns
-------
F-value : float
The computed F-value of the test.
p-value : float
The associated p-value from the F-distribution.
Notes
-----
The ANOVA test has important assumptions that must be satisfied in order
for the associated p-value to be valid.
1. The samples are independent
2. Each sample is from a normally distributed population
3. The population standard deviations of the groups are all equal. This
property is known as homoscedasticity.
If these assumptions are not true for a given set of data, it may still be
possible to use the Kruskal-Wallis H-test (`scipy.stats.kruskal`_) although
with some loss of power.
The algorithm is from Heiman[2], pp.394-7.
See ``scipy.stats.f_oneway`` that should give the same results while
being less efficient.
References
----------
.. [1] Lowry, Richard. "Concepts and Applications of Inferential
Statistics". Chapter 14.
http://faculty.vassar.edu/lowry/ch14pt1.html
.. [2] Heiman, G.W. Research Methods in Statistics. 2002.
"""
n_classes = len(args)
args = [as_float_array(a) for a in args]
n_samples_per_class = np.array([a.shape[0] for a in args])
n_samples = np.sum(n_samples_per_class)
ss_alldata = sum(safe_sqr(a).sum(axis=0) for a in args)
sums_args = [np.asarray(a.sum(axis=0)) for a in args]
square_of_sums_alldata = sum(sums_args) ** 2
square_of_sums_args = [s ** 2 for s in sums_args]
sstot = ss_alldata - square_of_sums_alldata / float(n_samples)
ssbn = 0.
for k, _ in enumerate(args):
ssbn += square_of_sums_args[k] / n_samples_per_class[k]
ssbn -= square_of_sums_alldata / float(n_samples)
sswn = sstot - ssbn
dfbn = n_classes - 1
dfwn = n_samples - n_classes
msb = ssbn / float(dfbn)
msw = sswn / float(dfwn)
constant_features_idx = np.where(msw == 0.)[0]
if (np.nonzero(msb)[0].size != msb.size and constant_features_idx.size):
warnings.warn("Features %s are constant." % constant_features_idx,
UserWarning)
f = msb / msw
# flatten matrix to vector in sparse case
f = np.asarray(f).ravel()
prob = special.fdtrc(dfbn, dfwn, f)
return f, prob
def polynomtest(x, y, degree=2):
y_prime = y - y.mean()
ss_tot = np.sum(y_prime**2)
print('ss_tot: ' + str(ss_tot))
### first linear regression
b_linear, rsq_linear = linreg.linreg(x, y)
df_linear = len(y) - 2
ypred_linear = b_linear[1] * x + b_linear[0]
error_linear = y - ypred_linear
error_ss_linear = np.sum(error_linear**2)
rsq_linear2 = 1. - (error_ss_linear / ss_tot)
df_linear = len(y) - 2
print('df_linear: ' + str(df_linear))
print('b_linear: ' + str(b_linear))
print('rsq_linear: ' + str(rsq_linear))
print('rsq_linear2: ' + str(rsq_linear2))
print('error_ss_linear: ' + str(error_ss_linear))
print('')
if degree <= 1:
return b_linear
else:
### next quadratic
quadratic_b = np.polyfit(x, y, 2)
ypred_quadratic = np.polyval(quadratic_b, x)
error_quadratic = y - ypred_quadratic
error_ss_quadratic = np.sum(error_quadratic**2)
rsq_quadratic = 1. - (error_ss_quadratic / ss_tot)
df_quadratic = len(y) - 3
fstat2_quadratic = (error_ss_quadratic - error_ss_linear) / (
error_ss_quadratic / df_quadratic)
f_stat_quadratic = df_quadratic * (rsq_quadratic -
rsq_linear) / (1. - rsq_quadratic)
p_quadratic = special.fdtrc(2, df_quadratic, f_stat_quadratic)
print('df_quadratic: ' + str(df_quadratic))
print('quadratic_b: ' + str(quadratic_b))
print('rsq_quadratic: ' + str(rsq_quadratic))
print('error_ss_quadratic: ' + str(error_ss_quadratic))
print('fstat2_quadratic: ' + str(fstat2_quadratic))
print('f_stat_quadratic: ' + str(f_stat_quadratic))
print('p_quadratic: ' + str(p_quadratic))
print('')
if degree <= 2:
return quadratic_b
else:
### next cubic
cubic_b = np.polyfit(x, y, 3)
ypred_cubic = np.polyval(cubic_b, x)
error_cubic = y - ypred_cubic
error_ss_cubic = np.sum(error_cubic**2)
rsq_cubic = 1. - (error_ss_cubic / ss_tot)
df_cubic = len(y) - 4
f_stat_cubic = df_cubic * (rsq_cubic - rsq_quadratic) / (1. -
rsq_cubic)
p_cubic = special.fdtrc(2, df_cubic, f_stat_cubic)
print('cubic_b: ' + str(cubic_b))
print('rsq_cubic: ' + str(rsq_cubic))
print('f_stat_cubic: ' + str(f_stat_cubic))
print('p_cubic: ' + str(p_cubic))
return cubic_b