def get_coef(data, pretype, econamelist, quatile):
#获得分位数回归线性关系
#注意xnamelist 最多只能容纳5个变量,yname是str
#n=len(xnamelist)
n = len(econamelist)
if n == 1:
mod = smf.quantreg('%s ~ %s' % (pretype, econamelist[0]), data)
elif n == 2:
mod = smf.quantreg(
'%s ~ %s+%s' % (pretype, econamelist[0], econamelist[1]), data)
elif n == 3:
mod = smf.quantreg(
'%s ~ %s+%s+%s' %
(pretype, econamelist[0], econamelist[1], econamelist[2]),
data)
elif n == 4:
mod = smf.quantreg(
'%s ~ %s+%s+%s+%s' % (pretype, econamelist[0], econamelist[1],
econamelist[2], econamelist[3]), data)
elif n == 5:
mod = smf.quantreg(
'%s ~ %s+%s+%s+%s+%s' %
(pretype, econamelist[0], econamelist[1], econamelist[2],
econamelist[3], econamelist[4]), data)
res = mod.fit(q=quatile)
# print(res.summary())
#返回分位点，截距，各个参数系数 和 各个参数lb,ub
return quatile, res.params['Intercept'], res.params[
econamelist], res.conf_int().loc[econamelist]
def __construct_from_points(self, points):
import statsmodels.formula.api as smf
normed_pnts = self.__get_normed_pnts(points)
dat_pnts = pd.DataFrame(normed_pnts, columns=('x', 'y', 'z'))
mod_y = smf.quantreg('y ~ x + I(x**2.0) + I(x**3.0) + I(x**4.0)',
dat_pnts)
mod_z = smf.quantreg('z ~ x + I(x**2.0) + I(x**3.0) + I(x**4.0)',
dat_pnts)
self.res_y = mod_y.fit(q=0.5)
self.res_z = mod_z.fit(q=0.5)
def fit(self, y_name, features_name):
if np.linalg.matrix_rank(self.temp[['mileage',
'weight_mileage']]) == 1:
return None
if self.temp is not None:
try:
model = smf.quantreg(y_name + '~' + features_name, self.temp)
res = model.fit(q=.5, max_iter=10000)
self.res = res
except:
self.res = None
return None
if self.res.params['mileage'] <= 0 or \
self.res.params['weight_mileage'] <= 0 or \
self.res.params['Intercept'] <= 0:
dirs = 'output/QR/' + str(self.start_cityid) + '/no/'
if not os.path.exists(dirs):
os.makedirs(dirs)
self.show_result(dirs)
return None
dirs = 'output/QR/' + str(self.start_cityid) + '/yes/'
if not os.path.exists(dirs):
os.makedirs(dirs)
self.show_result(dirs)
return self.res
def calcuTD(x, O, Y, SeqDepth, Grid, Tau):
TauGroup, D = Grid[x]
D = int(D)
try:
polyX, centre, scale, alpha, beta = poly.poly(O, D)
except Exception:
polyX = None
if polyX is not None:
colVars = ['var_' + str(j) for j in range(D)]
polydata = pd.concat([pd.DataFrame({'Y':Y}), pd.DataFrame(polyX, columns=colVars)], axis=1)
try:
rqfit = smf.quantreg('Y~' + '+'.join(colVars), polydata).fit(q=TauGroup)
revX = poly.predict_poly(polyX, centre, scale, alpha, beta, SeqDepth)
revX = pd.DataFrame(revX, columns=colVars)
pdvalsrq = rqfit.predict(revX)
if min(pdvalsrq) > 0:
S = QuantReg(pdvalsrq.values, tools.add_constant(SeqDepth)).fit(q=Tau).params[1]
else:
S = -50
except Exception:
S = -50
else:
S = -50
return S
def quantile_regression(categorical_mrna, categorical_protein):
data = pd.DataFrame(columns=['mrna', 'protein'])
data['mrna'] = categorical_mrna
data['protein'] = categorical_protein
mod = smf.quantreg('mrna ~ protein', data)
res = mod.fit(q=.5)
return res.prsquared
def __qfit_l(self):
""" Fit a quantile regression at every quantile and horizon """
# Prepare a container for each individual fit (convenient later)
QFit = namedtuple('Qfit', ['depvar', 'horizon', 'tau', 'qfit'])
qfit_l = list() # Container
for h, depvar in zip(self.horizon_l, self.depvar_l):
reg_f = self.regform_d[depvar] # Formula
for tau in self.quantile_l: # For every tau
# Estimate the quantile regression
p = {'q':tau, 'maxiter':1000, 'p_tol':1e-05}
qfit = smf.quantreg(formula=reg_f, data=self.data).fit(**p)
# Package it into a container
nt = {'depvar':depvar, 'horizon':h, 'tau':tau, 'qfit':qfit}
qfit_l.append(QFit(**nt))
print(f'{len(qfit_l)} quantile regressions estimated '
f'for {len(self.horizon_l)} horizons '
f'and {len(self.quantile_l)} quantiles')
return(qfit_l)
def fitMinSpline(self, Yvar, Xvar, smoothingWindow, plot=False, plotVar = None):
'''
This function is to fit/interpolate a spline in the data
'''
# use patsy class to define a matrix
X = np.asarray(patsy.dmatrix("cr(x, df=7)-1", {"x": Xvar}))
# redefine dataframe
modDat = pd.DataFrame(X, index=Yvar.index)
# redefine our data into X1-X7
modDat.columns = ['X1', 'X2', 'X3', 'X4', 'X5', 'X6', 'X7']
modDatTrunc = modDat.iloc[self._smoothingWindow/2:-self._smoothingWindow/2].copy()
window = np.ones(self._smoothingWindow)/float(self._smoothingWindow)
modDatTrunc['Y'] = np.convolve(Yvar, window, 'same')[self._smoothingWindow/2:-self._smoothingWindow/2]
mod = smf.quantreg('Y~X1+X2+X3+X4+X5', modDatTrunc)
res = mod.fit(q=0.01)
preds = pd.Series(res.predict(modDat), index = Xvar.index)
if plot:
plotDF = pd.concat([plotVar, Yvar, preds],1)
print(plotDF.columns)
plotDF.columns = [plotVar.name, Yvar.name, 'fitted']
p = ggplot(aes(x=plotVar.name, y=Yvar.name), data=plotDF) + geom_line() +\
geom_line(aes(y='fitted'), color='red')+\
ylim(0,5) +\
xlab('') + ylab('Sensor (V)')
print(p)
#return regression predictors
return(preds)
def fitMinSpline(Yvar, Xvar, smoothingWindow, plot=False, plotVar = None):
'''
Function returns minimal interpolation spline
Inputs:
Yvar : dependent variables that needed to be fit
Xvar : independent variables that needed to be fit
smoothingWindow : the smoothing time average
plot = boolean value to plot or not, default is not to plot
plotVar = plot a specific variable, default none
'''
X = np.asarray(patsy.dmatrix("cr(x, df=7)-1", {"x": Xvar}))
modDat = pd.DataFrame(X, index=Yvar.index)
modDat.columns = ['X1', 'X2', 'X3', 'X4', 'X5', 'X6', 'X7']
modDatTrunc = modDat.iloc[smoothingWindow/2:-smoothingWindow/2].copy()
window = np.ones(smoothingWindow)/float(smoothingWindow)
modDatTrunc['Y'] = np.convolve(Yvar, window, 'same')[smoothingWindow/2:-smoothingWindow/2]
mod = smf.quantreg('Y~X1+X2+X3+X4+X5', modDatTrunc)
res = mod.fit(q=0.01)
preds = pd.Series(res.predict(modDat), index = Xvar.index)
if plot:
plotDF = pd.concat([plotVar, Yvar, preds],1)
print(plotDF.columns)
plotDF.columns = [plotVar.name, Yvar.name, 'fitted']
p = ggplot(aes(x=plotVar.name, y=Yvar.name), data=plotDF) + geom_line() +\
geom_line(aes(y='fitted'), color='red')+\
ylim(0,5) +\
xlab('') + ylab('Sensor (V)')
print(p)
return(preds)
def QR_beta(f,g,df=merge1):
reg_p=[]
Y=df[f].astype(float)
for i in g:
X=df[i].astype(float)
tryme2=smf.quantreg('Y~X',data=df).fit(maxiter=100000,q=0.5)
reg_p.append(str(round(tryme2.params[1],8))+" ("+str(round(tryme2.pvalues[1],4))+" )" )#reg_p.append(tryme2.pvalues[1] )
return reg_p
def QR(f,g,df=merge1):
reg_p=[]
Y=df[f].astype(float)
for i in g:
X=df[i].astype(float)
tryme2=smf.quantreg('Y~X',data=df).fit(maxiter=100000,q=0.5)
reg_p.append(tryme2.pvalues[1] )
return reg_p
def quant_summary(self, q=0.5):
'''
Func:分位数回归概要\n
q --> 分位数
'''
mod = smf.quantreg(formula=self.formula, data=self.df)
res = mod.fit(q=q)
return res.summary()
def fit_quanmod(df: pd.DataFrame, q: Number) -> List[float]:
"""
- quantile regression
- returns array of floats [Intercept, NDVI]
"""
mod = smf.quantreg('STR ~ NDVI', df)
res = mod.fit(q=q)
return [res.params['Intercept'], res.params['NDVI']]
def quant_pred(q, data, **params):
mod = smf.quantreg(params['formula'], data)
reg_res = mod.fit(q=q, **params['method_args'])
out = pd.DataFrame({
'x': [data['x'].min(), data['x'].max()],
'quantile': q,
'group': '{}-{}'.format(data['group'].iloc[0], q)})
out['y'] = reg_res.predict(out)
return out
def quant_pred(q, data, **params):
mod = smf.quantreg(params['formula'], data)
reg_res = mod.fit(q=q, **params['method_args'])
out = pd.DataFrame({
'x': [data['x'].min(), data['x'].max()],
'quantile': q,
'group': '{}-{}'.format(data['group'].iloc[0], q)})
out['y'] = reg_res.predict(out)
return out
def quantile_q(d, p, c, s):
underage_cost = p - c
overage_cost = c - s
ratio = underage_cost / (underage_cost + overage_cost)
tmp = d.copy()
tmp['y'] = d
tmp['ones'] = np.ones(len(d))
mod = smf.quantreg('y ~ ones', tmp)
res = mod.fit(q=ratio)
return res.params['Intercept']
def quantile_reg(df, quantile):
mod = smf.quantreg(df.columns[1] + '~' + df.columns[0], df)
res = mod.fit(q = quantile)
print(res.summary())
# get_y = lambda a, b: a + b * df.iloc[:,0].values
# pre_y = get_y(res.params[0], res.params[1])
qre_df = pd.DataFrame(data = [[quantile, res.params[0], res.params[1]] + res.conf_int().iloc[1].tolist()],
index = ['quantile_reg'],
columns = ['qt','intercept','x_coef','cf_lower_bound','cf_upper_bound',])
return qre_df
def quantile_regression_q(d, p, c, s):
underage_cost = p - c
overage_cost = c - s
ratio = underage_cost / (underage_cost + overage_cost)
tmp = d.copy()
tmp['ones'] = np.ones(tmp.shape)
mod = smf.quantreg('y ~ ones', tmp)
res = mod.fit(q=ratio)
print(res.summary())
return res
def __qfit_dict(self):
""" Estimate the quantile fit for every quantile """
qfit_dict = dict()
for tau in self.quantile_list:
reg_f = self.reg_formula
qfit = smf.quantreg(formula=reg_f,
data=self.data).fit(q=tau,
maxiter=2000,
p_tol=1e-05)
qfit_dict[tau] = qfit
return (qfit_dict)
def ols_annotations(x,
y,
data=None,
ax=None,
color='black',
font_size=8,
textxy=[0.05, 0.95],
textva='top',
method='quantreg',
stats=['N', 'slope', 'slope_p']):
import statsmodels.api as sm
import statsmodels.formula.api as smf
if data is None:
data = pandas.DataFrame({'X': x, 'Y': y})
x = 'X'
y = 'Y'
data = data.sort_values(x)
if method == 'ols':
X = sm.add_constant(data.loc[:, x])
Y = data.loc[:, y]
mod = sm.OLS(Y, X)
res = mod.fit()
elif method == 'quantreg':
mod = smf.quantreg(y + ' ~ ' + x, data)
res = mod.fit(q=0.5)
N = data.shape[0]
slope = res.params[x]
slope_p = res.pvalues[x]
rsquared = res.rsquared_adj
rsquared_p = res.f_pvalue
text = ''
for stat in stats:
if stat == 'N':
text += 'N = {:,}\n'.format(N)
if stat == 'slope':
text += 'slope = {}\n'.format('%.2f' % Decimal(slope))
if stat == 'slope_p':
text += 'P = {}\n'.format('%.2E' % Decimal(slope_p))
if stat == 'rsquared':
text += 'R2 = {}\n'.format('%.2f' % Decimal(rsquared))
if stat == 'rsquared_p':
text += 'P = {}\n'.format('%.2E' % Decimal(rsquared_p))
ax.text(textxy[0],
textxy[1],
text,
transform=ax.transAxes,
va=textva,
color=color,
fontsize=font_size)
xmin = data.loc[:, x].min()
xmax = data.loc[:, x].max()
ax.plot(data[x].values[[0, N - 1]], res.predict()[[0, N - 1]], color=color)
def fit(self, X, y=None):
"""
:param X: covariate dataframe
:param y: currently unused
"""
# Build formula for prediction
formula = 'num_det_target ~ np.log(num_det+1)'
if self.covariates:
formula += ' + ' + ' + '.join(self.covariates)
self.fit_result = smf.quantreg(formula, data=X).fit(q=self.quantile)
return self.fit_result
def time_varying_delta_covar_regression(macroData, instData, quantile,
instName, writeToFile):
data = macroData.merge(instData, on='5_Day_Dates')
mod = smf.quantreg(
str(instName) +
' ~ Change_3_M_TR + Change_TR_Slope + TED + Baa_3_M_TR + SP_500 + RE_excess_FS + SP_500_Vol',
data)
varqres = mod.fit(q=quantile)
var50res = mod.fit(q=0.5)
mod = smf.quantreg(
'Fin_Sec_Loss ~ Change_3_M_TR + Change_TR_Slope + TED + Baa_3_M_TR + SP_500 + RE_excess_FS + SP_500_Vol + '
+ str(instName), data)
covarqres = mod.fit(q=quantile)
if writeToFile:
f = open(
str(instName) + ' Time Varying Delta CoVaR Parameters.txt', 'w')
f.write(str(quantile) + ' Quantile VaR for institution')
f.write('\n')
f.write(str(varqres.summary()))
f.write('\n')
f.write('\n')
f.write('0.5 Quantile VaR for institution')
f.write('\n')
f.write(str(var50res.summary()))
f.write('\n')
f.write('\n')
f.write(str(quantile) + ' Quantile CoVaR for system given institution')
f.write('\n')
f.write(str(covarqres.summary()))
f.close()
return {
'VaRqParams': varqres.params,
'VaR50Params': var50res.params,
'CoVaRqParams': covarqres.params
}
def getcoef(data, q=0.5):
'''
Pega o coeficiente angular da regressão
'''
data.columns = ['income', 'depend']
# por algum motivo a tabela não estava fazendo a regreção corretamente, estava entendendo o eixo
# das variáveis independentes como vários eixos e não apenas um eixo
table = {'income': data['income'].values.tolist(), 'depend': data['depend'].values.tolist()}
mod = smf.quantreg('depend ~ income', table)
res = mod.fit(q=q)
return res.params['income']
def quantile(self, q=0.5):
'''
Func:不准用！！!
'''
mod = smf.quantreg(formula=self.formula, data=self.df)
res = mod.fit(q=q)
df_lu = res.conf_int()
df_lu.columns = ['lb', 'ub']
result_dict = df_lu.to_dict()
result_dict['params'] = dict(res.params)
result_dict['pvalue'] = dict(res.pvalues)
result_dict['q'] = str(res.q)[:4]
result_dict['Pseudo R-squared'] = res.prsquared
return pd.DataFrame(result_dict)
def fit_model(self):
"""
fit the linear quantile regression model using the train dataset
Returns
-------
output: statsmodels.regression.linear_model.RegressionResultsWrapper object
the linear quantile regression model
"""
x_columns = list(self.x.columns.values)
equation = self.y.name + '~' + '+'.join(x_columns)
df = pd.concat([self.y, self.x], axis=1)
self.linear_quantile = smf.quantreg(equation, data=df)
self.linear_quantile = self.linear_quantile.fit(q=self.qt)
return self.linear_quantile
def fit(self, X, y):
# Build the design matrix via a tensor basis expansion of natural spline bases
data = {'x{}'.format(i + 1): x for i, x in enumerate(X.T)}
design_matrix = dmatrix(
"te(" + ",".join([
'cr(x{}, df={})'.format(i + 1, self.df)
for i in range(X.shape[1])
]) + ", constraints='center')", data)
# Save the design information for future predictions
self.design_info = design_matrix.design_info
# Fit the model using the basis
mod = smf.quantreg('y ~ x - 1', {'y': y, 'x': design_matrix})
if np.isscalar(self.quantiles):
self.model = mod.fit(q=self.quantiles)
else:
self.model = [mod.fit(q=q) for q in self.quantiles]
def table_rq_res(formula, taus, data, alpha, R, n, sigma, jacobian):
m = len(taus)
tab = pd.DataFrame([], index=[0])
setab = pd.DataFrame([], index=[0])
for i in range(m):
fit_model = smf.quantreg(formula, data)
fit = fit_model.fit(q=taus[i])
coeff = np.dot(R.T, np.array(fit.params))
tab[str(i)] = coeff
sigmatau = sigma(data, n, taus[i], fit.resid)
jacobtau = jacobian(data, n, taus[i], fit.resid, alpha)
solved_jacobtau = np.linalg.inv(jacobtau)
V = np.dot(np.dot(solved_jacobtau, sigmatau), solved_jacobtau) / n
secoeff = np.float(np.dot(np.dot(R.T, V), R))**.5
setab[str(i)] = secoeff
tab = tab.transpose()
setab = setab.transpose()
return (tab, setab)
def time_constant_delta_covar_regression(macroData, instData, quantile,
instName, writeToFile):
data = macroData.merge(instData, on='5_Day_Dates')
mod = smf.quantreg('Fin_Sec_Loss ~ ' + str(instName), data)
res = mod.fit(q=quantile)
var50 = data[str(instName)].quantile(0.5)
varq = data[str(instName)].quantile(quantile)
if writeToFile:
f = open(str(instName) + ' Constant Time Delta CoVaR Summary.txt', 'w')
f.write(str(quantile) + ' Quantile')
f.write('\n')
f.write(str(res.summary()))
f.write('\n')
f.write('Delta Covar ' + str(quantile) + " : " + str(res.params[1] *
(varq - var50)))
f.close()
def quantCV(q, alpha, L1_wt, data, folds):
import statsmodels.formula.api as smf
# from statsmodels.regression.quantile_regression import QuantReg
from sklearn.cross_validation import KFold
from sklearn.metrics import mean_squared_error as MSE
import warnings
warnings.filterwarnings("ignore")
## KFold
kf = KFold(len(np.unique(data.index)), n_folds=folds, random_state=0)
score = np.zeros(folds)
ct = 0
## Train Model
for train_index, test_index in kf:
data_train = data[np.array(
pd.DataFrame(data.index).isin(train_index).values.tolist())]
data_test = data[np.array(
pd.DataFrame(data.index).isin(test_index).values.tolist())]
mod = smf.quantreg(
'Delay_100_Mile ~ TC + ATP + IP + TC_TC + TC_ATP + TC_IP + ATP_ATP + ATP_IP + IP_IP',
data_train)
res = mod.fit_regularized(q=q,
alpha=alpha,
L1_wt=L1_wt,
maxiter=3000,
random_state=0,
cnvrg_tol=1e-08)
## Predict Values
features_predict = data_test.groupby(by=['TC', 'ATP', 'IP'])[data.drop(
['Delay_100_Mile'], axis=1).columns].mean()
params = res.params
delay_predicted = params[0] + np.dot(features_predict, params[1:])
## Corresponding Value of Same Percentile
target_per = data_test.groupby(
by=['TC', 'ATP', 'IP'])['Delay_100_Mile'].quantile(q)
# score[ct]= MSE(np.expm1(target_per),np.expm1(delay_predicted))**.5
score[ct] = MSE(target_per, delay_predicted)**.5
ct += 1
return np.mean(score)
def quantile_fit(xi, yi, q=0.5):
"""Perform quantile regression.
See for instance:
https://www.statsmodels.org/dev/examples/notebooks/generated/quantile_regression.html
(valid on 2091-04-16)
Parametes:
xi, yi np.array, x and y values
Returns:
slope regression slope estimate
intercept regression intercept estimate
"""
data = {'xi': xi, 'yi': yi}
df = pd.DataFrame.from_dict(data=data)
mod = smf.quantreg('yi ~ xi', df)
res = mod.fit(q=q)
# return slope, intercept, covariance_matrix
return res.params['xi'], res.params['Intercept'], res.cov_params().values
def fitMinSpline(Yvar, Xvar, smoothingWindow, plot=False, plotVar = None):
X = np.asarray(patsy.dmatrix("cr(x, df=7)-1", {"x": Xvar}))
modDat = pd.DataFrame(X, index=Yvar.index)
modDat.columns = ['X1', 'X2', 'X3', 'X4', 'X5', 'X6', 'X7']
modDatTrunc = modDat.iloc[smoothingWindow/2:-smoothingWindow/2].copy()
window = np.ones(smoothingWindow)/float(smoothingWindow)
modDatTrunc['Y'] = np.convolve(Yvar, window, 'same')[smoothingWindow/2:-smoothingWindow/2]
mod = smf.quantreg('Y~X1+X2+X3+X4+X5', modDatTrunc)
res = mod.fit(q=0.01)
preds = pd.Series(res.predict(modDat), index = Xvar.index)
if plot:
plotDF = pd.concat([plotVar, Yvar, preds],1)
print(plotDF.columns)
plotDF.columns = [plotVar.name, Yvar.name, 'fitted']
p = ggplot(aes(x=plotVar.name, y=Yvar.name), data=plotDF) + geom_line() +\
geom_line(aes(y='fitted'), color='red')+\
ylim(0,5) +\
xlab('') + ylab('Sensor (V)')
print(p)
return(preds)
def fit(self, train, quantiles=[0.025, 0.975], startx=None, endx=None):
"""
Uses the statsmodel implementation of quantile regression. Quantile weighted least squares.
Possibility to only fit the exponential decay beyond a certain leadtime
Works on dataframe with resetted index. (i.e. leadtime as a column)
"""
train = train.reset_index('leadtime')
if startx is not None:
train = train.loc[train[self.predcol] >= startx, :]
if endx is not None:
train = train.loc[train[self.predcol] <= endx, :]
mod = smf.quantreg(self.obscol + ' ~ np.log(' + self.predcol + ')',
train)
self.fits = pd.DataFrame(np.zeros((len(quantiles), 2)),
index=quantiles,
columns=self.model_coefs)
for q in quantiles:
res = mod.fit(q=q)
self.fits.loc[q, :] = res.params.values
def subsamplek(formula, V, tau, coeffs, data, n, b, B, R):
k = np.zeros(B)
RVR = (np.float(np.dot(np.dot(R.T, V), R) / b))**(-1 / 2)
probs = np.array(data['perwt']) / np.sum(np.array(data['perwt']))
for s in range(B):
sing = 0
while sing == 0:
sample = np.random.choice(np.arange(0, n),
size=int(b),
replace=True,
p=probs)
sdata = data.iloc[sample, :]
x = sdata[["educ", "exper", "exper2", "black", "perwt"]]
x = x.as_matrix()
sing = np.linalg.det(np.dot(x.T, x))
# Didn't use weights here
sqr_model = smf.quantreg(formula, sdata)
sqr = sqr_model.fit(q=tau)
k[s] = np.abs(np.dot(np.dot(RVR, R.T), coeffs - np.array(sqr.params)))
return (k)
def CoVar():
df = pd.read_csv("Data/Index_data.csv", sep=";")
df["Date"] = pd.to_datetime(df["Date"])
df = df.dropna().ffill().set_index("Date")
# data = np.log(df).diff().dropna()[['Nordea Bank','Sydbank','Danske Bank','Jyske Bank','Novo Nordisk B']]
data = np.log(df).diff().dropna()
data = data.rename(columns={"S&P": "SP"})
data = data.replace(np.inf, 0).replace(-np.inf, 0)
mCovar = np.zeros((len(data.columns), len(data.columns)))
q = 0.05
for nr1, j in enumerate(data.columns):
for nr2, k in enumerate(data.columns):
if nr1 != nr2:
mod = smf.quantreg(str(j) + "~" + str(k), data)
res = mod.fit(q=q)
var5 = mod.fit(q=q).params[0]
var5 = np.percentile(data[k], q)
var50 = mod.fit(q=0.5).params[0]
covar = res.params[0] + res.params[1] * var5
print covar
print res.summary()
dcovar = mod.fit(q=q).params[1] * (var5 - var50)
# res = mod.fit(q=0.5)
mCovar[nr1, nr2] = round(dcovar, 3)
icepts = []
for i in np.arange(0.01, 1, 0.01):
res = mod.fit(q=i)
icepts.append(res.params[1])
plt.plot(np.arange(0.01, 1, 0.01), icepts)
# plt.ylim(0,1)
print j, k
plt.show()
else:
mCovar[nr1, nr2] = np.nan
# mCovar[nr1,nr2]
print pd.DataFrame(mCovar, columns=data.columns, index=data.columns)
def _set_quantiles(self, data):
#Compute quantiles for the transformed power conditional on the transformed power prediction
#for a specific location and a specific lead time.
#smf.quantreg generates warning - see documentation for more details
#warning off just for this section
warnings.filterwarnings("ignore")
#Performs the actual quantile regression and stores the variables of
prob = np.concatenate([[0.001],np.arange(0.05,0.951,0.05),[0.999]])
self.betas = expando()
for location in data.metadata.id_nodes:
print(location)
setattr(self.betas, location, expando())
for ileadT, leadT in enumerate(data.metadata.fore_leadT, start = 1):
clim_concurr_loc_leadT = getattr(getattr(self.clim.concurr, location), leadT)
betas_aux = pd.DataFrame(0, columns = ['probabilities','intercept', 'coefficient'],
index = range(len(prob)))
betas_aux.loc[:,('probabilities')] = prob
#For solar cases, all quantiles are kepts to zeros
if not np.all(clim_concurr_loc_leadT.observations == 0.):
mod = smf.quantreg('observations ~ predictions', clim_concurr_loc_leadT)
for iq,q in enumerate(prob):
res = mod.fit(q=q)
betas_aux.loc[iq,('intercept')] = res.params['Intercept']
betas_aux.loc[iq,('coefficient')] = res.params['predictions']
del res
del mod
setattr(getattr(self.betas,location), leadT, betas_aux)
del betas_aux
gc.collect()
#warning on
warnings.filterwarnings("always")
pass
# -*- coding: utf-8 -*-'''
from __future__ import print_function
import patsy
import numpy as np
import pandas as pd
import statsmodels.api as sm
import statsmodels.formula.api as smf
import matplotlib.pyplot as plt
from statsmodels.regression.quantile_regression import QuantReg
from matplotlib import rc
data = sm.datasets.engel.load_pandas().data
print(data.head())
mod = smf.quantreg('foodexp ~ income', data)
res = mod.fit(q=.5)
print(res.summary())
quantiles = np.arange(.05, .96, .1)
def fit_model(q):
res = mod.fit(q=q)
return [q, res.params['Intercept'], res.params['income']] + \
res.conf_int().ix['income'].tolist()
models = [fit_model(x) for x in quantiles]
models = pd.DataFrame(models, columns=['q', 'a', 'b','lb','ub'])
ols = smf.ols('foodexp ~ income', data).fit()
ols_ci = ols.conf_int().ix['income'].tolist()
ols = dict(a = ols.params['Intercept'],
def do_GLM(self, disp=1):
"""
Generaliesd Linear Models
This fits a GLM to the training data set and then fits it to the testing dataset.
Different families and links can be included if need be simply using the statsmodels
simple API.
"""
import statsmodels.api as sm
import statsmodels.formula.api as smf
import statsmodels.genmod as smg
# Decide the family
if self.family_name == "Gamma":
if self.link == "log":
self.family = sm.families.Gamma(link=smg.families.links.log)
else:
self.family = sm.families.Gamma()
elif self.family_name == "Quantile":
self.family = self.family_name
self.link = "None"
else:
logger.info("You can only pick the family: Gamma and Quantile")
# Decide the formula
poly = lambda x, power: x**power
if not self.formula:
formula = "redshift ~ poly(PC1, 2) +"
for i in range(self.num_components):
if i<self.num_components-1:
formula += "PC{0}*".format(i+1)
else:
formula += "PC{0}".format(i+1)
self.formula = formula
self.logger.info("Family: {0} with \tformula: {1}\tlink: {2}".format(self.family_name, self.formula, self.link))
self.logger.info("Fitting...")
t1 = time.time()
if self.family == "Quantile":
# Quantile regression
model = smf.quantreg(formula=self.formula, data=self.data_frame_train)
results = model.fit(q=.5)
if verbose:
self.logger.info(results.summary())
else:
model = smf.glm(formula=self.formula, data=self.data_frame_train, family=self.family)
results = model.fit()
self.logger.info(results.summary())
t2 = time.time()
self.dt = (t2-t1)
self.logger.info("Time taken: {0} seconds".format(self.dt))
#Plot the model with our test data
## Prediction
if self.cross_validate:
self.logger.info("Cross validating")
self.measured = np.array(self.data_frame_test["redshift"].values)
self.predicted = results.predict(self.data_frame_test)
else:
self.measured = np.array(self.data_frame_train["redshift"].values)
self.predicted = results.predict(self.data_frame_train)
self.fitted = results.predict(self.data_frame_test)
## Outliers
## (z_phot - z_spec)/(1+z_spec)
self.deltas = abs(self.predicted - self.measured)
self.median = np.median(self.deltas)
self.std = np.std(self.deltas)
# First we will remove the outliers
mega_out_indx = (self.deltas/(1+self.measured)) > 0.15
self.num_mega_outliers = mega_out_indx.sum() / (1.0*len(self.deltas))
self.average = np.mean(self.deltas[mega_out_indx.__invert__()])
self.rms = np.sqrt(np.mean(self.deltas**2))
self.rms_outliers = np.sqrt(np.mean(self.deltas[mega_out_indx.__invert__()]**2))
self.std_outliers = np.std(self.deltas[mega_out_indx.__invert__()])
self.bias_outliers = np.mean(self.deltas[mega_out_indx.__invert__()])
self.logger.info("Median (dz):.............................................{0}".format(self.median))
self.logger.info("Standard deviation (dz):.................................{0}".format(self.std))
self.logger.info("RMS (dz).................................................{0}".format(self.rms))
self.logger.info("............................................................")
self.logger.info("Number of outliers removed...............................{0}".format(self.num_mega_outliers))
self.logger.info("Average (removed outliers for > 0.15) (dz):..............{0}".format(self.average))
self.logger.info("Standard deviation (removed outliers for > 0.15) (dz):...{0}".format(self.std_outliers))
self.logger.info("RMS (removed outliers for z > 0.15)......................{0}".format(self.rms_outliers))
self.logger.info("Bias (removed outliers for z > 0.15).....................{0}".format(self.bias_outliers))
self.outliers = (self.predicted - self.measured) / (1.0 + self.measured)
# R code
# Out<-100*length(PHAT0.Pred$fit[(abs(PHAT0.test.PCA$redshift-PHAT0.Pred$fit))>0.15*(1+PHAT0.test.PCA$redshift)])/length(PHAT0.Pred$fit)
self.catastrophic_error = 100.0*(abs(self.measured-self.predicted) > (0.15*(1+self.measured))).sum()/(1.0*self.measured.shape[0])
self.logger.info("Catastrophic Error:......................................{0}%".format(self.catastrophic_error))
plt.yticks(())
plt.xlabel("x")
plt.ylabel("y and predicted y")
plt.title("Linear regression on data with non-constant variance")
## Quantile regression for the median, 0.5th quantile
import pandas as pd
data = pd.DataFrame(data = np.hstack([x_, y_]), columns = ["x", "y"])
print data.head()
import statsmodels.formula.api as smf
mod = smf.quantreg('y ~ x', data)
res = mod.fit(q=.5)
print(res.summary())
## Build the model for other quantiles
quantiles = np.arange(0.1,1,0.1)
print quantiles
models = []
params = []
for qt in quantiles:
print qt
res = mod.fit(q = qt )
models.append(res)
params.append([qt, res.params['Intercept'], res.params['x']] + res.conf_int().ix['x'].tolist())
print()
print(u'-'*30)
print(u'Variable for close distance:', d_dist)
# NO CONTROL
ols_res = smf.ols('pct_rr ~ {:s}'.format(d_dist), data = df_compa).fit()
#print()
#print(ols_res.summary())
ls_res = []
ls_quantiles = [0.25, 0.5, 0.75] # use 0.7501 if issue
for quantile in ls_quantiles:
#print()
#print(quantile)
#print(smf.quantreg('pct_rr~d_dist_5', data = df_repro_compa).fit(quantile).summary())
ls_res.append(smf.quantreg('pct_rr ~ {:s}'.format(d_dist),
data = df_compa[~df_compa[d_dist].isnull()]).fit(quantile))
print(summary_col([ols_res] + ls_res,
stars=True,
float_format='%0.2f',
model_names=['OLS'] + [u'Q{:2.0f}'.format(quantile*100) for quantile in ls_quantiles],
info_dict={'N':lambda x: "{0:d}".format(int(x.nobs)),
'R2':lambda x: "{:.2f}".format(x.rsquared)}))
# WITH CONTROLS
ols_res_ctrl = smf.ols('pct_rr ~ {:s} + {:s}'.format(d_dist, str_ev),
data = df_compa).fit()
#print()
#print(ols_res_ctrl.summary())
ls_res_ctrl = ([smf.quantreg('pct_rr ~ {:s} + {:s}'.format(d_dist, str_ev),
slope, intercept, r_value, p_value, std_err = stats.linregress(y,dur)
correlation[q,sea_ID,state,2]=slope
correlation[q,sea_ID,state,3]=p_value
correlation[q,sea_ID,state,4]=intercept
#print slope, intercept, r_value, p_value, std_err
#plt.plot(y,dur,'o')
#plt.plot(y,intercept+slope*y,'r')
df=pd.DataFrame(data={'dur':dur,'y':y})
mod = smf.quantreg('dur ~ y', df)
for qu,qui in zip(quantiles,range(5)):
try:
res = mod.fit(q=qu)
slope,p_value,interc=res.params['y'],res.pvalues['y'],res.params['Intercept']
correlation_qu[q,sea_ID,state,qui,:]=[slope,p_value,interc]
#plt.plot(y,interc+slope*y,'b--')
except:
pass
#plt.show()
#asdasd
out_file='data/_TMean/91_7/gridded/91_7_TMean_duration_'+variable+'_cor.nc'
def quant_mincer(q, data):
r = smf.quantreg('logwk ~ educ + black + exper + exper2 + wt - 1', data)
result = r.fit(q = q)
coef = result.params['educ']
se = result.bse['educ']
return [coef, se]
def elast_calc(self, key, Y, X, P, stub='', parts=100):
"""
Add elasticities using log-log quantile regressions
number of elasticities will be that of hypothetical delimiters
in parts i.e parts-1
key - household key
Y - dependent variable - resource consumption
X - independent variable - income
P - household population weights
stub - sufix to name variables containing quantiles
and elasticities
parts - number of parts
"""
dt = self.dataset
quantstub = 'quant' + stub
elaststub = 'elast' + stub
print '\nElasticity calculator started - please be patient'
# take the logs of Y and X
dt['__lnY'] = np.log(dt[Y])
dt['__lnX'] = np.log(dt[X])
# log of 0 is -infinite, replace with missing (NaN)
dt['__lnY'][dt[Y] == 0] = np.NaN
dt['__lnX'][dt[X] == 0] = np.NaN
# rescale and round weights to inform replication
dt['__' + P] = dt[P]/dt[P].min()
dt['__rdwgt'] = dt['__' + P].round()
# define quantiles based on parts and mark
dt.sort(Y, inplace=True)
dt[quantstub] = (dt['__' + P].cumsum() /
dt['__' + P].sum() *
parts).astype(int) / float(parts)
dt.sort(key, inplace=True)
# the quantile of the regression, can't be 0 or 1
# unique() is sorted as dt, get the smallest non zero quantile
# and the larger < 1
quantiles = dt[quantstub].unique()
quantiles.sort()
quantiles = quantiles[1:-1]
dt[quantstub][dt[quantstub] == 0] = quantiles[0]
dt[quantstub][dt[quantstub] == 1] = quantiles[-1]
# dataframe with replications
print 'Replicating observations, {} to {}...'.format(
dt['__rdwgt'].count(), int(dt['__rdwgt'].sum()))
lnY, lnX = pd.Series(), pd.Series()
for i in xrange(len(dt)):
lnY = lnY.append(pd.Series((dt['__lnY'][i],) *
int(dt['__rdwgt'][i])))
lnX = lnX.append(pd.Series((dt['__lnX'][i],) *
int(dt['__rdwgt'][i])))
estdt = pd.DataFrame()
estdt['lnY'] = lnY
estdt['lnX'] = lnX
del lnY, lnX
# calculate elasticities
print 'Fitting models...'
model = smf.quantreg('lnY ~ lnX', estdt)
elastseries = ()
#elasterrors = ()
print 'Quantile\telasticity\tse_elast\tintercept\tse_intercept'
for quantile in quantiles:
elast = model.fit(quantile)
elastseries += (elast.params[1],)
print '{}\t{:8.6f}\t{:8.6f}\t{:8.6f}\t{:8.6f}'.format(
quantile, elast.params[1], elast.bse[1], elast.params[0],
elast.bse[0],)
elastdt = pd.DataFrame()
elastdt[quantstub] = quantiles
elastdt[elaststub] = elastseries
# add elasticities and clean dataset
todrop = [var for var in dt.keys() if '__' in var]
self.dataset = pd.merge(dt, elastdt, on=quantstub)
self.dataset.sort(key, inplace=True)
self.dataset.reset_index(drop=True, inplace=True)
self.dataset.drop(todrop, axis=1, inplace=True)
self.seedvars += [quantstub, elaststub]
def trend_CI(x_var, y_var, n_boot=1000, ci=95, trendtype="linreg", q=0.5, frac=0.6, it=3, autocorr=None, CItype="bootstrap"):
"""calculates bootstrap confidence interval and significance level for trend, ignoring autocorrelation or accounting for it
Parameters
----------
x_var : list
independent variable
y_var : list
dependent variable, same length as x_var
q : int, optional, only if trendtype==quantreg
quantile for which regression is to be calculated
n : int, optional
number of bootstrap samples
ci : int, optional
confidence level. Default is for 95% confidence interval
frac : int, optional, only if trendtype==lowess
lowess parameter (fraction of time period length used in local regression)
it : int, optional, only if trendtype==lowess
lowess parameter (numbre of iterations)
autocorr : str, optional
way of accounting for autocorrelation, possible values: None, "bootstrap"
trendtype : str, optional
method of trend derivation, possible values: lowess, linreg, quantreg, TheilSen
CItype : str, optional
method of CI derivation, possible values: "analytical" and "bootstrap".
if trendtype is "lowess", CItype will be set to None
if CItype is "analytical": autocorrelation will be set to None
Results
-------
returns library with following elements:
slope - slope of the trend
CI_high - CI on the slope value
CI_low - as above
pvalue - trend's significance level
trend - trend line, or rather its y values for all x_var
trendCI_high - confidence interval for each value of y
trendCI_low - as above
Remarks
-------
the fit function ocassionally crashes on resampled data. The workaround is to use try statement
"""
import numpy as np
import pandas as pd
#for linreg
import statsmodels.api as sm
from statsmodels.regression.linear_model import OLS
#for arima
import statsmodels.tsa as tsa
#for quantreg
import statsmodels.formula.api as smf
from statsmodels.regression.quantile_regression import QuantReg
#for lowess
import statsmodels.nonparametric.api as npsm
#other
from statsmodels.distributions.empirical_distribution import ECDF
from scipy.stats import mstats, mannwhitneyu, t, kendalltau
from arch.bootstrap import StationaryBootstrap, IIDBootstrap
#preparing data
if CItype=="analytical" and trendtype=="TheilSen":
CItype="bootstrap"
x_var=np.array(x_var)
y_var=np.ma.masked_invalid(y_var)
n_data=len(y_var)
ci_low=(100-ci)/2
ci_high=100-ci_low
#setting bootstrapping function
if autocorr=="bootstrap":
bs=StationaryBootstrap(3, np.array(range(len(y_var))))
else:
bs=IIDBootstrap(np.array(range(len(y_var))))
if trendtype=="quantreg":
print "Quantile regression, CI type: "+CItype+", autocorrelation adjustment: "+str(autocorr)+"\n"
xydata=pd.DataFrame(np.column_stack([x_var, y_var]), columns=['X', 'Y'])
model=smf.quantreg('Y ~ X', xydata)
res=model.fit(q=q)
intcpt=res.params.Intercept
slope=res.params.X
pvalue=res.pvalues[1]
CI_low=res.conf_int()[0]['X']
CI_high=res.conf_int()[1]['X']
y_pred=res.predict(xydata)
#calculating residuals
resids=y_var-y_pred
#calculate autocorrelation indices
autocorr_test(x_var, resids)
if CItype=="bootstrap":
#bootstrapping
bs_trends=np.copy(y_pred).reshape(-1,1)
bs_slopes=[]
bs_intcpts=[]
for data in bs.bootstrap(n_boot):
ind=data[0][0]
model = smf.quantreg('Y ~ X', xydata.ix[ind,:])
try:
res = model.fit(q=q)
bs_slopes=bs_slopes+[res.params.X]
bs_intcpts=bs_intcpts+[res.params.Intercept]
bs_trends=np.append(bs_trends,res.predict(xydata).reshape(-1,1), 1)
except:
goingdownquietly=1
if trendtype=="linreg":
print "Linear regression, CI type: "+CItype+", autocorrelation adjustment: "+str(autocorr)+"\n"
x_varOLS = sm.add_constant(x_var)
model = sm.OLS(y_var, x_varOLS, hasconst=True, missing='drop')
res = model.fit()
intcpt,slope=res.params
pvalue=res.pvalues[1]
CI_low,CI_high=res.conf_int()[1]
y_pred=res.predict(x_varOLS)
#calculating residuals
resids=y_var-y_pred
#calculate autocorrelation indices
autocorr_test(x_var, resids)
if CItype=="bootstrap":
#bootstrapping for confidence intervals
bs_slopes=[]
bs_intcpts=[]
bs_trends=np.copy(y_pred).reshape(-1,1)
for data in bs.bootstrap(n_boot):
ind=data[0][0]
model = sm.OLS(y_var[ind], x_varOLS[ind,:], hasconst=True, missing='drop')
try:
res = model.fit()
bs_slopes=bs_slopes+[res.params[1]]
bs_intcpts=bs_intcpts+[res.params[0]]
bs_trends=np.append(bs_trends,res.predict(x_varOLS).reshape(-1,1), 1)
except:
goingdownquietly=1
if trendtype=="TheilSen":
# print "Theil-Sen slope, CI type: "+CItype+", autocorrelation adjustment: "+str(autocorr)+"\n"
#significance of MK tau
tau,pvalue=kendalltau(x_var, y_var)
# print "raw MK tau:", tau, "raw MK pvalue:", pvalue
#TS slope and confidence intervals
slope,intercept,CI_low,CI_high=mstats.theilslopes(y_var, x_var, alpha=0.95)
#getting slope line's y values
y_pred=intercept+slope*x_var
#calculating residuals
resids=y_var-y_pred
#calculate autocorrelation indices
autocorr_test(x_var, resids)
if CItype=="bootstrap":
#bootstrapping for confidence intervals
bs_slopes=[]
bs_intcpts=[]
bs_trends=np.copy(y_pred).reshape(-1,1)
for data in bs.bootstrap(n_boot):
ind=data[0][0]
res=mstats.theilslopes(y_var[ind], x_var[ind], alpha=0.95)
bs_slopes=bs_slopes+[res[0]]
bs_intcpts=bs_intcpts+[res[1]]
bs_trends=np.append(bs_trends, (res[1]+res[0]*x_var).reshape(-1,1), 1)
if trendtype=="lowess":
print "Lowess\n"
temp=dict(npsm.lowess(y_var, x_var, frac=frac, it=it, missing="drop"))
y_pred=np.array(map(temp.get, x_var)).astype("float").reshape(-1,1)
bs_trends=np.copy(y_pred)
for data in bs.bootstrap(n_boot):
ind=data[0][0]
try:
temp = dict(npsm.lowess(y_var[ind], x_var[ind], frac=frac, it=it, missing="drop"))
temp=np.array(map(temp.get, x_var)).astype("float").reshape(-1,1)
pred=pd.DataFrame(temp, index=x_var)
temp_interp=pred.interpolate().values
bs_trends=np.append(bs_trends, temp_interp, 1)
except:
goingdownquietly=1
#calculating final values of CI and p-value
#skipping when lowess
if trendtype=="lowess":
CI_low=np.nan
CI_high=np.nan
slope=np.nan
intcpt=np.nan
pvalue=np.nan
confint=np.nanpercentile(bs_trends, [ci_low,ci_high], 1)
trendCI_low=confint[:,0]
trendCI_high=confint[:,1]
else:
if CItype=="bootstrap":
#values for slope, intercept and trend can be obtained as medians of bootstrap distributions, but normally analytical parameters are used instead
# it the bootstrap bias (difference between analytical values and bootstap median) is strong, it might be better to use bootstrap values.
# These three lines would need to be uncommented then
# slope=np.median(bs_slopes)
# intcpt=np.median(bs_intcpts)
# trend=intcpt+slope*x_var
#these are from bootstrap too, but needs to be used for this accounts for autocorrelation, which is the point of this script
CI_low,CI_high=np.percentile(bs_slopes, [5, 95])
ecdf=ECDF(bs_slopes)
pvalue=ecdf(0)
#this makes sure we are calculating p-value on the correct side of the distribution. That will be one-sided pvalue
if pvalue>0.5:
pvalue=1-pvalue
confint=np.nanpercentile(bs_trends, [ci_low,ci_high], 1)
print "bs_trends:", bs_trends.shape, confint.shape
trendCI_low=confint[:,0]
trendCI_high=confint[:,1]
else:
#this is for analytical calculation of trend confidence interval
#it happens in the same way for each of the trend types, thus it is done here, not under the trendtype subroutines
#making sure x are floats
xtemp=np.array(x_var)*1.0
#squared anomaly
squanom=(xtemp-np.mean(xtemp))**2
temp=((1./len(x_var))+(squanom/sum(squanom)))**0.5
#standard error of estmation
see=(np.nansum((np.array(y_var)-np.nanmean(y_pred))**2)/len(x_var))**0.5
#adjusting ci
ci_adj=1-((1-ci/100.)/2)
#accounting for uncertainty in mean through student's t
tcomp=t.ppf(ci_adj, len(x_var)-2)
#confidence interval
cint=tcomp*see*temp
#for trend only
trendCI_high=y_pred+cint
trendCI_low=y_pred-cint
print trendtype, "slope:",slope, "pvalue (one sided):", pvalue, "conf interval:", CI_low, CI_high, "autocorrelation adjustment:", autocorr, "\n"
output={"slope":slope, "CI_high":CI_high, "CI_low":CI_high, "pvalue":pvalue, "trend": y_pred, "trendCI_low":trendCI_low, "trendCI_high":trendCI_high}
return output
