def getTStat(X,y,alpha,lam,nSamp=100): # here we are doing residual bootstrap # to identify the std err and report # the t-stat (mean/st err) nObs,nRegs = X.shape # sd is done by res boot so we need to get the res enm = enet.fit(X,y, alpha,lambdas=[lam]) yHat = enm.predict(X)[:,0] res = y - yHat resCent = res-np.mean(res) ySample = np.zeros((nObs,nSamp)) # now we need the samples for i in range(nSamp): resSample = st.sampleWR(resCent) ySample[:,i] = yHat+resSample # residual bs time sc = np.zeros(nRegs) sSqc = np.zeros(nRegs) for i in range(nSamp): # need the coef # they change so we need to map the back to the original tmpEnm = enet.fit(X,ySample[:,i], alpha,lambdas=[lam]) sc[tmpEnm.indices] = sc[tmpEnm.indices] + tmpEnm.coef[:,0] sSqc[tmpEnm.indices] = sSqc[tmpEnm.indices] + tmpEnm.coef[:,0]**2 # get averages and variances aveCoef = sc/float(nSamp) sdCoef = np.sqrt(sSqc/float(nSamp) - aveCoef**2) # get tstat # due to the sparsity of lasso # its possible for a coef to be zero # on all samples, thus a zero st error # we are going to remove the zeros sdCoef[sdCoef<1E-52] = 1E-52 tStat = np.abs(aveCoef/sdCoef) return tStat
def estStErr(self,nSamp=100): X = self._X y = self._y nObs,nRegs = X.shape lam = self._lam yHat = self._yHat intercept= self._intercept globalCoef = self._globalCoef coefIndex = self._coefIndex notEmpty = self._notEmpty alpha = self._alpha # get the bootstrap residual response samples res = y - yHat resCent = res-np.mean(res) ySample = np.zeros((nObs,nSamp)) self._ySample = ySample for i in range(nSamp): resSample = st.sampleWR(resCent) ySample[:,i] = yHat+resSample if notEmpty: # working on subset now Xhat = X[:,coefIndex] self._Xhat = Xhat nObs,nRegsHat = Xhat.shape sdXhat = np.sqrt(np.var(Xhat,0)) self._sdXhat = sdXhat # residual bs time sumErr = 0 sumSqErr = 0 sumNullErr = 0 sumSqNullErr = 0 sc = np.zeros(nRegsHat) sSqc = np.zeros(nRegsHat) sumSup = np.zeros(nRegsHat) for i in range(nSamp): # cv to get the errors err,tmpEnm,tmpallVals = fitSampling(Xhat,ySample[:,i],alpha,10,method='cv',lambdas=[lam]) sumErr = err.mErr[0] + sumErr sumSqErr = err.mErr[0]**2 + sumSqErr # cv over this thing to get the null model errors nullErr,a = fitSamplingNull(ySample[:,i],10, method='cv') sumNullErr = sumNullErr + nullErr sumSqNullErr = sumSqNullErr + nullErr**2 # need the coef # they change so we need to map the back to the original tmpEnm = enet.fit(Xhat,ySample[:,i], alpha,lambdas=[lam]) sc[tmpEnm.indices] = sc[tmpEnm.indices] + tmpEnm.coef[:,0] sSqc[tmpEnm.indices] = sSqc[tmpEnm.indices] + tmpEnm.coef[:,0]**2 # find supports occur = np.zeros(len(tmpEnm.coef[:,0])) occur[abs(tmpEnm.coef[:,0])>1E-25] = 1.0 sumSup[tmpEnm.indices] = sumSup[tmpEnm.indices] + occur # get averages and variances aveErr = sumErr/nSamp self._aveErr = aveErr self._sdErr = np.sqrt(sumSqErr/nSamp - aveErr**2) aveNullErr = sumNullErr/nSamp self._aveNullErr=aveNullErr self._sdNullErr = np.sqrt(sumSqNullErr/nSamp - aveNullErr**2) aveCoef = sc/nSamp self._aveCoef = aveCoef self._sdCoef = np.sqrt(sSqc/nSamp - aveCoef**2) self._pSup = sumSup/nSamp else: # residual bs time sumNullErr = 0 sumSqNullErr = 0 for i in range(nSamp): # cv over this thing to get the null model errors nullErr,a = fitSamplingNull(ySample[:,i],10, method='cv') sumNullErr = sumNullErr + nullErr sumSqNullErr = sumSqNullErr + nullErr**2 # get averages and variances aveNullErr = sumNullErr/nSamp sdNullErr = np.sqrt(sumSqNullErr/nSamp - aveNullErr**2) self._aveNullErr = aveNullErr self._sdNullErr = sdNullErr self._aveErr = aveNullErr self._sdErr = sdNullErr
def estModel(XFull,y,nSamp=100,alphaList=np.array([1]),estErr=True,estImp=False,reduceX=False,params=[]):
"""Estimate a mean and standard deviation
for an elastic net model using bootstrap
residual.
Note: Bootstrap resampling is used to select
model parameters, then the bs res at these
params is used on the full feature set X
to calculate means and standard errors.
Note: if estErr then 10 fold CV is used to estimate
the prediction error at each iteration of the bs.
This is ten extra iterations at each bs res
sample, but reduces the bias in prediction error.
The mean and sdDev of the CV error is then reported.
Note: If params are passed then we assume its a tuple
with the (lambda,alpha) model parameters. In this case
model selection is bipassed. and these params are used.
"""
nObs,nRegsFull = XFull.shape
# select full model values
if len(params)==2:
lam,alpha = params
enm = enet.fit(XFull,y,alpha,lambdas=[lam])[0]
else:
enm = select(XFull,y,nSamp,alphaList)
lam = enm.lambdas[0]
yHat = enm.predict(XFull)
intercept = enm.intercept[0]
globalCoef =enm.coef[np.abs(enm.coef)>1E-21]
coefIndex = enm.indices[np.abs(enm.coef)>1E-21]
alpha = enm.alpha
# now is when we reduce the x if we need too!
if reduceX:
nRegs = len(coefIndex)
if nRegs > 0:
X = XFull[:,coefIndex]
nObs, _ = X.shape
else:
X = XFull
nRegs = nRegsFull
# get the bootstrap residual response samples
res = y - yHat
resCent = res-np.mean(res)
ySample = np.zeros((nObs,nSamp))
for i in range(nSamp):
resSample = st.sampleWR(resCent)
ySample[:,i] = yHat+resSample
if nRegs > 0:
# residual bs time
if estErr:
sumErr = 0
sumSqErr = 0
sumNullErr = 0
sumSqNullErr = 0
sc = np.zeros(nRegs)
sSqc = np.zeros(nRegs)
ac = lil_matrix((nRegs,nSamp))
sumSup = np.zeros(nRegs)
for i in range(nSamp):
# cv to get the errors
if estErr:
err,tmpEnm,tmpallVals = fitSampling(X,ySample[:,i],alpha,10,method='cv',lambdas=[lam])
sumErr = err.mErr[0] + sumErr
sumSqErr = err.mErr[0]**2 + sumSqErr
# cv over this thing to get the null model errors
nullErr,a = fitSamplingNull(ySample[:,i],10, method='cv')
sumNullErr = sumNullErr + nullErr
sumSqNullErr = sumSqNullErr + nullErr**2
# need the coef
# they change so we need to map the back to the original
tmpEnm = enet.fit(X,ySample[:,i], alpha,lambdas=[lam])
sc[tmpEnm.indices] = sc[tmpEnm.indices] + tmpEnm.coef[:,0]
sSqc[tmpEnm.indices] = sSqc[tmpEnm.indices] + tmpEnm.coef[:,0]**2
if len(tmpEnm.indices)>0:
ac[tmpEnm.indices,i] = tmpEnm.coef
# find supports
occur = np.zeros(len(tmpEnm.coef[:,0]))
occur[abs(tmpEnm.coef[:,0])>1E-25] = 1.0
sumSup[tmpEnm.indices] = sumSup[tmpEnm.indices] + occur
# get averages and variances
if estErr:
aveErr = sumErr/nSamp
sdErr = np.sqrt(sumSqErr/nSamp - aveErr**2)
aveNullErr = sumNullErr/nSamp
sdNullErr = np.sqrt(sumSqNullErr/nSamp - aveNullErr**2)
aveCoef = sc/nSamp
sdCoef = np.sqrt(sSqc/nSamp - aveCoef**2)
#some crazy stuff here becase of the way scipy mat is shaped
medCoef = np.array(np.median(ac.todense(),1))[:,0]
pSup = sumSup/nSamp
indices = np.arange(nRegs)[np.abs(medCoef)>1E-21]
# put it in a dict for simplicity
solution = {}
if estErr:
solution['aveErr'] = aveErr
solution['sdErr'] = sdErr
solution['aveNullErr'] = aveNullErr
solution['sdNullErr'] = sdNullErr
if reduceX:
# need to go back to the original indicies
solution['aveCoef'] = np.zeros(nRegsFull)
solution['sdCoef'] = np.zeros(nRegsFull)
solution['medCoef'] = np.zeros(nRegsFull)
solution['pSup'] = np.zeros(nRegsFull)
solution['aveCoef'][coefIndex] = aveCoef
solution['sdCoef'][coefIndex] = sdCoef
solution['medCoef'][coefIndex] = medCoef
solution['pSup'][coefIndex] = pSup
solution['indices'] = coefIndex[indices]
else:
solution['aveCoef'] = aveCoef
solution['sdCoef'] = sdCoef
solution['medCoef'] = medCoef
solution['pSup'] = pSup
solution['indices'] = indices
nRegsHat = len(indices)
if nRegsHat>0 and estImp:
Xhat = X[:,indices]
# lets do the leave one out importance deal
errOutHat = np.zeros(nRegsHat)
if nRegsHat>1:
for j in range(nRegsHat):
Xprime = np.delete(Xhat,j,axis=1)
# residual bs time
sumErr = 0
sumSqErr = 0
for i in range(nSamp):
# cv to get the errors
err,tmpenm,tmpallVals = fitSampling(Xprime,ySample[:,i],alpha,10,method='cv',lambdas=[lam])
sumErr = err.mErr[0] + sumErr
sumSqErr = err.mErr[0]**2 + sumSqErr
errOutHat[j] = sumErr/nSamp
elif nRegsHat==1:
errOutHat[0] = aveNullErr
# lets do leave only one
errInHat = np.zeros(nRegsHat)
for j in range(nRegsHat):
Xprime = np.zeros((nObs,1))
Xprime[:,0] = Xhat[:,j]
# residual bs time
sumErr = 0
sumSqErr = 0
for i in range(nSamp):
# cv to get the errors
err,tmpenm,tmpallVals = fitSampling(Xprime,ySample[:,i],alpha,10,method='cv',lambdas=[lam])
sumErr = err.mErr[0] + sumErr
sumSqErr = err.mErr[0]**2 + sumSqErr
errInHat[j] = sumErr/nSamp
errOut = np.zeros(nRegs)
errOut[indices] = errOutHat
solution['errOut'] = errOut
errIn = np.zeros(nRegs)
errIn[indices] = errInHat
solution['errIn'] = errIn
else:
solution = {}
if estErr:
sumNullErr = 0
sumSqNullErr = 0
for i in range(nSamp):
# cv over this thing to get the null model errors
nullErr,a = fitSamplingNull(ySample[:,i],10, method='cv')
sumNullErr = sumNullErr + nullErr
sumSqNullErr = sumSqNullErr + nullErr**2
# get averages and variances
aveNullErr = sumNullErr/nSamp
sdNullErr = np.sqrt(sumSqNullErr/nSamp - aveNullErr**2)
aveErr = aveNullErr
sdErr = sdNullErr
solution['aveErr'] = aveErr
solution['sdErr'] = sdErr
solution['aveNullErr'] = aveNullErr
solution['sdNullErr'] = sdNullErr
solution['aveCoef'] = np.zeros(nRegsFull)
solution['sdCoef'] = np.zeros(nRegsFull)
solution['medCoef'] = np.zeros(nRegsFull)
solution['pSup'] = np.zeros(nRegsFull)
solution['indices'] = np.array([])
return solution, enm
def runTest(X,y):
nSamp = 250
nObs,nRegs = X.shape
# selection via bootstrap
err,enm,allVals = fitSampling(X,y,1,nSamp,method='bs')
errV = err.mErr
tmpIndex = np.argmin(errV)
# get the bootstrap full values
bsAll = allVals[tmpIndex,:]
# other important values
lam = enm.lambdas[tmpIndex]
yHat = enm.predict(X)[:,tmpIndex]
coefIndex = enm.indices
# get the bootstrap residual response samples
res = y - yHat
resCent = res-np.mean(res)
ySample = np.zeros((nObs,nSamp))
for i in range(nSamp):
resSample = st.sampleWR(resCent)
ySample[:,i] = yHat+resSample
# get the cv error estimated over bs residual responses
errSample = np.zeros(nSamp)
for i in range(nSamp):
err,tmp,tmpallVals = fitSampling(X,ySample[:,i],1,10,method='cv',lambdas=[lam])
errV = err.mErr
#should be only one value here
if len(errV)>1:
raise ValueError('something wrong with bs res cv')
errSample[i] = errV[0]
bsResAll = errSample
#now let repeat this stuff on the selected sample
Xhat = X[:,coefIndex]
err,enm,allVals = fitSampling(Xhat,y,1,nSamp,method='bs',lambdas=[lam])
bsSub = allVals
# get the cv error estimated over bs residual responses
errSample = np.zeros(nSamp)
for i in range(nSamp):
err,tmpenm,tmpallVals = fitSampling(Xhat,ySample[:,i],1,10,method='cv',lambdas=[lam])
errV = err.mErr
#should be only one value here
if len(errV)>1:
raise ValueError('something wrong with bs res cv')
errSample[i] = errV[0]
bsResSub = errSample
vals = np.zeros((4,nSamp))
vals[0,:] = bsAll
vals[1,:] = bsResAll
vals[2,:] = bsSub
vals[3,:] = bsResSub
return vals
def run(X,y,name):
nSamp = 100
alphaList = np.array([1])#np.arange(.1,1.1,.1)
nObs,nRegs = X.shape
sdY = np.sqrt(np.var(y))
# selection via bootstrap
bestMin = 1E10
for a in alphaList:
tmpErr,tmpEnm,allVals = fitSampling(X,y,a,nSamp,method='bs')
tmpErrV = tmpErr.mErr
tmpMin = np.min(tmpErrV)
print tmpMin
if tmpMin < bestMin:
bestMin = tmpMin
modelIndex = np.argmin(tmpErrV)
enm = tmpEnm
err = tmpErr
alpha = a
# important values
lam = enm.lambdas[modelIndex]
yHat = enm.predict(X)[:,modelIndex]
intercept = enm.intercept[modelIndex]
globalCoef = enm.coef[np.abs(enm.coef[:,modelIndex])>1E-21,modelIndex]
coefIndex = enm.indices[np.abs(enm.coef[:,modelIndex])>1E-21]
notEmpty = len(coefIndex) > 0
# get the bootstrap residual response samples
res = y - yHat
resCent = res-np.mean(res)
ySample = np.zeros((nObs,nSamp))
for i in range(nSamp):
resSample = st.sampleWR(resCent)
ySample[:,i] = yHat+resSample
notEmpty = len(coefIndex) > 0
if notEmpty:
# working on subset now
Xhat = X[:,coefIndex]
nObs,nRegsHat = Xhat.shape
sdXhat = np.sqrt(np.var(Xhat,0))
# residual bs time
sumErr = 0
sumSqErr = 0
sumNullErr = 0
sumSqNullErr = 0
sc = np.zeros(nRegsHat)
sSqc = np.zeros(nRegsHat)
sumSup = np.zeros(nRegsHat)
for i in range(nSamp):
# cv to get the errors
err,tmpEnm,tmpallVals = fitSampling(Xhat,ySample[:,i],alpha,10,method='cv',lambdas=[lam])
sumErr = err.mErr[0] + sumErr
sumSqErr = err.mErr[0]**2 + sumSqErr
# cv over this thing to get the null model errors
nullErr,a = fitSamplingNull(ySample[:,i],10, method='cv')
sumNullErr = sumNullErr + nullErr
sumSqNullErr = sumSqNullErr + nullErr**2
# need the coef
# they change so we need to map the back to the original
tmpEnm = enet.fit(Xhat,ySample[:,i], alpha,lambdas=[lam])
sc[tmpEnm.indices] = sc[tmpEnm.indices] + tmpEnm.coef[:,0]
sSqc[tmpEnm.indices] = sSqc[tmpEnm.indices] + tmpEnm.coef[:,0]**2
# find supports
occur = np.zeros(len(tmpEnm.coef[:,0]))
occur[abs(tmpEnm.coef[:,0])>1E-25] = 1.0
sumSup[tmpEnm.indices] = sumSup[tmpEnm.indices] + occur
# get averages and variances
aveErr = sumErr/nSamp
sdErr = np.sqrt(sumSqErr/nSamp - aveErr**2)
aveNullErr = sumNullErr/nSamp
sdNullErr = np.sqrt(sumSqNullErr/nSamp - aveNullErr**2)
aveCoef = sc/nSamp
sdCoef = np.sqrt(sSqc/nSamp - aveCoef**2)
pSup = sumSup/nSamp
# let do the leave one out importance deal
codN = np.zeros(nRegsHat)
if nRegsHat>1:
for j in range(nRegsHat):
Xprime = np.delete(Xhat,j,axis=1)
# residual bs time
sumErr = 0
sumSqErr = 0
for i in range(nSamp):
# cv to get the errors
err,tmpenm,tmpallVals = fitSampling(Xprime,ySample[:,i],alpha,10,method='cv',lambdas=[lam])
sumErr = err.mErr[0] + sumErr
sumSqErr = err.mErr[0]**2 + sumSqErr
codN[j] = sumErr/nSamp
elif nRegsHat==1:
codN[0] = aveNullErr
# lets do leave only one
cod1 = np.zeros(nRegsHat)
for j in range(nRegsHat):
Xprime = np.zeros((nObs,1))
Xprime[:,0] = Xhat[:,j]
# residual bs time
sumErr = 0
sumSqErr = 0
for i in range(nSamp):
# cv to get the errors
err,tmpenm,tmpallVals = fitSampling(Xprime,ySample[:,i],alpha,10,method='cv',lambdas=[lam])
sumErr = err.mErr[0] + sumErr
sumSqErr = err.mErr[0]**2 + sumSqErr
cod1[j] = sumErr/nSamp
# now we are going to estimate
# some pvalues. it should
# be noted: that we want to use
# permutation, to get a real feel
# for random or unrelated data
# but we dont want to run a bs
# for each perm (but we should)
# so in here we are using the
# ols stderr to get the test stat
# we will record a bunch of stuff
# from here to look at latter
p,tStat,tStatPerm,olsSE = regStat.netTTestPermute(Xhat,y,lam,alpha,nperm=1000)
n,m = tStatPerm.shape
#*****
# would like to check if any values are nan
# this most likly means the gpd failed in goodness of fit for tail
# will use direct permutation values as the estimate in that case
# *** some other form of automated checking might be good here
for i in range(n):
if np.isnan(p[i]):
z = tStatPerm[i,:]
tmp = np.sum(z>tStat[i])
p[i] = float(tmp)/float(m)
else:
# residual bs time
sumNullErr = 0
sumSqNullErr = 0
for i in range(nSamp):
# cv over this thing to get the null model errors
nullErr,a = fitSamplingNull(ySample[:,i],10, method='cv')
sumNullErr = sumNullErr + nullErr
sumSqNullErr = sumSqNullErr + nullErr**2
# get averages and variances
aveNullErr = sumNullErr/nSamp
sdNullErr = np.sqrt(sumSqNullErr/nSamp - aveNullErr**2)
aveErr = aveNullErr
sdErr = sdNullErr
# we have it all, lets print it
f = open('SLR2run_'+name+'.dat','w')
lam.tofile(f,sep="\t")
f.write("\n")
alpha.tofile(f,sep="\t")
f.write("\n")
intercept.tofile(f,sep="\t")
f.write("\n")
aveErr.tofile(f,sep="\t")
f.write("\n")
sdErr.tofile(f,sep="\t")
f.write("\n")
aveNullErr.tofile(f,sep="\t")
f.write("\n")
sdNullErr.tofile(f,sep="\t")
f.write("\n")
sdY.tofile(f,sep="\t")
f.write("\n")
if notEmpty:
coefIndex.tofile(f,sep="\t")
f.write("\n")
sdXhat.tofile(f,sep="\t")
f.write("\n")
globalCoef.tofile(f,sep="\t")
f.write("\n")
aveCoef.tofile(f,sep="\t")
f.write("\n")
sdCoef.tofile(f,sep="\t")
f.write("\n")
pSup.tofile(f,sep="\t")
f.write("\n")
codN.tofile(f,sep="\t")
f.write("\n")
cod1.tofile(f,sep="\t")
f.write("\n")
p.tofile(f,sep="\t")
f.write("\n")
olsSE.tofile(f,sep="\t")
f.write("\n")
f.close()
def estModel(XFull,y,nSamp=100,alphaList=np.array([1]),indType='coef',estErr=True,estImp=True,reduceX=False,params=[],):
"""Estimate a mean, median and standard deviation
for an elastic net model using bootstrap
residual.
Bootstrap resampling is used to select
model parameters, then the bs res at these
params is used on the full feature set X
to calculate the stats. nSamp is used for
selection and stat estimates.
Options
*indType* determines which stat to use for indicies.
Indices report the non zero entries in the sparse
regression model. Possible types:
coef - use coefs from full fit after the selection
(defult)
ave - use the avereage coefs after the bs, typically
includes many more regressors, not recomended
as the average removes sparsity benifit.
med - use the median value after the bs, typically
fewer regressors chosen then 'coef'
if *estErr* then 10 fold CV is used to estimate
the prediction error at each iteration of the bs.
This is ten extra iterations at each bs res
sample, but reduces the bias in prediction error.
The mean and sdDev of the CV error is then reported.
If *estImp* then the importance of each selected
regressor is estimated. For errOut this is the error
if the regressor is removed, multi varriate error.
For errIn this is the error if the regressor is alone,
univariate error.
If *reduceX* then the regressor matrix is ruduced
based on the full model fit after selection. Only
non zero coef are kept, much faster, but biases the
other stats.
NOTE: This was never tested after the last
migration, its possible the indices in the solution
do not match the orginal ones
If *params* are passed then we assume its a tuple
with the (lambda,alpha) model parameters. In this case
model selection is bipassed. and these params are used.
"""
nObs,nRegsFull = XFull.shape
# select full model values
if len(params)==2:
lam,alpha = params
enm = enet.fit(XFull,y,alpha,lambdas=[lam])[0]
else:
enm = select(XFull,y,nSamp,alphaList)
lam = enm.lambdas[0]
yHat = enm.predict(XFull)
intercept = enm.intercept[0]
globalCoef =enm.coef[np.abs(enm.coef)>1E-21]
coefIndex = enm.indices[np.abs(enm.coef)>1E-21]
alpha = enm.alpha
# now is when we reduce the x if we need too!
if reduceX:
nRegs = len(coefIndex)
if nRegs > 0:
X = XFull[:,coefIndex]
nObs, _ = X.shape
else:
X = XFull
nRegs = nRegsFull
# get the bootstrap residual response samples
res = y - yHat
resCent = res-np.mean(res)
ySample = np.zeros((nObs,nSamp))
for i in range(nSamp):
resSample = st.sampleWR(resCent)
ySample[:,i] = yHat+resSample
if nRegs > 0:
# residual bs time
if estErr:
sumErr = 0
sumSqErr = 0
sumNullErr = 0
sumSqNullErr = 0
sc = np.zeros(nRegs)
sSqc = np.zeros(nRegs)
ac = lil_matrix((nRegs,nSamp))
sumSup = np.zeros(nRegs)
for i in range(nSamp):
# cv to get the errors
if estErr:
err,tmpEnm,tmpallVals = fitSampling(X,ySample[:,i],alpha,10,method='cv',lambdas=[lam])
sumErr = err.mErr[0] + sumErr
sumSqErr = err.mErr[0]**2 + sumSqErr
# cv over this thing to get the null model errors
nullErr,a = fitSamplingNull(ySample[:,i],10, method='cv')
sumNullErr = sumNullErr + nullErr
sumSqNullErr = sumSqNullErr + nullErr**2
# need the coef
# they change so we need to map the back to the original
tmpEnm = enet.fit(X,ySample[:,i], alpha,lambdas=[lam])
sc[tmpEnm.indices] = sc[tmpEnm.indices] + tmpEnm.coef[:,0]
sSqc[tmpEnm.indices] = sSqc[tmpEnm.indices] + tmpEnm.coef[:,0]**2
if len(tmpEnm.indices)>0:
ac[tmpEnm.indices,i] = tmpEnm.coef
# find supports
occur = np.zeros(len(tmpEnm.coef[:,0]))
occur[abs(tmpEnm.coef[:,0])>1E-25] = 1.0
sumSup[tmpEnm.indices] = sumSup[tmpEnm.indices] + occur
# get averages and variances
if estErr:
aveErr = sumErr/nSamp
sdErr = np.sqrt(sumSqErr/nSamp - aveErr**2)
aveNullErr = sumNullErr/nSamp
sdNullErr = np.sqrt(sumSqNullErr/nSamp - aveNullErr**2)
aveCoef = sc/nSamp
sdCoef = np.sqrt(sSqc/nSamp - aveCoef**2)
#some crazy stuff here becase of the way scipy mat is shaped
medCoef = np.array(np.median(ac.todense(),1))[:,0]
pSup = sumSup/nSamp
# lets do the selection
if indType=='coef':
indices = coefIndex
elif indType=='med':
indices = np.arange(nRegs)[np.abs(medCoef)>1E-21]
elif indType=='ave':
indices = np.arange(nRegs)[np.abs(aveCoef)>1E-21]
else:
raise ValueError('The indType '+indType+' is not valid.')
# put it in a dict for simplicity
solution = {}
if estErr:
solution['aveErr'] = aveErr
solution['sdErr'] = sdErr
solution['aveNullErr'] = aveNullErr
solution['sdNullErr'] = sdNullErr
if reduceX:
# need to go back to the original indicies
solution['aveCoef'] = np.zeros(nRegsFull)
solution['sdCoef'] = np.zeros(nRegsFull)
solution['medCoef'] = np.zeros(nRegsFull)
solution['pSup'] = np.zeros(nRegsFull)
solution['aveCoef'][coefIndex] = aveCoef
solution['sdCoef'][coefIndex] = sdCoef
solution['medCoef'][coefIndex] = medCoef
solution['pSup'][coefIndex] = pSup
solution['indices'] = coefIndex[indices]
else:
solution['aveCoef'] = aveCoef
solution['sdCoef'] = sdCoef
solution['medCoef'] = medCoef
solution['pSup'] = pSup
solution['indices'] = indices
nRegsHat = len(indices)
if nRegsHat>0 and estImp:
Xhat = X[:,indices]
# lets do the leave one out importance deal
errOutHat = np.zeros(nRegsHat)
if nRegsHat>1:
for j in range(nRegsHat):
Xprime = np.delete(Xhat,j,axis=1)
# residual bs time
sumErr = 0
sumSqErr = 0
for i in range(nSamp):
# cv to get the errors
err,tmpenm,tmpallVals = fitSampling(Xprime,ySample[:,i],alpha,10,method='cv',lambdas=[lam])
sumErr = err.mErr[0] + sumErr
sumSqErr = err.mErr[0]**2 + sumSqErr
errOutHat[j] = sumErr/nSamp
elif nRegsHat==1:
errOutHat[0] = aveNullErr
# lets do leave only one
errInHat = np.zeros(nRegsHat)
for j in range(nRegsHat):
Xprime = np.zeros((nObs,1))
Xprime[:,0] = Xhat[:,j]
# residual bs time
sumErr = 0
sumSqErr = 0
for i in range(nSamp):
# cv to get the errors
err,tmpenm,tmpallVals = fitSampling(Xprime,ySample[:,i],alpha,10,method='cv',lambdas=[lam])
sumErr = err.mErr[0] + sumErr
sumSqErr = err.mErr[0]**2 + sumSqErr
errInHat[j] = sumErr/nSamp
errOut = np.zeros(nRegs)
errOut[indices] = errOutHat
solution['errOut'] = errOut
errIn = np.zeros(nRegs)
errIn[indices] = errInHat
solution['errIn'] = errIn
else:
solution = {}
if estErr:
sumNullErr = 0
sumSqNullErr = 0
for i in range(nSamp):
# cv over this thing to get the null model errors
nullErr,a = fitSamplingNull(ySample[:,i],10, method='cv')
sumNullErr = sumNullErr + nullErr
sumSqNullErr = sumSqNullErr + nullErr**2
# get averages and variances
aveNullErr = sumNullErr/nSamp
sdNullErr = np.sqrt(sumSqNullErr/nSamp - aveNullErr**2)
aveErr = aveNullErr
sdErr = sdNullErr
solution['aveErr'] = aveErr
solution['sdErr'] = sdErr
solution['aveNullErr'] = aveNullErr
solution['sdNullErr'] = sdNullErr
solution['aveCoef'] = np.zeros(nRegsFull)
solution['sdCoef'] = np.zeros(nRegsFull)
solution['medCoef'] = np.zeros(nRegsFull)
solution['pSup'] = np.zeros(nRegsFull)
solution['indices'] = np.array([])
return solution, enm