def ll_q(params=[None,None,None],data=[None,None,None],H=100,verbose=1,expmethod='alglin',expmethodsecond='pade',loga=1,grid='default',positive=1,dominance=0.5,threshold=1e-5,numberprecision=128,thresholdfrerot=1e-5):
"""
Computes the likelihood when given the data, conditioned you never reach fixation until the last sampling time.
"""
Hsmall=H-2
if verbose:
#if 1:
print "data I,M,T",data
print "params t0,gamma,Ne",params
print "dominance ",dominance
print "H ",H
print "Hsmall ",Hsmall
raw_input(" Press a key to continue:here,now ")
#------------- define parameters -------------------------------
t_=params[0];gamma=params[1];Ne=params[2];
#-------------- redefine expmethod H ----------------------------
expmethodOri=[expmethod][0]
expmethod,H=funcs.process_expmethod(Ne=Ne,gamma=gamma,dominance=dominance,grid=grid,gammathreshold=40,H=H,expmethod=expmethod,expmethodsecond=expmethodsecond)
if expmethodOri!=expmethod:
print "expmethod adjusted because high gamma"
print "expmethod new,H,dominance ",expmethod,H,dominance
Hsmall=H-2
if verbose:
print "after processing...."
print "data I,M,T",data
print "params t0,gamma,Ne",params
print "H ",H
print "Hsmall ",Hsmall
#raw_input(" Press a key to continue ")
#------------- define data -------------------------------------
I=data[0];M=data[1];T=data[2]
#---- check allele age is appropriate, if not return np.nan ----
I,M,T=preprocess(time=t_,Iori=I,Mori=M,Tori=T,verbose=0)
if verbose:
print "Input data after preprocessing I,M,T",I,M,T
print "input allele age ",t_
if I==None and M==None and T==None:
if verbose:
print "likelihood is",0
print "OUTPUT: ",np.nan
return 5*[np.nan] #Attention! number of outputs.
# Compute all t[j]-t[j-1]/2Ne (store in DeltaT).
DeltaT=list((np.array(T)-np.array([t_]+T[:-1]))/(2.0*Ne))
if verbose: print "DeltaT ",DeltaT
DeltaT.append(sum(DeltaT))
# -----------------Define the space grids -----------------------
# xx is for the grid for transition from any frequ
# oriFI is the index of the 1/2Ne freq for the transition from 1/2Ne
# xxSmall is for the grid for transition from any frequ, without boundaries
# oriFI-1 is the index of the 1/2Ne freq for the transition from 1/2Ne
if grid=='default':
xx,oriFI=Grids.Ne_grid(H,Ne)
elif grid=='symmetric':
xx=Grids.symmetric_grid(H)
elif grid=='uniform':
xx,oriFI=Grids.uniform_grid(H,Ne)
elif grid=='expo':
indice=int(0.10*H)
xx,oriFI=Grids.exponential_grid_Ne(indice=indice,H=H,Ne=Ne)
xxSmall=xx[1:-1]
maxi=max(np.diff(xx))
if verbose:
print "grid ",grid
print "xxSmall ",xxSmall[0:10],'...',xxSmall[-10:]
print "orginal frequency ",xxSmall[oriFI-1]
print "what the frq should be ",1./(2*Ne)
#Check gamma is appopropriate, gamma more than 60 gives unstabilities ---------------------------
#if abs(gamma)>60:
# raise ValueError("gamma is too high or too small for current double precision, max is 60")
#elif gamma>=1./maxi or gamma<=-1./maxi:
# raise ValueError("gamma is too high or too small for grid space, max is %f"%(1./maxi))
Qmat,Deltamat,Betamat=AlgLin.Qmatrix(gamma=gamma,xx=xx,verbose=1,h=dominance)
qmat=Qmat[1:-1,1:-1]
if verbose:
print "xx.shape ",xx.shape
print "Qmat.shape ",Qmat.shape
print "rate out 1/2Ne of qmat\n ",qmat[oriFI-1,oriFI]
print "rate out 1/2Ne of Qmat\n ",Qmat[oriFI,oriFI+1]
# --------- expqt for all t --------------------------------
#---------- matrix diagonalization-babik--------------------
if expmethod=='alglin':
# d,dinv,s,o,oT,lam=AlgLin.tools_q_expo(Q=Qmat,Beta=Betamat,Delta=Deltamat)
PtMatrices,flag=AlgLin.ExpMatrices_q(Qmat=Qmat,Betamat=Betamat,Deltamat=Deltamat,Times=DeltaT,verbose=verbose,threshold=threshold)
if verbose:
print "FLAG: ",flag
if flag == 'warning':
print "warning, the exponentiation seems problematic"
#----------- pade approximation ---------------------------
elif expmethod=="pade":
PtMatrices=[AlgLin.expm((dt)*qmat) for dt in DeltaT]
#---------- high precision call ----------------------------
elif expmethod=='prec':
if grid=="default":
argu_frerot=[numberprecision,thresholdfrerot,gamma,dominance,H,1,Ne]+DeltaT
argu_frerot=" ".join([str(w) for w in argu_frerot])
else:
raise ValueError("only grid implemented is the default grid")
command="./ancientSelectionApaSmallQ %s"%argu_frerot
print command
os.system(command)
PtMatrices=[np.loadtxt('exp_Qt_%i.dat'%dtindex, dtype=np.float64,delimiter=" ") for dtindex in range(len(DeltaT))]
[os.system("rm exp_Qt_%i.dat"%dtindex) for dtindex in range(len(DeltaT))]
if len(PtMatrices)!=len(T)+1:
raise ValueError("something went wrong with matrix computation")
#PtMatrices=[] #where all matrices are stored
#for dtindex,dt in enumerate(DeltaT):
# if verbose: print 'Interval of time dt ',dt
# if expmethod=="babik":
# Ptmatrice=AlgLin.expBabikq(d=d,dinv=dinv,o=o,ot=oT,lam=lam,time=dt,positive=True)
# elif expmethod=="pade":
# Ptmatrice=AlgLin.expm((dt)*qmat)
# elif expmethod=="frerot":
# #import them from the right file
# matname='exp_Qt_%i.dat'%dtindex
# print matname
# Ptmatrice=np.eye(Hsmall)
# #Ptmatrice=np.loadtxt(matname, dtype=np.float64,delimiter=" ")
# if verbose:
# print "shape of Ptmatrice ",Ptmatrice.shape
# PtMatrices.append(Ptmatrice)
Ptfinal=PtMatrices[-1] ## "renormalisation"
PtOri=PtMatrices[0] ## I.C.
ExpMat=PtMatrices[1:-1]## all others
if verbose:
#check starting point, i.e. that grids works well
print "starting point ",(2.*Ne)*xxSmall[oriFI-1]
print "PtOri ",PtOri
#----------- nofixation proba -----------------------------
prob_nofix=np.sum(Ptfinal[oriFI-1,])
#----------- initial conditions ---------------------------
IC=[]
for j1 in range(Hsmall):
#print funcs.sampling(n=M[0],mut=I[0],f=xxSmall[j1])
#print PtOri[oriFI-1,j1]
IC.append(funcs.sampling(n=M[0],mut=I[0],f=xxSmall[j1])*PtOri[oriFI-1,j1])
#----------- Loop over next times ---------------------------
L=IC # store in L, elements of the sum
if verbose:
print "IC ",L
print "len(L) ",len(L)
for ind in range(1,len(T)):
Pt=ExpMat[ind-1];n=M[ind];mut=I[ind];
Lnext=[]
if verbose:
print "Pt.shape ",Pt.shape
print "Pt sum rows ",np.sum(Pt,axis=1)
for j in range(Hsmall):
somme =sum(Pt[:,j]*L)
echant=funcs.sampling(mut=mut,n=n,f=xxSmall[j])
#echant=1
Lnext.append(echant*somme)
L=Lnext
if verbose:
print "L\n",L
#----------------------------------------- return values -----------------------------------
if prob_nofix==0 and prob_nofix==sum(L):
proba_norm=0
else:
proba_norm=sum(L)/prob_nofix
if loga:
if verbose:
print "Returning -log lik................"
print "sum(L) ",sum(L)
print "prob_nofix ",prob_nofix
print "lik ",proba_norm
print "OUTPUT: -log lik ",-np.log(proba_norm)
return -np.log(proba_norm),-np.log(sum(L)),PtOri,ExpMat,prob_nofix
else:
if verbose:
print "Returning lik..................."
print "not loga "
print "len(L) ",len(L)
print "sum(L) ",sum(L)
print "prob_nofix ",prob_nofix
print "OUTPUT: sum(L)/prob_nofix ",proba_norm
return proba_norm,sum(L),PtOri,ExpMat,prob_nofix
def ll(params=[None,None,None],data=[None,None,None],H=100,verbose=0,expmethod='alglin',expmethodsecond='pade',loga=0,grid='default',dominance=0.5,threshold=1e-5,numberprecision=128,thresholdfrerot=1e-5):
"""
Computes the (unconditional) likelihood when given the data.
"""
if verbose:
print "data I,M,T",data
print "params t0,gamma,Ne",params
print "H ",H
raw_input(" Press a key to continue ")
#------------- define parameters -------------------------------
t_=params[0];gamma=params[1];Ne=params[2];
#-------------- redefine expmethod H ----------------------------
expmethod,H=funcs.process_expmethod(Ne=Ne,gamma=gamma,dominance=dominance,grid=grid,gammathreshold=40,H=H,expmethod=expmethod,expmethodsecond=expmethodsecond)
if verbose:
print "expmethod,H,dominance,verbose ",expmethod,H,dominance,verbose
if verbose:
print "after processing...."
print "data I,M,T",data
print "params t0,gamma,Ne",params
print "H ",H
#raw_input(" Press a key to continue ")
#------------- define data -------------------------------------
I=data[0];M=data[1];T=data[2]
#---- check allele age is appropriate, if not return np.nan ----
I,M,T=preprocess(time=t_,Iori=I,Mori=M,Tori=T,verbose=0)
if verbose:
print "Input data after preprocessing I,M,T",I,M,T
print "input allele age ",t_
if I==None and M==None and T==None:
if verbose:
print "likelihood is",0
print "OUTPUT: ",np.nan
return 4*[np.nan] #Attention! number of outputs.
# --------Compute all t[j]-t[j-1]/2Ne (store in DeltaT).--------
DeltaT=list((np.array(T)-np.array([t_]+T[:-1]))/(2.0*Ne))
if verbose: print "DeltaT ",DeltaT
# ------------Define the space grids ---------------------------
if grid=='default':
xx,oriFI=Grids.Ne_grid(H,Ne)
elif grid=='symmetric':
xx=Grids.symmetric_grid(H)
elif grid=='uniform':
xx,oriFI=Grids.uniform_grid(H,Ne)
elif grid=='expo':
indice=int(0.10*H)
xx,oriFI=Grids.exponential_grid_Ne(indice=indice,H=H,Ne=Ne)
maxi=max(np.diff(xx))
# ---------Check gamma is appopropriate -------------------------
#if abs(gamma)>60:
# raise ValueError("gamma is too high or too small for current double precision, max is 60")
#elif gamma>=1./maxi or gamma<=-1./maxi:
# raise ValueError("gamma is too high or too small for grid space, max is %f"%(1./maxdiff))
#Compute the one and unique Q
Qmat,Deltamat,Betamat=AlgLin.Qmatrix(gamma=gamma,xx=xx,verbose=0,h=dominance)
# --------- expqt for all t --------------------------------
#---------- matrix diagonalization-babik--------------------
if expmethod=='alglin':
#print "HERE", sys.exit()
PtMatrices,flag=AlgLin.ExpMatrices_Q(Qmat=Qmat,Betamat=Betamat,Deltamat=Deltamat,Times=DeltaT,verbose=verbose,threshold=threshold)
if verbose:
print "FLAG: ",flag
if flag == 'warning':
print "warning, the exponentiation seems problematic"
#----------- pade approximation ---------------------------
elif expmethod=="pade":
PtMatrices=[AlgLin.expm((dt)*Qmat) for dt in DeltaT]
#---------- high precision call ----------------------------
elif expmethod=='prec':
if grid=="default":
argu_frerot=[numberprecision,thresholdfrerot,gamma,dominance,H,1,Ne]+DeltaT
argu_frerot=" ".join([str(w) for w in argu_frerot])
else:
raise ValueError("only grid implemented is the default grid")
command="./ancientSelectionApaBigQ %s"%argu_frerot
print command
os.system(command)
PtMatrices=[np.loadtxt('exp_Qt_%i.dat'%dtindex, dtype=np.float64,delimiter=" ") for dtindex in range(len(DeltaT))]
[os.system("rm exp_Qt_%i.dat"%dtindex) for dtindex in range(len(DeltaT))]
if len(PtMatrices)!=len(T):
print len(PtMatrices)
raise ValueError("something went wrong with matrix computation: %s")
PtOri=PtMatrices[0] ## I.C.
ExpMat=PtMatrices[1:] ## all others
#if verbose and expmethod=='babik':
# stepfinal=(T[-1]-t_)/(2.0*Ne))
# Ptfinal,flag=AlgLin.ExpMatrices_Q(Qmat=Qmat,Betamat=Betamat,Deltamat=Deltamat,Times=[stepfinal],verbose=1)[0]
# print "expected no fix",1-Ptfinal[oriFI,0]-Ptfinal[oriFI,-1]
#----------- initial conditions ---------------------------
IC=[]
for j1 in range(H):
#if verbose:
#print 'sampling1 ',sampling(n=M[0],mut=I[0],f=xxOri[j1])
IC.append(funcs.sampling(n=M[0],mut=I[0],f=xx[j1])*PtOri[oriFI,j1])
#----------- Loop over next times ---------------------------
L=IC
for ind in range(1,len(T)):
Pt=ExpMat[ind-1];n=M[ind];mut=I[ind];
Lnext=[]
for j in range(H):
somme =sum(Pt[:,j]*L)
echant=funcs.sampling(mut=mut,n=n,f=xx[j])
Lnext.append(echant*somme)
L=Lnext
if verbose:
print "L\n",L
#------------- return values --------------------------
if loga:
print "LOGA.............."
if verbose:
print "Returning -log lik................"
print "-log lik sum(L) ",-np.log(sum(L))
#print "prob_nofix ",prob_nofi
return -np.log(sum(L)),oriFI,PtOri,ExpMat
else:
if verbose:
print "Returning lik..................."
print "not loga "
print "len(L) ",len(L)
print "lik sum(L) ",sum(L)
print "lik ",sum(L)
return sum(L),oriFI,PtOri,ExpMat