def sample(counter=simulationCounter):
"""Sample new Parameter"""
alphaNew = prior() # sample from prior
"""Sample synthetic Data (Beta-coalescent)"""
P, q = re.P_and_q_lambda_beta(n_leaves, (alphaNew,))
coalescentNew = lc.simulateLambdaBeta(n_leaves, self.mutationRate, float("inf"), alphaNew, P, q)
counter[0] += 1 # increment simulation counter
return alphaNew, coalescentNew
Pi_1 = []
Pi_2 = []
coalescentType = coalescentType.lower()
print "Running %i simulations of a %s coalescent, with n=%i, theta=%s, alpha=%s, phi=%s..."%(trials,coalescentType,n,str(round(theta,3)),str(round(beta,3)),str(round(psi,3)))
t1 = time.time()
if coalescentType == 'xi_beta':
P,q = re.P_and_q_lambda_beta(n,(beta,))
for i in range(trials):
Pi_2.append(lc.simulateLambdaBeta_FourWay(n,theta/2.,T_max,beta,P,q))
elif coalescentType == 'lambda_beta' or coalescentType=='xi_lambda_beta':
P,q = re.P_and_q_lambda_beta(n,(beta,))
for i in range(trials):
Pi_2.append(lc.simulateLambdaBeta(n,theta/2.,T_max,beta,P,q))
elif coalescentType =='lambda_ew':
for i in range(trials):
Pi_2.append(lc.simulateLambdaEldonWakely(n,theta/2.,T_max,psi))
elif coalescentType == 'xi_ew':
for i in range(trials):
Pi_2.append(lc.simulateLambdaEldonWakely_FourWay(n,theta/2.,T_max,psi))
elif coalescentType == 'kingman' or coalescentType == 'xi_kingman':
for i in range(trials):
Pi_2.append(lc.simulateKingman(n,theta/2.,T_max))
elif coalescentType == 'lambda_pointmass':
for i in range(trials):
Pi_2.append(lc.simulateLambdaPoint(n,theta/2.,T_max,psi))
elif coalescentType == 'xi_pointmass':
for i in range(trials):
Pi_2.append(lc.simulateLambdaPoint_FourWay(n,theta/2.,T_max,psi))
