def hastings_factor(self):
"""
Compute the hastings factor.
"""
tau = (self.adaptive_scale_factor * self.proposal_sd)**2
cur_val = self.stochastic.value
last_val = self.stochastic.last_value
lp_for = pm.lognormal_like(cur_val, mu=np.log(last_val), tau=tau)
lp_bak = pm.lognormal_like(last_val, mu=np.log(cur_val), tau=tau)
if self.verbose > 1:
print((self._id + ': Hastings factor %f' % (lp_bak - lp_for)))
return lp_bak - lp_for
def hastings_factor(self):
"""
Compute the hastings factor.
"""
tau = (self.adaptive_scale_factor * self.proposal_sd) ** 2
cur_val = self.stochastic.value
last_val = self.stochastic.last_value
lp_for = pm.lognormal_like(cur_val, mu=np.log(last_val), tau=tau)
lp_bak = pm.lognormal_like(last_val, mu=np.log(cur_val), tau=tau)
if self.verbose > 1:
print self._id + ': Hastings factor %f' % (lp_bak - lp_for)
return lp_bak - lp_for
def get_likelihood_M0(map_M0, x, pwr, sigma, tau, obstype):
A0 = get_variables_M0(map_M0)
A0 = curve_fit_M0(x, pwr, A0, sigma)
if obstype == '.logiobs':
return pymc.normal_like(pwr, get_spectrum_M0(x, A0), tau)
else:
return pymc.lognormal_like(pwr, get_spectrum_M0(x, A0), tau)
def get_likelihood_M2(map_M2, x, pwr, sigma, tau, obstype):
A2 = get_variables_M2(map_M2)
A2 = curve_fit_M2(x, pwr, A2, sigma)
if obstype == '.logiobs':
return pymc.normal_like(pwr, get_spectrum_M2(x, A2), tau)
else:
return pymc.lognormal_like(pwr, get_spectrum_M2(x, A2), tau)
def get_likelihood_M1(map_M1, x, pwr, sigma, tau, obstype):
A1 = get_variables_M1(map_M1)
A1 = curve_fit_M1(x, pwr, A1, sigma)
if obstype == '.logiobs':
return pymc.normal_like(pwr, get_spectrum_M1(x, A1), tau)
else:
return pymc.lognormal_like(pwr, get_spectrum_M1(x, A1), tau)
def integrand(y, x):
#centered on x0,y0, delta around that
e1 = np.exp(pymc.lognormal_like(y+y0, np.log(m*(x+x0)), 1./sig**2))
e2 = np.exp(pymc.mv_normal_cov_like(np.array([x,y]), np.array([0,0]), cov))
return e1*e2
def get_likelihood_M0(map_M0, x, pwr, sigma, obstype):
tau = 1.0 / (sigma ** 2)
A0 = get_variables_M0(map_M0)[0:3]
A0 = curve_fit_M0(x, pwr, A0, sigma)
if obstype == '.logiobs':
return pymc.normal_like(pwr, get_spectrum_M0(x, A0), tau)
else:
return pymc.lognormal_like(pwr, get_spectrum_M0(x, A0), tau)
def SIR_simplex_sample(mu, tau, cutoff, sum_val, N, N_proposals=1000, N_samps=1000):
"""
Returns raw log-weights, indices chosen and SIR samples for sets of N draws
from a truncated lognormal distribution, conditioned so that their sum is
equal to sum_val.
This SIR algorithm will fail miserably unless sum_val is relatively likely
given N and the parameters of the lognormal distribution.
:Parameters:
- mu : float
The mean parameter.
- tau : float
The precision parameter.
- cutoff : float
The truncation value.
- sum_val : float
The sum that is being conditioned on.
- N : integer
The number of variates in each vector
- N_proposals : integer
The number of vectors to propose.
- N_samps : integer
The number of vectors to return.
"""
# Draw samples, compute missing values, evaluate log-weights.
samps = np.exp(geto_truncnorm(mu, tau, log(cutoff), (N-1,N_proposals)))
last_vals = sum_val - np.sum(samps,axis=0)
weights = np.array([pm.lognormal_like(last_val_now, mu, tau) for last_val_now in last_vals])
# Check that there are at least some positive weights.
where_pos = np.where(weights>-1e308)
if len(where_pos[0])==0:
raise RuntimeError, 'No weights are positive. You have used a shitty value for N.'
# Normalize and exponentiate log-weights.
weights[where(last_vals>cutoff)]=-np.Inf
weights -= log_sum(weights)
# Append missing values to samples.
samps = np.vstack((samps,last_vals))
# Slice and return.
ind=np.array(pm.rcategorical(p=np.exp(weights),size=N_samps),dtype=int)
return weights, ind, samps[:,ind]
def y(value=0.01, x=x):
return pymc.lognormal_like(value, mu=x[0], tau=1.)
def y(value=0.01, x=x):
return pymc.lognormal_like(value, mu=x[0], tau=1.)
def Y(x=X, z=z):
return mc.lognormal_like(
z - x,
1,
0.4,
)