def test_independent(self):
# Use IID data
x = [pymc.geweke(np.random.normal(size=1000), intervals=5)[0][1] for _ in range(10000)]
assert_approx_equal(np.var(x), 1, 1)
# If the model has converged, 95% the scores should lie
# within 2 standard deviations of zero, under standard normal model
intervals = 40
x = np.transpose(pymc.geweke(np.random.normal(size=10000), intervals=intervals))[1]
assert(sum(np.abs(x) < 2) >= int(0.9 * intervals))
def test_independent(self):
# Use IID data
x = [pymc.geweke(np.random.normal(size=1000),intervals=5, maxlag=5)[0][1]
for _ in range(1000)]
assert_approx_equal(np.var(x), 1, 1)
# If the model has converged, 95% the scores should lie
# within 2 standard deviations of zero, under standard normal model
intervals = 40
x = np.transpose(pymc.geweke(
np.random.normal(size=10000),intervals=intervals))[1]
assert(sum(np.abs(x) < 2) >= int(0.9 * intervals))
def convergence_diagnose_birt(m, a):
# birt_model = pymc.MCMC(...)
pymc.raftery_lewis(m.a, q=0.025, r=0.01)
scores = pymc.geweke(m.a, intervals=20)
pymc.Matplot.geweke_plot(scores)
pymc.gelman_rubin(m)
def analyzeConvergence(dbFilename, db, pn, burnin):
print 'ANALYZING {0}'.format(pn)
vals = np.array(getParameter(db, pn, burnin=burnin))
convDict = OrderedDict()
gw = pymc.geweke(vals)
gwDict = OrderedDict()
gwDict['scores'] = gw
frac2SD = len([x for x in gw if x[1] > -2 and x[1] < 2]) / float(len(gw))
gwDict['frac_2sd'] = frac2SD
convDict['geweke'] = gwDict
rl = pymc.raftery_lewis(vals, 0.025, r=0.01)
rlDict = OrderedDict()
rlDict['iter_req_acc'] = rl[0]
rlDict['thin_first_ord'] = rl[1]
rlDict['burnin'] = rl[2]
rlDict['iter_total'] = rl[3]
rlDict['thin_ind'] = rl[4]
convDict['raftery_lewis'] = rlDict
print ''
return convDict
def plot(temp_path, traces):
for i in range(len(traces)):
trace_name = 'trace_' + str(i)
pymc.Matplot.plot(traces[i], name=trace_name, path=temp_path, verbose=0)
summary(traces[i], trace_name)
try:
scores = pymc.geweke(traces[i])
pymc.Matplot.geweke_plot(scores, name='gweke_' + str(i), path=temp_path)
except:
print 'Failed to create Geweke plot.'
def geweke_test_problem(model):
for name, node_desc in model.iter_stochastics():
node = node_desc['node']
output = pm.geweke(node)
values = np.array(output)[:, 1]
if np.any(np.abs(values) > 2):
print
print "Geweke problem was found in: %s" % name
return True
return False
def geweke_test_problem(model):
for name, node_desc in model.iter_stochastics():
node = node_desc['node']
output = pm.geweke(node)
values = np.array(output)[:,1]
if np.any(np.abs(values) > 2):
print
print "Geweke problem was found in: %s" % name
return True
return False
def geweke_statistics(model_mcmc, features):
geweke_scores = []
# Geweke Test
for feature in features:
print feature
scores = pymc.geweke(model_mcmc.trace('b_'+feature)[:])
geweke_scores.append(scores)
return geweke_scores
# function to perform cross validation
"""
def check_geweke(model, assert_=True):
# Test for convergence using geweke method
for param in model.group_params.values():
geweke = np.array(pm.geweke(param))
if assert_:
assert (np.any(np.abs(geweke[:,1]) < 2)), 'Chain of %s not properly converged'%param
return False
else:
if np.any(np.abs(geweke[:,1]) > 2):
print("Chain of %s not properly converged" % param)
return False
return True
def check_geweke(model, assert_=True):
# Test for convergence using geweke method
for name, param in model.iter_stochastics():
geweke = np.array(pm.geweke(param['node']))
if np.any(np.abs(geweke[:,1]) > 2):
msg = "Chain of %s not properly converged" % param
if assert_:
raise AssertionError(msg)
else:
print msg
return False
return True
def check_geweke(model, assert_=True):
# Test for convergence using geweke method
for name, param in model.iter_stochastics():
geweke = np.array(pm.geweke(param['node']))
if np.any(np.abs(geweke[:, 1]) > 2):
msg = "Chain of %s not properly converged" % param
if assert_:
raise AssertionError(msg)
else:
print(msg)
return False
return True
def test_simple(self):
intervals = 20
scores = pymc.geweke(S, intervals=intervals)
a_scores = scores['a']
assert_equal(len(a_scores), intervals)
# Plot diagnostics (if plotting is available)
try:
from pymc.Matplot import geweke_plot as plot
plot(scores, path=DIR, verbose=0)
except ImportError:
pass
def check_geweke(model, assert_=True):
# Test for convergence using geweke method
for param in model.group_params.itervalues():
geweke = np.array(pm.geweke(param))
if assert_:
assert (np.any(np.abs(geweke[:, 1]) < 2)
), 'Chain of %s not properly converged' % param
return False
else:
if np.any(np.abs(geweke[:, 1]) > 2):
print "Chain of %s not properly converged" % param
return False
return True
def test_simple(self):
intervals = 20
scores = pymc.geweke(S, intervals=intervals, maxlag=5)
a_scores = scores['a']
assert_equal(len(a_scores), intervals)
# Plot diagnostics (if plotting is available)
try:
from pymc.Matplot import geweke_plot as plot
plot(scores, path=DIR)
except ImportError:
pass
def test_simple(self):
scores = pymc.geweke(S, intervals=20)
a_scores = scores['a']
assert_equal(len(a_scores), 20)
# If the model has converged, 95% the scores should lie
# within 2 standard deviations of zero, under standard normal model
assert(sum(np.abs(np.array(a_scores)[:, 1]) > 1.96) < 2)
# Plot diagnostics (if plotting is available)
try:
from pymc.Matplot import geweke_plot as plot
plot(scores, path=DIR, verbose=0)
except ImportError:
pass
def test_simple(self):
scores = pymc.geweke(S, intervals=20)
a_scores = scores['a']
assert_equal(len(a_scores), 20)
# If the model has converged, 95% the scores should lie
# within 2 standard deviations of zero, under standard normal model
assert(sum(np.abs(np.array(a_scores)[:,1]) > 1.96) < 2)
# Plot diagnostics (if plotting is available)
try:
from pymc.Matplot import geweke_plot as plot
plot(scores, path=DIR, verbose=0)
except ImportError:
pass
def plot_geweke(self, n_chains = None, burn = 20., n_trace = 1000, axes_style = "ticks", savefig = True, **kwds):
path = kwds.get("path", "Plots/")
name = kwds.get("name", self.model_name+"_Geweke")
format = kwds.get("format", ".png")
Stochs = []
if not hasattr(self, "_plot_traces"):
self._select_trace()
if len(self.LD.trace(self._plot_traces[0], chain = n_chains)[:])< n_trace:
n_trace = len(self.LD.trace(self._plot_traces[0], chain = n_chains)[:])
n_values = np.linspace(len(self.LD.trace(self._plot_traces[0], chain = n_chains)[:])*burn/100,
len(self.LD.trace(self._plot_traces[0], chain = n_chains)[:])-1,n_trace, dtype = int)
Stochs = self._plot_traces
rows = int(len(Stochs)/3+1)
fig, axs = plt.subplots(rows, 3, sharex=True, sharey=True, figsize = (13, 23))
for i, Stoch in enumerate(Stochs):
axa = axs[i/3,i- 3*(i/3)]
try:
geweke_val = pm.geweke(self.LD.trace(Stoch, chain = n_chains)[n_values])
self._plot_geweke_f(geweke_val, Stoch , ax = axa)
except ValueError:
print Stoch
continue
except LinAlgError:
print "Alg",Stoch
continue
if savefig == True:
if not os.path.exists(path):
os.makedirs(path)
plt.savefig(path+name+"_"+Stoch+format, transparent = True)
def geweke_problems(model, fname=None, **kwargs):
"""
return a list of nodes who were detected as problemtic according to the geweke test
Input:
fname : string (deafult - None)
Save result to file named fname
kwargs : keywords argument passed to the geweke function
"""
#search for geweke problems
g = pm.geweke(model.mc)
problems = []
for node, output in g.iteritems():
values = np.array(output)[:,1]
if np.any(np.abs(values) > 2):
problems.append(node)
#write results to file if needed
if fname is not None:
with open(fname, 'w') as f:
for node in problems:
f.write(node)
return problems
def geweke_problems(model, fname=None, **kwargs):
"""
return a list of nodes who were detected as problemtic according to the geweke test
Input:
fname : string (deafult - None)
Save result to file named fname
kwargs : keywords argument passed to the geweke function
"""
#search for geweke problems
g = pm.geweke(model.mc)
problems = []
for node, output in g.items():
values = np.array(output)[:, 1]
if np.any(np.abs(values) > 2):
problems.append(node)
#write results to file if needed
if fname is not None:
with open(fname, 'w') as f:
for node in problems:
f.write(node)
return problems
# return (cur_x, funEvals['funevals']) if returnFunEvals else cur_x
if __name__ == '__main__':
npr.seed(1)
import pylab as pl
import pymc
D = 10
fn = lambda x: -0.5 * np.sum(x**2)
iters = 1000
samps = np.zeros((iters, D))
for ii in xrange(1, iters):
samps[ii, :] = slice_sample(samps[ii - 1, :],
fn,
sigma=0.1,
step_out=False,
doubling_step=True,
verbose=False)
ll = -0.5 * np.sum(samps**2, axis=1)
scores = pymc.geweke(ll)
pymc.Matplot.geweke_plot(scores, 'test')
pymc.raftery_lewis(ll, q=0.025, r=0.01)
pymc.Matplot.autocorrelation(ll, 'test')
def plot_traces(db=db,path='./diagnostics',format='png'):
'''Plot the traces of the unknown variables to check for convergence.
Also compute several convergence methods and print them out.'''
lw = 1 #line width
# Specify variables to include in each figure and subplot
# Each sublist is a figure. Each OrderedDict is a subplot with the
# key as the trace name and the val as the LaTeX string name.
var_names = []
var_names.append([OrderedDict([('f_a1', r'$f:a_1$'), ('f_a2', r'$f:a_2$')])])
var_names[0].append(OrderedDict([('f_b1', r'$f:b_1$'), ('f_b2', r'$f:b_2$'),
('g_aw', r'$g:a_w$'), ('g_bw', r'$g:b_w$')]))
var_names[0].append(OrderedDict([('sig_x', r'$\sigma_x$'), ('sig_y', r'$\sigma_y$'),
('sig_xl', r'local $\sigma_x$'),
('sig_yl', r'local $\sigma_y$')]))
var_names[0].append(OrderedDict([('corr', r'$\rho$'), ('corr_l', r'local $\rho$'),
('lam', r'$\lambda$')]))
var_names.append([OrderedDict([('xi', r'$\xi$'), ('em_obs_prob', r'emerg obs prob'),
('grid_obs_prob', r'grid obs prob')])])
sent_names = []
for name in db.trace_names[0]:
if name[:13] == 'sent_obs_prob':
id = name[-1]
sent_names.append((name, id))
var_names[1].append(OrderedDict(sent_names))
plt.figure()
plt.hold(True)
f_clrs = [0.3, 0.7]
g_clrs = [0.1, 0.9]
sig_clrs = [0.01, 0.99, 0.25, 0.75]
corr_lam_clrs = [0.01, 0.25, 0.5]
probs_clrs = [0.01, 0.5, 0.99]
clrs_list = [f_clrs, f_clrs+g_clrs, sig_clrs, corr_lam_clrs, probs_clrs]
plt.title("Traces of unknown model parameters")
for ii in range(len(var_names[0])):
plt.subplot(len(var_names[0]), 1, ii+1)
cnt = 0
for name, label in var_names[0][ii].items():
plt.plot(db.trace(name, chain=None)[:], label="trace of "+label,
c=cmap(clrs_list[ii][cnt]), lw=lw)
cnt += 1
leg = plt.legend(loc="upper left")
leg.get_frame().set_alpha(0.7)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
plt.draw()
plt.pause(0.0001)
plt.figure()
plt.hold(True)
plt.subplot(211)
plt.title("Traces of unknown Bayesian model parameters")
# xi, em_obs_prob, grid_obs_prob
cnt = 0
for name, label in var_names[1][0].items():
plt.plot(db.trace(name, chain=None)[:], label="trace of "+label,
c=cmap(probs_clrs[cnt]), lw=lw)
cnt += 1
leg = plt.legend(loc="upper right")
leg.get_frame().set_alpha(0.7)
# sent_obs_probs
plt.subplot(212)
cnt = 0
for name, label in var_names[1][1].items():
plt.plot(db.trace(name, chain=None)[:], label="trace of prob field "+label,
c=cmap(.10+cnt*.16), lw=lw)
cnt += 1
leg = plt.legend(loc="upper right")
leg.get_frame().set_alpha(0.7)
plt.draw()
##### Convergence tests #####
# Geweke
f, axarr = plt.subplots(len(var_names[0]), sharex=True)
axarr[0].set_title('Geweke Plots')
axarr[0].hold(True)
for ii in range(len(var_names[0])):
cnt = 0
ymax = 0
ymin = 0
for name, label in var_names[0][ii].items():
scores = pm.geweke(db.trace(name, chain=None)[:])
x, y = np.transpose(scores)
axarr[ii].scatter(x.tolist(), y.tolist(), label=label,
c=cmap(clrs_list[ii][cnt]))
ymax = max(ymax, np.max(y))
ymin = min(ymin, np.min(y))
cnt += 1
# Legend
leg = axarr[ii].legend(loc="upper left",prop={'size':9})
leg.get_frame().set_alpha(0.7)
# Labels
axarr[ii].set_ylabel('Z-score')
# Plot lines at +/- 2 std from zero
axarr[ii].plot((np.min(x), np.max(x)), (2, 2), '--')
axarr[ii].plot((np.min(x), np.max(x)), (-2, -2), '--')
# Plot bounds
axarr[ii].set_ylim(min(-2.5, ymin), max(2.5, ymax))
axarr[ii].set_xlim(0, np.max(x))
axarr[-1].set_xlabel('First iteration')
plt.hold(False)
if not os.path.exists(path):
os.mkdir(path)
if not path.endswith('/'):
path += '/'
plt.savefig("{}.{}".format(path+'_Geweke',format),dpi=200)
plt.draw()
@pm.deterministic
def theta(a=alpha, b=beta, d=dose):
"""theta = inv_logit(a+b)"""
return pm.invlogit(a+b*d)
"""deaths ~ binomial(n, p)"""
deaths = pm.Binomial('deaths', n=n, p=theta, value=x, observed=True)
my_model = [alpha, beta, theta, deaths]
# Instantiate and run sampler
S = pm.MCMC(my_model)
S.sample(10000, burn=5000)
# Calculate and plot Geweke scores
scores = pm.geweke(S, intervals=20)
pm.Matplot.geweke_plot(scores)
# Geweke plot for a single parameter
trace = S.trace('alpha')[:]
alpha_scores = pm.geweke(trace, intervals=20)
pm.Matplot.geweke_plot(alpha_scores, 'alpha')
# Calculate Raftery-Lewis diagnostics
pm.raftery_lewis(S, q=0.025, r=0.01)
"""
Sample output:
========================
Raftery-Lewis Diagnostic
{**feed_dict, x_start:samples[enum]}
)
return samples, log_probs
num_samples = 8192
samples, log_probs = run_mcmc(test_means, num_samples)
emp_means = np.mean(samples, axis=0)
emp_cov = np.cov(samples.T)
print(emp_means, '\n\n', test_cov, '\n\n', emp_cov, '\n\n',
test_cov / emp_cov)
import pylab as pl
import pymc
scores = pymc.geweke(log_probs)
pymc.Matplot.geweke_plot(scores, 'test')
pymc.raftery_lewis(log_probs, q=0.025, r=0.01)
pymc.Matplot.autocorrelation(log_probs, 'test')
pl.show()
bp()
# ==============================================
# Developers' Section
# ==============================================
# ------------ Scrap work goes here ------------
'''
# 'Stepping in' with a mode sophisticated stopping criterion.
def step_in(self, local_fn, threshold, upper, lower, dtype=None):
if (dtype is None): dtype = threshold.dtype
direction = direction / np.sqrt(np.sum(direction**2))
new_x = direction_slice(direction, init_x)
if scalar:
return float(new_x[0])
else:
return new_x
if __name__ == '__main__':
npr.seed(1)
import pylab as pl
D = 10
fn = lambda x: -0.5*np.sum(x**2)
iters = 1000
samps = np.zeros((iters,D))
for ii in xrange(1,iters):
samps[ii,:] = slice_sample(samps[ii-1,:], fn, sigma=0.1, step_out=False, doubling_step=True, verbose=False)
ll = -0.5*np.sum(samps**2, axis=1)
scores = pymc.geweke(ll)
pymc.Matplot.geweke_plot(scores, 'test')
pymc.raftery_lewis(ll, q=0.025, r=0.01)
pymc.Matplot.autocorrelation(ll, 'test')
mcmc.cont(BAOh.trace('omega_M_0')[:],BAOh.trace('w')[:],color='blue',nsmooth=sm)
mcmc.cont(AllBAOh.trace('omega_M_0')[:],AllBAOh.trace('w')[:],color='red',nsmooth=sm)
xx=np.linspace(0,1,1000)
plot(xx,xx*0-1,'k:')
#### convergence checking
# Geweke: mean in segments compared with global mean
scores=pymc.geweke(BAOh,intervals=10)
pymc.Matplot.geweke_plot(scores)
# Raftery-Lewis
pymc.raftery_lewis(BAOh,q=0.68,r=0.01)
ft=scipy.fft(BAOh.trace('w')[:])
ps=abs(ft)**2
clf()
xscale('log')
yscale('log')
plot(ps)
for t in things:
print(db.trace(t).stats())
print("means:")
for t in things:
print(t, "\t", db.trace(t).stats()['mean'])
print("#samples: %d" % db.trace('mg_pv_K').stats()['n'])
pymc.raftery_lewis(S, q=0.025, r=0.01)
b = 1
t = 1
scores = pymc.geweke(S, intervals=20)
pymc.Matplot.trace(db.trace('deviance',
chain=None).gettrace(burn=1000,
thin=t,
chain=None),
'deviance',
rows=2,
columns=9,
num=1)
pymc.Matplot.trace(db.trace('mg_pv_K',
chain=None).gettrace(thin=t, chain=None),
'mg_pv_K',
rows=2,
columns=9,
def plot(dirname,
data,
bkgd,
resmat,
trace,
nuisancetrace,
lower=[],
upper=[]):
import os
if not os.path.exists(dirname):
os.makedirs(dirname)
dirname = os.path.normpath(dirname) + os.sep
plt.imshow(resmat, interpolation='none', origin='lower', alpha=0.5)
plt.savefig(dirname + 'resmat.png')
plt.close()
ndim = len(data)
# overlay data and background
x = arange(0.5, ndim + 0.5)
plt.plot(x, data, 'k', label='data', drawstyle='steps-mid')
if len(bkgd) > 0:
plt.plot(x,
array(bkgd).sum(axis=0),
'b',
label='background',
drawstyle='steps-mid')
plt.ylim([0., max(data) * 1.3])
plt.xlim([0., len(data)])
plt.savefig(dirname + 'databckg.png')
plt.close()
# plot traces and autocorrelation
#for ii,bckg in enumerate(bckgtrace):
#mcplot(bckg,common_scale=False,suffix='_summary',path=dirname,format='eps')
#plt.close()
for name, nuisance in nuisancetrace.items():
plothistandtrace(dirname + name, nuisance, -5., 5.)
nbins = len(trace)
for bin in xrange(nbins):
## need to be fixed
##mcplot(trace,common_scale=False,suffix='_summary',path=dirname,format='eps')
##plt.close()
scores = pymc.geweke(trace[bin])
# plot geweke test
geweke_plot(scores,
'truth',
path=dirname,
format='png',
suffix='bin%d-geweke' % bin)
plt.close()
# raftery lewis test
##not very useful
## pymc.raftery_lewis(scores, q=0.975, r=0.005)
plothistandtrace(dirname + 'bin%d' % bin, trace[bin], lower[bin],
upper[bin])
for name, nuisance in nuisancetrace.items():
plt.plot(trace[bin], nuisance, ',')
plt.savefig(dirname + '%s_bin%d.png' % (name, bin))
plt.close()
def plot_geweke_scores(mcmc_database, keys, working_dir):
for key in keys:
print('plotting geweke scores for %s...' % key)
scores = pymc.geweke(mcmc_database.trace(key)[:])
pymc.Matplot.geweke_plot(scores, name=key, path=working_dir)
return None
plt.close()
# plot autocorrelation
os.chdir(proj_dir + "/outputs/model results/simple random effects by state/mcmc plots/autocorrelation/")
for p in plot_me:
mc.Matplot.autocorrelation(p, suffix="_autocorrelation")
if len(p.shape) == 0:
plt.close()
else:
for i in range(np.int(np.ceil(p.shape[0] / 4.0))):
plt.close()
# plot geweke
os.chdir(proj_dir + "/outputs/model results/simple random effects by state/mcmc plots/geweke/")
for p in plot_me:
scores = mc.geweke(p, intervals=20)
mc.Matplot.geweke_plot(scores, p.__name__, suffix="_geweke")
if len(p.shape) == 0:
plt.close()
else:
for i in range(np.int(np.ceil(p.shape[0] / 4.0))):
plt.close()
"""
# plot predictions
pp = PdfPages(proj_dir + 'outputs/model results/epi transition by state/predictions.pdf')
for g in g_list:
d = output[output.state == g]
fig = plt.figure()
axis_num = 0
for t in things:
print db.trace(t).stats()
print "means:"
for t in things:
print t,"\t",db.trace(t).stats()['mean']
print "#samples: %d" % db.trace('mg_pv_K').stats()['n']
pymc.raftery_lewis(S, q=0.025, r=0.01)
b = 1
t = 1
scores = pymc.geweke(S, intervals=20)
pymc.Matplot.trace(db.trace('deviance',chain=None).gettrace(burn=1000,thin=t,chain=None),'deviance',rows=2,columns=9,num=1)
pymc.Matplot.trace(db.trace('mg_pv_K',chain=None).gettrace(thin=t,chain=None),'mg_pv_K',rows=2,columns=9,num=2)
pymc.Matplot.histogram(np.array(db.trace('mg_pv_K',chain=None).gettrace(burn=b,chain=None)),'mg_pv_K',rows=2,columns=9,num=11)
pymc.Matplot.trace(db.trace('mg_pv_K_prime',chain=None).gettrace(thin=t,chain=None),'mg_pv_K_prime',rows=2,columns=9,num=3)
pymc.Matplot.histogram(np.array(db.trace('mg_pv_K_prime',chain=None).gettrace(burn=b,chain=None)),'mg_pv_K_prime',rows=2,columns=9,num=12)
pymc.Matplot.trace(db.trace('mg_pv_G',chain=None).gettrace(thin=t,chain=None),'mg_pv_G',rows=2,columns=9,num=4)
pymc.Matplot.histogram(np.array(db.trace('mg_pv_G',chain=None).gettrace(burn=b,chain=None)),'mg_pv_G',rows=2,columns=9,num=13)
pymc.Matplot.trace(db.trace('mg_pv_G_prime',chain=None).gettrace(thin=t,chain=None),'mg_pv_G_prime',rows=2,columns=9,num=5)
pymc.Matplot.histogram(np.array(db.trace('mg_pv_G_prime',chain=None).gettrace(burn=b,chain=None)),'mg_pv_G_prime',rows=2,columns=9,num=14)
# approximation (but not exactly the same):
normal = pymc.NormApprox(make_poisson(5, 1., 20.))
normal.fit() # optimizes and saves results as attributes
# Use MCMC for posterior sampling via MCMC; store samples in a Python
# pickle file:
mcmc = pymc.MCMC(make_poisson(5, 1., 20.), db='pickle')
# Run 3 chains:
for i in range(3):
mcmc.sample(iter=10000, burn=5000, thin=1)
print # to handle missing newline from progress bar
# Generate a dict of Geweke test z scores for each RV, here using early
# segments 10% of the chain length, a final segment 50% of the length,
# and producing scores for 10 early intervals.
scores = pymc.geweke(mcmc, first=0.1, last=0.5, intervals=10)
# The Matplot functions automatically produce new figures for each plot.
pymc.Matplot.geweke_plot(scores['rate'], 'rate')
pymc.Matplot.geweke_plot(scores['mu'], 'mu')
print 'Rhat values:', pymc.gelman_rubin(mcmc)
# Plot credible regions and R values:
pymc.Matplot.summary_plot(mcmc)
def make_on_off(n_off, expo_off, n_on, expo_on, mean0):
"""
Make a PyMC model for inferring a Poisson signal rate parameter, `s`, for
'on-off' observations with uncertain background rate, `b`.
listTraces=[['Age1','Age2','Age2','Age4','Age6','Age7'],['ACAR','LV1AR','LV2AR','B211AR','B503AR','SAAR'],['err1','err2','err3','err4','err6','err7']]
for k in range(6):
for i in range(3):
tracePlot=plt.subplot(gs[k,i])
trace=mcmc.trace(listTraces[i][k])[extraburn::thin]
tracePlot.plot(range(trace.size),trace,lw=1)
tracePlot.set_title(listTraces[i][k])
fig.savefig(('6SectionsData_tset_traceFig_ACSET.pdf'), format='pdf', dpi=300)
#%%
variables=['velocity1','velocity2','velocity3','velocity6','velocity7','Age','RR','err1']
for i in variables:
burn=0
thin=1
trace=mcmc.trace(i)[burn::thin]
test=pm.geweke(trace, intervals=20)
pm.Matplot.geweke_plot(test,'test',lw=1)
#%%
class HRAM(pm.Gibbs):
def __init__(self, stochastic, proposal_sd=None, verbose=None):
pm.Metropolis.__init__(self, stochastic, proposal_sd=proposal_sd,
verbose=verbose, tally=False)
self.proposal_tau = self.proposal_sd**-2.
self.n = 0
self.N = 11
self.value = pm.rnormal(self.stochastic.value, self.proposal_tau, size=tuple([self.N] + list(self.stochastic.value.shape)))
def step(self):
x0 = self.value[self.n]
u = pm.rnormal(np.zeros(self.N), 1.)