def test_mixture_list_of_poissons(self):
with Model() as model:
w = Dirichlet("w",
floatX(np.ones_like(self.pois_w)),
shape=self.pois_w.shape)
mu = Gamma("mu", 1.0, 1.0, shape=self.pois_w.size)
Mixture(
"x_obs",
w,
[Poisson.dist(mu[0]), Poisson.dist(mu[1])],
observed=self.pois_x)
step = Metropolis()
trace = sample(5000,
step,
random_seed=self.random_seed,
progressbar=False,
chains=1)
assert_allclose(np.sort(trace["w"].mean(axis=0)),
np.sort(self.pois_w),
rtol=0.1,
atol=0.1)
assert_allclose(np.sort(trace["mu"].mean(axis=0)),
np.sort(self.pois_mu),
rtol=0.1,
atol=0.1)
def createHistogramFitModel(data_bins, simulation_bins, scaleGuess):
scale = Normal('scale', mu=scaleGuess, tau=sigToTau(.10 * scaleGuess))
scaled_sim = scale * simulation_bins
baseline_observed = Poisson("baseline_observed",
mu=scaled_sim,
value=data_bins,
observed=True)
return locals()
def set_models(self):
"""Define models for each group.
:return: None
"""
for group in ['control', 'variant']:
self.stochastics[group] = Poisson(
group,
self.stochastics[group + '_mu'],
value=getattr(self, group),
observed=True)
])
# Switchpoint
switch = DiscreteUniform('switch', lower=0, upper=110)
# Early mean
early_mean = Exponential('early_mean', beta=1)
# Late mean
late_mean = Exponential('late_mean', beta=1)
@deterministic(plot=False)
def rates(s=switch, e=early_mean, l=late_mean):
"""Allocate appropriate mean to time series"""
out = np.empty(len(disasters_array))
# Early mean prior to switchpoint
out[:s] = e
# Late mean following switchpoint
out[s:] = l
return out
# The inefficient way, using the Impute function:
# D = Impute('D', Poisson, disasters_array, mu=r)
# The efficient way, using masked arrays:
# Generate masked array. Where the mask is true,
# the value is taken as missing.
masked_values = masked_array(disasters_array, mask=disasters_array == -999)
# Pass masked array to data stochastic, and it does the right thing
disasters = Poisson('disasters', mu=rates, value=masked_values, observed=True)
from pymc import DiscreteUniform, Exponential, deterministic, Poisson, Uniform
import numpy as np
disasters_array = np.array([ 4, 5, 4, 0, 1, 4, 3, 4, 0, 6, 3, 3, 4, 0, 2, 6,
3, 3, 5, 4, 5, 3, 1, 4, 4, 1, 5, 5, 3, 4, 2, 5,
2, 2, 3, 4, 2, 1, 3, 2, 2, 1, 1, 1, 1, 3, 0, 0,
1, 0, 1, 1, 0, 0, 3, 1, 0, 3, 2, 2, 0, 1, 1, 1,
0, 1, 0, 1, 0, 0, 0, 2, 1, 0, 0, 0, 1, 1, 0, 2,
3, 3, 1, 1, 2, 1, 1, 1, 1, 2, 4, 2, 0, 0, 1, 4,
0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1])
switchpoint = DiscreteUniform('switchpoint', lower=0, upper=110,
doc='Switchpoint[year]')
early_mean = Exponential('early_mean', beta=1.)
late_mean = Exponential('late_mean', beta=1.)
@deterministic(plot=False)
def rate(s=switchpoint, e=early_mean, l=late_mean):
out = np.empty(len(disasters_array))
out[:s] = e
out[s:] = l
return out
disasters = Poisson('disasters', mu=rate, value=disasters_array, observed=True)
import gen
pathways = gen.pathways()
features = gen.features_dict()
detected = gen.detected_features()
evidence = gen.evidence()
ap = {p.name: Gamma('p_' + p.name, p.rate, 1) for p in pathways}
#bmp = [Gamma('b_{' + str(i) + '}', 1, ap[i]) for i in range(3)]
bmp = {
p.name: {
feat: Gamma('b_{' + p.name + ',' + str(feat) + '}', ap[p.name], 1)
for feat in p.mets
}
for p in pathways
}
print bmp
#g_bmp = {feat : Poisson('g_' + str(feat), sum([bmp[pname][feat] for pname in pathways])) for feat, pathways in features.iteritems()}
g_bmp = {}
for feat, pathways in features.iteritems():
if detected(feat):
print feat, "was detected"
g_bmp[feat] = Poisson('g_' + str(feat),
sum([bmp[pname][feat] for pname in pathways]),
value=1,
observed=True)
else:
print feat, "was not detected"
g_bmp[feat] = Poisson('g_' + str(feat),
sum([bmp[pname][feat] for pname in pathways]))
print g_bmp
# produces basically the same result as the exponential priors
mu = np.average(linear_array)
linear_mean = TruncatedNormal('linear_mean', a=0, b=10, mu=mu, tau=1., value=mu)
mu = np.average(spacewatch_array)
spacewatch_mean = TruncatedNormal('spacewatch_mean', a=0, b=10, mu=mu, tau=1., value=mu)
mu = np.average(catalina_array)
catalina_mean = TruncatedNormal('catalina_mean', a=0, b=10, mu=mu, tau=1., value=mu)
mu = 1.25
panstarrs_mean = TruncatedNormal('panstarrs_mean', a=0, b=10, mu=mu, tau=1., value=mu)
mu = 2.25
neowise_mean = TruncatedNormal('neowise_mean', a=0, b=10, mu=mu, tau=1., value=mu)
mu = np.average(other_array)
other_mean = TruncatedNormal('other_mean', a=0, b=10, mu=mu, tau=1., value=mu)
linear_hits = Poisson('linear_hits', mu=linear_mean,
value=linear_array, observed=True)
spacewatch_hits = Poisson('spacewatch_hits', mu=spacewatch_mean,
value=spacewatch_array, observed=True)
catalina_hits = Poisson('catalina_hits', mu=catalina_mean,
value=catalina_array, observed=True)
panstarrs_hits = Poisson('panstarrs_hits', mu=panstarrs_mean,
value=panstarrs_array, observed=True)
neowise_hits = Poisson('neowise_hits', mu=neowise_mean,
value=neowise_array, observed=True)
other_hits = Poisson('other_hits', mu=other_mean,
value=other_array, observed=True)
linear_next = Poisson('linear_next', mu=linear_mean)
spacewatch_next = Poisson('spacewatch_next', mu=spacewatch_mean)
catalina_next = Poisson('catalina_next', mu=catalina_mean)
panstarrs_next = Poisson('panstarrs_next', mu=panstarrs_mean)
disasters: D[t] ~ Poisson(early if t <= s, l otherwise)
"""
__all__ = ['s', 'e', 'l', 'r', 'D']
from pymc import DiscreteUniform, Exponential, deterministic, Poisson, Uniform
import numpy as np
disasters_array = np.array([
4, 5, 4, 0, 1, 4, 3, 4, 0, 6, 3, 3, 4, 0, 2, 6, 3, 3, 5, 4, 5, 3, 1, 4, 4,
1, 5, 5, 3, 4, 2, 5, 2, 2, 3, 4, 2, 1, 3, 2, 2, 1, 1, 1, 1, 3, 0, 0, 1, 0,
1, 1, 0, 0, 3, 1, 0, 3, 2, 2, 0, 1, 1, 1, 0, 1, 0, 1, 0, 0, 0, 2, 1, 0, 0,
0, 1, 1, 0, 2, 3, 3, 1, 1, 2, 1, 1, 1, 1, 2, 4, 2, 0, 0, 1, 4, 0, 0, 0, 1,
0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1
])
s = DiscreteUniform('s', lower=0, upper=110)
e = Exponential('e', beta=1)
l = Exponential('l', beta=1)
@deterministic(plot=False)
def r(s=s, e=e, l=l):
"""Concatenate Poisson means"""
out = np.empty(len(disasters_array))
out[:s] = e
out[s:] = l
return out
D = Poisson('D', mu=r, value=disasters_array, observed=True)
y = [(random.random() < pi) * random.poisson(theta) for i in range(n)]
def remcache(s):
s._cache_depth = 0
s.gen_lazy_function()
p = Beta('p', 1, 1)
z = Bernoulli('z', p, value=array(y) > 0, plot=False)
theta_hat = Uniform('theta_hat', 0, 100, value=3)
t = z * theta
counts = Poisson('counts', t, value=y, observed=True)
model = [p, z, theta_hat, counts]
#disable caching for all the nodes
v = model + [t]
for s in v:
remcache(s)
def pymc_logp():
return logp_of_set(model)
def pymc_dlogp():
return logp_gradient_of_set(model)
def __init__(self, fname, playedto=None):
super(LeagueMultiHomeModel, self).__init__()
league = League(fname, playedto)
N = len(league.teams)
def outcome_eval(home=None, away=None):
if home > away:
return 1
if home < away:
return -1
if home == away:
return 0
def clip_rate(val):
if val > 0.2: return val
else: return 0.2
self.goal_rate = np.empty(N, dtype=object)
self.home_adv = np.empty(N, dtype=object)
self.def_rate = np.empty(N, dtype=object)
self.match_rate = np.empty(len(league.games) * 2, dtype=object)
self.outcome_future = np.empty(len(league.games), dtype=object)
self.match_goals_future = np.empty(len(league.future_games) * 2,
dtype=object)
self.league = league
fmesh = np.arange(0., league.n_days + 2.)
for t in league.teams.values():
self.goal_rate[t.team_id] = Exponential('goal_rate_%i' % t.team_id,
beta=1.)
self.def_rate[t.team_id] = Normal('def_rate_%i' % t.team_id,
tau=1.,
mu=0.)
self.home_adv[t.team_id] = Normal('home_adv_%i' % t.team_id,
tau=1.,
mu=0.)
for game in range(len(league.games)):
self.match_rate[2 * game] = Poisson(
'match_rate_%i' % (2 * game),
mu=Deterministic(
eval=clip_rate,
parents={
'val':
self.goal_rate[league.games[game].hometeam.team_id] -
self.def_rate[league.games[game].awayteam.team_id] +
self.home_adv[league.games[game].hometeam.team_id]
},
doc='clipped goal rate',
name='clipped_h_%i' % game),
value=league.games[game].homescore,
observed=True)
self.match_rate[2 * game + 1] = Poisson(
'match_rate_%i' % (2 * game + 1),
mu=Deterministic(
eval=clip_rate,
parents={
'val':
self.goal_rate[league.games[game].awayteam.team_id] -
self.def_rate[league.games[game].hometeam.team_id]
},
doc='clipped goal rate',
name='clipped_a_%i' % game),
value=league.games[game].awayscore,
observed=True)
for game in range(len(league.future_games)):
self.match_goals_future[2 * game] = Poisson(
'match_goals_future_%i_home' % game,
mu=Deterministic(
eval=clip_rate,
parents={
'val':
self.goal_rate[league.future_games[game][0].team_id] -
self.def_rate[league.future_games[game][1].team_id] +
self.home_adv[league.future_games[game][0].team_id]
},
doc='clipped goal rate',
name='clipped_fut_h_%i' % game))
self.match_goals_future[2 * game + 1] = Poisson(
'match_goals_future_%i_away' % game,
mu=Deterministic(
eval=clip_rate,
parents={
'val':
self.goal_rate[league.future_games[game][1].team_id] -
self.def_rate[league.future_games[game][0].team_id]
},
doc='clipped goal rate',
name='clipped_fut_a_%i' % game))
self.outcome_future[game] = Deterministic(
eval=outcome_eval,
parents={
'home': self.match_goals_future[2 * game],
'away': self.match_goals_future[2 * game + 1]
},
name='match_outcome_future_%i' % game,
dtype=int,
doc='The outcome of the match')
def __init__(self, fname, playedto=None):
super(LeagueFullModel, self).__init__()
league = League(fname, playedto)
N = len(league.teams)
def outcome_eval(home=None, away=None):
if home > away:
return 1
if home < away:
return -1
if home == away:
return 0
def clip_rate(val):
if val > 0.2: return val
else: return 0.2
def linfun(x, c):
return 0. * x + c
# The covariance dtrm C is valued as a Covariance object.
#@pm.deterministic
#def C(eval_fun = gp.matern.euclidean, diff_degree=diff_degree, amp=amp, scale=scale):
# return gp.NearlyFullRankCovariance(eval_fun, diff_degree=diff_degree, amp=amp, scale=scale)
self.goal_rate = np.empty(N, dtype=object)
self.def_rate = np.empty(N, dtype=object)
self.goal_var = np.empty(N, dtype=object)
self.def_var = np.empty(N, dtype=object)
self.match_rate = np.empty(len(league.games) * 2, dtype=object)
self.outcome_future = np.empty(len(league.games), dtype=object)
self.match_goals_future = np.empty(len(league.future_games) * 2,
dtype=object)
self.home_adv = Uniform(name='home_adv', lower=0., upper=2.0)
self.league = league
fmesh = np.arange(0., league.n_days + 2.)
for t in league.teams.values():
# Prior parameters of C
diff_degree_g = pm.Uniform('diff_degree_g_%i' % t.team_id, 1., 3)
amp_g = pm.Uniform('amp_g_%i' % t.team_id, .01, 2.)
scale_g = pm.Uniform('scale_g_%i' % t.team_id, 1., 10.)
diff_degree_d = pm.Uniform('diff_degree_d_%i' % t.team_id, 1., 3)
amp_d = pm.Uniform('amp_d_%i' % t.team_id, .01, 2.)
scale_d = pm.Uniform('scale_d_%i' % t.team_id, 1., 10.)
@pm.deterministic(name='C_d%i' % t.team_id)
def C_d(eval_fun=gp.matern.euclidean,
diff_degree=diff_degree_d,
amp=amp_d,
scale=scale_d):
return gp.NearlyFullRankCovariance(eval_fun,
diff_degree=diff_degree,
amp=amp,
scale=scale)
@pm.deterministic(name='C_g%i' % t.team_id)
def C_g(eval_fun=gp.matern.euclidean,
diff_degree=diff_degree_g,
amp=amp_g,
scale=scale_g):
return gp.NearlyFullRankCovariance(eval_fun,
diff_degree=diff_degree,
amp=amp,
scale=scale)
self.goal_rate[t.team_id] = Exponential('goal_rate_%i' % t.team_id,
beta=1)
self.def_rate[t.team_id] = Exponential('def_rate_%i' % t.team_id,
beta=1)
@pm.deterministic(name='M_d%i' % t.team_id)
def M_d(eval_fun=linfun, c=self.def_rate[t.team_id]):
return gp.Mean(eval_fun, c=c)
@pm.deterministic(name='M_g%i' % t.team_id)
def M_g(eval_fun=linfun, c=self.goal_rate[t.team_id]):
return gp.Mean(eval_fun, c=c)
self.def_var[t.team_id] = gp.GPSubmodel('smd_%i' % t.team_id, M_d,
C_d, fmesh)
self.goal_var[t.team_id] = gp.GPSubmodel('smg_%i' % t.team_id, M_g,
C_g, fmesh)
for game in range(len(league.games)):
gd = int(game / (league.n_teams / 2))
assert (gd < league.n_days)
self.match_rate[2 * game] = Poisson(
'match_rate_%i' % (2 * game),
mu=Deterministic(
eval=clip_rate,
parents={
'val':
self.goal_var[
league.games[game].hometeam.team_id].f_eval[gd] -
self.def_var[
league.games[game].awayteam.team_id].f_eval[gd] +
self.home_adv
},
doc='clipped goal rate',
name='clipped_h_%i' % game),
value=league.games[game].homescore,
observed=True)
self.match_rate[2 * game + 1] = Poisson(
'match_rate_%i' % (2 * game + 1),
mu=Deterministic(
eval=clip_rate,
parents={
'val':
self.goal_var[
league.games[game].awayteam.team_id].f_eval[gd] -
self.def_var[
league.games[game].hometeam.team_id].f_eval[gd]
},
doc='clipped goal rate',
name='clipped_a_%i' % game),
value=league.games[game].awayscore,
observed=True)
for game in range(len(league.future_games)):
gd = league.n_days
self.match_goals_future[2 * game] = Poisson(
'match_goals_future_%i_home' % game,
mu=Deterministic(
eval=clip_rate,
parents={
'val':
self.goal_var[league.future_games[game]
[0].team_id].f_eval[gd] -
self.def_var[league.future_games[game]
[1].team_id].f_eval[gd] + self.home_adv
},
doc='clipped goal rate',
name='clipped_fut_h_%i' % game))
self.match_goals_future[2 * game + 1] = Poisson(
'match_goals_future_%i_away' % game,
mu=Deterministic(eval=clip_rate,
parents={
'val':
self.goal_var[league.future_games[game]
[1].team_id].f_eval[gd] -
self.def_var[league.future_games[game]
[0].team_id].f_eval[gd]
},
doc='clipped goal rate',
name='clipped_fut_a_%i' % game))
self.outcome_future[game] = Deterministic(
eval=outcome_eval,
parents={
'home': self.match_goals_future[2 * game],
'away': self.match_goals_future[2 * game + 1]
},
name='match_outcome_future_%i' % game,
dtype=int,
doc='The outcome of the match')
(Conversions_t | start_t, before_rate, after_rate) ~ Poisson(rate_t)
start_t ~ DiscreteUniform(first_period, last_period) //can be any period with equal probability
rate_t = ( before_rate ... //start_t // .. after_rate)
'''
conversions_data = np.array(
[1, 2, 1, 2, 3, 4, 1, 2, 3, 5, 7, 3, 8, 7, 4, 5, 7])
start_t = DiscreteUniform("start_t", lower=0, upper=len(conversions_data))
before_mean = Exponential('before_mean', beta=1.)
after_mean = Exponential('after_mean', beta=1.)
@deterministic(plot=False)
def rate(start_period=start_t,
before_period_mean=before_mean,
after_period_mean=after_mean):
output = np.empty(len(conversions_data))
output[:start_period] = before_period_mean
output[start_period:] = after_period_mean
return output
conversions = Poisson("conversions",
mu=rate,
value=conversions_data,
observed=True)