def test_empty_parameter(self):
model_code = """
parameters {
real y;
vector[3] x;
vector[0] a;
vector[2] z;
}
model {
y ~ normal(0,1);
}
"""
if pystan_version() == 2:
from pystan import StanModel # pylint: disable=import-error
model = StanModel(model_code=model_code)
fit = model.sampling(iter=500,
chains=2,
check_hmc_diagnostics=False)
else:
import stan # pylint: disable=import-error
model = stan.build(model_code)
fit = model.sample(num_samples=500, num_chains=2)
posterior = from_pystan(posterior=fit)
test_dict = {
"posterior": ["y", "x", "z", "~a"],
"sample_stats": ["diverging"]
}
fails = check_multiple_attrs(test_dict, posterior)
assert not fails
def run_or_load_model(m_type, m_dict, iters, warmup, c_params):
if m_type not in ['car', 'tobit']:
raise Exception('Invalid model type!')
name = 'crash_{}_{}-{}_delta_{}_max_{}'.format(m_type, iters, warmup,
c_params['adapt_delta'],
c_params['max_treedepth'])
try:
model = load(Path('cache/' + name + '_model.joblib'))
except:
model = StanModel(file=Path(
'models/crash_{}.stan'.format(m_type)).open(),
extra_compile_args=["-w"],
model_name=name.split('-')[0])
dump(model, Path('cache/' + name + '_model.joblib'))
try:
fit = load(Path('cache/' + name + '_fit.joblib'))
except:
fit = model.sampling(data=m_dict,
iter=iters,
warmup=warmup,
control=c_params,
check_hmc_diagnostics=True)
info = fit.stansummary()
with open(Path('logs/' + name + '.log'), 'w') as c_log:
c_log.write(info)
dump(fit, Path('cache/' + name + '_fit.joblib'))
return model, fit
def simple_car_model(tobit_data: pd.DataFrame, ad_matrix):
"""
In the model of the researchers, phi is distributed around phi_bar
is this handled by the multi_normal_prec??? Need to understand docs and adjust if not.
- seems to be legit. Documentation of WinBUGS does it in a similar way.
https://mc-stan.org/docs/2_19/functions-reference/multivariate-normal-distribution-precision-parameterization.html
- find out what the CAR prior in car.normal is. Right now I just have 2/-2 ...
- Unfortunately, there is no information available. Just need to set something that works.
"""
car_model = StanModel(file=Path('models/tobit_car_students.stan').open(),
extra_compile_args=["-w"])
car_dict = get_datadict()
car_dict['W'] = ad_matrix
car_dict['U'] = 800
# this smaller run still took 25 mins to sample...
# And still getting too low E-BFMI values
car_fit = car_model.sampling(data=car_dict,
iter=2000,
warmup=500,
chains=4)
dump(car_fit, Path('data/car_students_2000.joblib'))
car_res = car_fit.extract()
print('β_0: {}'.format(car_res['beta_zero'][501:].mean()))
print('β: {}'.format(car_res['beta'][501:].mean(axis=0)))
# getting many rejections - bad? Phi is a bit like a covariance matrix
# -> only in the beginning, after 200 iterations all fine.
# result from the run: chains have not mixed, might need to re-parametrize...
# am I contraining the variables too much??? Need to center somehow?
return car_fit, car_model
def compile(self):
"""Compile the Stan model."""
# Note: we deliberately use a centered parameterization for the
# thetas at the moment. This is sub-optimal in terms of estimation,
# but allows us to avoid having to add extra logic to detect and
# handle intercepts in X.
spec = f"""
data {{
int<lower=1> N;
int<lower=1> K;
vector[N] y;
int<lower=1,upper=K> id[N];
int<lower=1> C;
matrix[K, C] X;
vector[N] sigma;
}}
parameters {{
vector[C] beta;
vector[K] theta;
real<lower=0> tau2;
}}
transformed parameters {{
vector[N] mu;
mu = theta[id] + X * beta;
}}
model {{
y ~ normal(mu, sigma);
theta ~ normal(0, tau2);
}}
"""
from pystan import StanModel
self.model = StanModel(model_code=spec)
def fit(self, iterations=5000, control=default_control):
self.stan_model = StanModel('../stan/player_scoring.stan')
self.samples = self.stan_model.sampling(self.stan_data,
iter=iterations,
chains=4,
refresh=1,
control=control)
def scaled_spare_car(tobit_data: pd.DataFrame, ad_matrix):
"""
will try with values closer to 0 now.
sigma was 67.3 with stdev 3.74
even worse - E-BMFI is still small, but now also much treedepth saturation (OK)
and chain divergence (bad!) would need to check energy-plots and what correlates...
TODO: if I scale, I have the danger of missing not hitting the condition for U...
-> should not be a problem if I have zeros there as lower bound
"""
tobit_data['ones'] = np.ones(tobit_data.shape[0])
trans = MaxAbsScaler().fit_transform(tobit_data[new_preds + ['apt']])
data_centered = pd.DataFrame(trans, columns=new_preds + ['apt'])
is_800 = tobit_data['apt'] == 800
not_800 = tobit_data['apt'] != 800
ii_obs = tobit_data[not_800]['id']
ii_cens = tobit_data[is_800]['id']
# After using vectorisation: Gradient takes 0.0003 seconds.
c_sparse_dict = {
'X': data_centered[new_preds],
'n': tobit_data.shape[0],
'n_obs': not_800.sum(),
'n_cens': is_800.sum(),
'y_obs': data_centered[not_800]['apt'],
'ii_obs': ii_obs,
'ii_cens': ii_cens,
'p': len(new_preds),
'y_cens': data_centered[is_800]['apt'],
'W': ad_matrix,
'U': 1,
'W_n': ad_matrix.sum() // 2
}
# or just 'models/sparse_tcar_students_without_QR.stan'
c_sp_model = StanModel(file=Path('sparse_tobitcar_students.stan').open(),
verbose=False,
extra_compile_args=["-w"])
c_params = {'adapt_delta': 0.95, 'max_treedepth': 12}
# no more saturation, but still divergence...
# trying to constrain the model: α <= 0.99 instead <=1, σ >= 0.001
c_sp_fit = c_sp_model.sampling(c_sparse_dict,
iter=4000,
warmup=500,
control=c_params)
c_sp_res = c_sp_fit.extract()
print(c_sp_fit.stansummary())
dump(c_sp_fit, 'data/c_sp_4000.joblib')
plt.scatter(c_sp_fit['lp__'], c_sp_fit['sigma'])
# sigma looks very correlated.
simpler_csp = c_sp_res.copy()
del simpler_csp['phi']
del simpler_csp['y_cens']
del simpler_csp['beta']
del simpler_csp['y']
if 'theta' in simpler_csp:
del simpler_csp['theta']
c_sp_df = pd.DataFrame.from_dict(simpler_csp)
sns.pairplot(c_sp_df)
return c_sp_fit, c_sp_model
def _fit_stan_model(self, vb: bool, sm: StanModel, data_dict: Dict,
pars: List, gen_init: Union[str, Callable],
nchain: int, niter: int, nwarmup: int, nthin: int,
adapt_delta: float, stepsize: float,
max_treedepth: int, ncore: int) -> Any:
"""Fit the stan model.
Parameters
----------
vb
Whether to perform variational Bayesian analysis.
sm
The StanModel object to use to fit the model.
data_dict
Dict holding the data to pass to Stan.
pars
List specifying the parameters of interest.
gen_init
String or function to specify how to generate the initial values.
nchain
Number of chains to run.
niter
Number of iterations per chain.
nwarmup
Number of warm-up iterations.
nthin
Use every `i == nthin` sample to generate posterior distribution.
adapt_delta
Advanced control argument for sampler.
stepsize
Advanced control argument for sampler.
max_treedepth
Advanced control argument for sampler.
ncore
Argument for parallel computing while sampling multiple chains.
Returns
-------
fit
The fitted result returned by `vb` or `sampling` function.
"""
if vb:
return sm.vb(data=data_dict, pars=pars, init=gen_init)
else:
return sm.sampling(data=data_dict,
pars=pars,
init=gen_init,
chains=nchain,
iter=niter,
warmup=nwarmup,
thin=nthin,
control={
'adapt_delta': adapt_delta,
'stepsize': stepsize,
'max_treedepth': max_treedepth
},
n_jobs=ncore)
def verify_stan():
"""
Simplest model to verify the stan installation
"""
model_code = 'parameters {real y;} model {y ~ normal(0,1);}'
model = StanModel(model_code=model_code)
y = model.sampling().extract()['y']
print('If this worked, you will see a value near 0 now:')
print(y.mean())
def _bayes_sampling(x, y, distribution='normal'):
"""
Helper function.
Args:
x (array_like): sample of a treatment group
y (array_like): sample of a control group
distribution: name of the KPI distribution model, which assumes a
Stan model file with the same name exists
Returns:
tuple:
- the posterior samples
- sample size of x
- sample size of y
- absolute mean of x
- absolute mean of y
"""
# Checking if data was provided
if x is None or y is None:
raise ValueError('Please provide two non-None samples.')
# Coercing missing values to right format
_x = np.array(x, dtype=float)
_y = np.array(y, dtype=float)
mu_x = np.nanmean(_x)
mu_y = np.nanmean(_y)
n_x = statx.sample_size(_x)
n_y = statx.sample_size(_y)
if distribution == 'normal':
fit_data = {'Nc': n_y, 'Nt': n_x, 'x': _x, 'y': _y}
elif distribution == 'poisson':
fit_data = {
'Nc': n_y,
'Nt': n_x,
'x': _x.astype(int),
'y': _y.astype(int)
}
else:
raise NotImplementedError
model_file = __location__ + '/../models/' + distribution + '_kpi.stan'
sm = StanModel(file=model_file)
fit = sm.sampling(data=fit_data,
iter=25000,
chains=4,
n_jobs=1,
seed=1,
control={
'stepsize': 0.01,
'adapt_delta': 0.99
})
traces = fit.extract()
return traces, n_x, n_y, mu_x, mu_y
def main():
schools_dat = {
'J': 8,
'y': [28, 8, -3, 7, -1, 1, 18, 12],
'sigma': [15, 10, 16, 11, 9, 11, 10, 18]
}
sm = StanModel(file='model.stan')
fit = sm.sampling(data=schools_dat, iter=1000, chains=4, seed=555)
with open(DATA_FILE_NAME, 'wb') as f:
pickle.dump({'model': sm, 'fit': fit}, f)
def sparse_car_model(tobit_data: pd.DataFrame, ad_matrix):
sparse_dict = get_sparse_modeldict(tobit_data, ad_matrix)
sparse_model = StanModel(
file=Path('models/sparse_tobitcar_students.stan').open(),
extra_compile_args=["-w"])
sparse_fit = sparse_model.sampling(sparse_dict,
iter=4000,
warmup=500,
chains=4)
print(sparse_fit.stansummary())
return sparse_fit, sparse_model
def coin_model():
"""
Example from „Kruschke: Doing Bayesian Data Analysis”.
"""
coin_model = StanModel(file=Path('models/bernoulli_example.stan').open())
# generate some data
N = 50
z = 10
y = [1] * z + [0] * (N - z)
coin_data = {'y': y, 'N': N}
# warmup is the same as burnin in JAGS
return coin_model.sampling(data=coin_data, chains=3, iter=1000, warmup=200)
def stanTopkl():
if os.path.isfile('log_normal.pkl'):
os.remove('log_normal.pkl')
sm = StanModel(file='log_normal.stan')
with open('log_normal.pkl', 'wb') as f:
pickle.dump(sm, f)
if os.path.isfile('log_t.pkl'):
os.remove('log_t.pkl')
sm = StanModel(file='log_t.stan')
with open('log_t.pkl', 'wb') as f:
pickle.dump(sm, f)
def test_init_zero_exception_inf_grad(self):
code = """
parameters {
real x;
}
model {
target += 1 / log(x);
}
"""
sm = StanModel(model_code=code)
with self.assertRaises(RuntimeError):
sm.sampling(init='0', iter=1, chains=1)
def test_init_zero_exception_inf_grad(self):
code = """
parameters {
real x;
}
model {
target += 1 / log(x);
}
"""
sm = StanModel(model_code=code)
with self.assertRaises(RuntimeError):
sm.sampling(init='0', iter=1, chains=1)
def test_init_zero_exception_inf_grad(self):
code = """
parameters {
real x;
}
model {
lp__ <- 1 / log(x);
}
"""
sm = StanModel(model_code=code)
assertRaisesRegex = self.assertRaisesRegexp if PY2 else self.assertRaisesRegex
with assertRaisesRegex(RuntimeError, 'divergent gradient'):
sm.sampling(init='0', iter=1)
def test_init_zero_exception_inf_grad(self):
code = """
parameters {
real x;
}
model {
lp__ <- 1 / log(x);
}
"""
sm = StanModel(model_code=code)
assertRaisesRegex = self.assertRaisesRegexp if PY2 else self.assertRaisesRegex
with assertRaisesRegex(RuntimeError, 'divergent gradient'):
sm.sampling(init='0', iter=1)
def linear_model():
"""
1st example from Stan User's Guide
"""
linear_model = StanModel(file=Path('models/linear_example.stan').open(),
extra_compile_args=["-w"])
x = list(range(10))
y = [1.1, 2.04, 3.07, 3.88, 4.95, 6.11, 7.03, 7.89, 8.91, 10]
linear_data = {'x': x, 'y': y, 'N': 10}
linear_fit = linear_model.sampling(data=linear_data)
linear_res = linear_fit.extract()
print('α : {}'.format(np.mean(linear_res['alpha'])))
print('β : {}'.format(np.mean(linear_res['beta'])))
return linear_fit
def bnb_stan(dataset, oos_dataset, warmup=20000, n_iter=25000):
Y_data, ratings_data, expectations_data, team_dummies_data, pct = (
extract_data(dataset))
_, oos_ratings_data, oos_expectations_data, oos_team_dummies_data, oos_pct = \
extract_data(oos_dataset)
ratings_data = ratings_data.squeeze()
oos_ratings_data = oos_ratings_data.squeeze()
ratings_data, oos_ratings_data = normalize(ratings_data, oos_ratings_data)
ratings_data = np.stack((ratings_data, np.square(ratings_data)), axis=1)
oos_ratings_data = np.stack(
(oos_ratings_data,
np.sign(oos_ratings_data) * np.square(oos_ratings_data)),
axis=1)
pct, oos_pct = normalize(pct, oos_pct)
expectations_data, oos_expectations_data = normalize(
expectations_data, oos_expectations_data)
home_team_dummies = team_dummies_data[::, 0, ::]
away_team_dummies = team_dummies_data[::, 1, ::]
stan_data = {
'n_rows': Y_data.shape[0],
'n_teams': team_dummies_data.shape[2],
'm_ratings': ratings_data.shape[1],
'max_goals': 10,
'home_team_dummies': home_team_dummies,
'away_team_dummies': away_team_dummies,
'expectations': expectations_data,
'pct': pct,
'ratings': ratings_data,
'Y': Y_data.astype(np.int16),
'oos_n_rows': oos_ratings_data.shape[0],
'oos_home_team_dummies': oos_team_dummies_data[::, 0, ::],
'oos_away_team_dummies': oos_team_dummies_data[::, 1, ::],
'oos_expectations': oos_expectations_data,
'oos_ratings': oos_ratings_data,
'oos_pct': oos_pct
}
stan_model = StanModel('../stan/games.stan')
samples = stan_model.sampling(stan_data,
warmup=warmup,
iter=n_iter,
chains=4,
refresh=1,
control={
'adapt_delta': 0.99,
'max_treedepth': 15
})
preds = samples['predicted_probabilities']
mean_preds = np.mean(preds, axis=0)
return samples, mean_preds
def stanTopkl():
"""
The function complies 'stan' models first and avoids re-complie of the model.
"""
if os.path.isfile('log_normal.pkl'):
os.remove('log_normal.pkl')
sm = StanModel(file='log_normal.stan')
with open('log_normal.pkl', 'wb') as f:
pickle.dump(sm, f)
if os.path.isfile('log_t.pkl'):
os.remove('log_t.pkl')
sm = StanModel(file='log_t.stan')
with open('log_t.pkl', 'wb') as f:
pickle.dump(sm, f)
def compile_stan_model(stan_model_name):
"""
Compile stan model and save as pkl
"""
source_model = pkg_resources.resource_filename(
'orbit', 'stan/{}.stan'.format(stan_model_name))
compiled_model = pkg_resources.resource_filename(
'orbit', 'stan_compiled/{}.pkl'.format(stan_model_name))
# updated for py3
os.makedirs(os.path.dirname(compiled_model), exist_ok=True)
# compile if stan source has changed
if not os.path.isfile(compiled_model) or \
os.path.getmtime(compiled_model) < os.path.getmtime(source_model):
with open(source_model, encoding="utf-8") as f:
model_code = f.read()
sm = StanModel(model_code=model_code)
with open(compiled_model, 'wb') as f:
pickle.dump(sm, f, protocol=pickle.HIGHEST_PROTOCOL)
return None
def get_or_compile_stan_model(model_file, distribution):
"""
Creates Stan model. Compiles a Stan model and saves it to .pkl file to the folder selected by tempfile module if
file doesn't exist yet and load precompiled model if there is a model file in temporary dir.
Args:
model_file: model file location
distribution: name of the KPI distribution model, which assumes a
Stan model file with the same name exists
Returns:
returns compiled Stan model for the selected distribution or normal distribution
as a default option
Note: compiled_model_file is the hardcoded file path which may cause some issues in future.
There are 2 alternative implementations for Stan models handling:
1. Using global variables
2. Pre-compiling stan models and adding them as a part of expan project
(3). Using temporary files with tempfile module is not currently possible, since it
generates a unique file name which is difficult to track.
However, compiled modules are saved in temporary directory using tempfile module
which vary based on the current platform and settings. Cleaning up a temp dir is done on boot.
"""
python_version = '{0[0]}.{0[1]}'.format(sys.version_info)
compiled_model_file = tempfile.gettempdir() + '/expan_early_stop_compiled_stan_model_' \
+ distribution + '_' + python_version + '.pkl'
if os.path.isfile(compiled_model_file):
sm = pickle.load(open(compiled_model_file, 'rb'))
else:
sm = StanModel(file=model_file)
with open(compiled_model_file, 'wb') as f:
pickle.dump(sm, f)
return sm
def test_bernoulli_compile_time(self):
model_code = self.bernoulli_model_code
t0 = time.time()
model = StanModel(model_code=model_code)
self.assertIsNotNone(model)
msg = "Compile time: {}s (vs. RStan 28s)\n".format(int(time.time()-t0))
logging.info(msg)
def test_stanc_exception(self):
model_code = 'parameters {real z;} model {z ~ no_such_distribution();}'
assertRaisesRegex = self.assertRaisesRegexp if PY2 else self.assertRaisesRegex
with assertRaisesRegex(ValueError, 'unknown distribution'):
stanc(model_code=model_code)
with assertRaisesRegex(ValueError, 'unknown distribution'):
StanModel(model_code=model_code)
def get_stan_model(model_name, recompile=False, **model_params):
"""
Compile a Stan probabilistic model, or load pre-compiled model from cache,
if available.
Parameters
----------
model_name : str
Then name of the model used
"bernoulli", "b": Bernoulli likelihood flat prior on probabilities
"beta-binomial", "bb": Binomial likelihood and Beta prior
recompile : boolean
If set to to True, always recompile the model, otherwise try to use
the cached pickle of the model.
"""
python_version = 'python{0[0]}.{0[1]}'.format(sys.version_info)
filename = "-".join([_f for _f in [model_name, python_version] if _f])
compiled_model_file = os.path.join(STAN_MODEL_CACHE, filename + ".pickle")
if os.path.isfile(compiled_model_file) and not recompile:
with open(compiled_model_file, 'rb') as m:
model = pickle.load(m)
else:
model_code = get_stan_model_code(model_name)
model = StanModel(model_code=model_code)
logging.info('Saving model to {}'.format(compiled_model_file))
with open(compiled_model_file, 'wb') as f:
pickle.dump(model, f)
return model
def __init__(self, context, rdd, prepare_data_callback, stan_file):
self.rdd = rdd
self.prepare_data_callback = prepare_data_callback
self.n_partitions = self.rdd.getNumPartitions()
sm = StanModel(file=stan_file)
pickle.dump(sm, open(PICKLE_FILENAME, "wb"))
context.addFile(PICKLE_FILENAME)
def tobit_vec_QR(tobit_data: pd.DataFrame, scaled: bool = False):
"""
vectorised version of the tobit model that combines the parameters for the censored
values with the uncensored values into a transformed y for more efficiency.
"""
vec_model = StanModel(
file=Path('models/tobit_students_vec_qr.stan').open(),
extra_compile_args=["-w"])
not_800 = tobit_data['apt'] != 800
is_800 = tobit_data['apt'] == 800
ii_obs = tobit_data[not_800]['id']
ii_cens = tobit_data[is_800]['id']
if not scaled:
vec_dict = {
'X': tobit_data[new_preds],
'n_obs': not_800.sum(),
'n_cens': is_800.sum(),
'U': 800,
'y_obs': tobit_data[not_800]['apt'],
'p': len(new_preds),
'ii_obs': ii_obs,
'ii_cens': ii_cens
}
else:
trans = MaxAbsScaler().fit_transform(tobit_data[new_preds + ['apt']])
data_centered = pd.DataFrame(trans, columns=new_preds + ['apt'])
vec_dict = {
'X': data_centered[new_preds],
'n_obs': not_800.sum(),
'n_cens': is_800.sum(),
'U': 800,
'y_obs': data_centered[not_800]['apt'],
'p': len(new_preds),
'ii_obs': ii_obs,
'ii_cens': ii_cens,
'X_cens': data_centered[is_800][new_preds]
}
vec_fit = vec_model.sampling(data=vec_dict,
iter=10000,
chains=4,
warmup=2000,
control=c_params)
print('β: {}'.format(vec_fit['beta'][501:].mean(axis=0)))
print(vec_fit.stansummary())
return vec_fit, vec_model
def tobit_simple_model(tobit_data: pd.DataFrame, scaled: bool = False):
"""
2) using a censored model. Has the same sigma - in the paper, the distinction
between ε_{it} ~ normal(0,σ^2and θ^m_{it} ~ normal(0, δ^2_m) is clearly made.
This looks quite close to the values from the tutorial:
Intercept: 209.5488
mydata$read: 2.6980, mydata$math: 5.9148
"""
censored_model = StanModel(
file=Path('models/tobit_students_split.stan').open(),
extra_compile_args=["-w"])
not_800 = tobit_data['apt'] != 800
is_800 = tobit_data['apt'] == 800
if not scaled:
cens_dict_ex = {
'X': tobit_data[not_800][new_preds],
'n': tobit_data.shape[0] - is_800.sum(),
'y': tobit_data[not_800]['apt'],
'n_cens': is_800.sum(),
'p': len(new_preds),
'X_cens': tobit_data[is_800][new_preds],
'y_cens': tobit_data[is_800]['apt'],
'U': 800
}
else:
trans = MaxAbsScaler().fit_transform(tobit_data[new_preds + ['apt']])
data_centered = pd.DataFrame(trans, columns=new_preds + ['apt'])
cens_dict_ex = {
'X': data_centered[not_800][new_preds],
'n': tobit_data.shape[0] - is_800.sum(),
'y': data_centered[not_800]['apt'],
'n_cens': is_800.sum(),
'p': len(new_preds),
'y_cens': data_centered[is_800]['apt'],
'U': 1,
'X_cens': tobit_data[is_800][new_preds]
}
censored_fit = censored_model.sampling(data=cens_dict_ex,
iter=2000,
chains=4,
warmup=500,
control=c_params)
censored_res = censored_fit.extract()
print('β: {}'.format(censored_res['beta'][501:].mean(axis=0)))
return censored_fit, censored_model
def build_stan_model(target_dir, model_dir=MODEL_DIR):
from pystan import StanModel
model_name = 'prophet.stan'
target_name = 'prophet_model.pkl'
with open(os.path.join(model_dir, model_name)) as f:
model_code = f.read()
sm = StanModel(model_code=model_code)
with open(os.path.join(target_dir, target_name), 'wb') as f:
pickle.dump(sm, f, protocol=pickle.HIGHEST_PROTOCOL)
def run_inference():
df = pd.read_csv('3gaussians-10k.csv')
X = np.array(df[['XX', 'YY']].values)
K = 3
data = {'D': 2,
'K': 3,
'N': 10000,
'Omega0': np.identity(2),
'alpha': K * [0.1],
'beta0': 0.1,
'dof0': 1.1,
'm0': np.zeros(2),
'x': X}
model = StanModel(file='finite_gaussian_mixture.stan')
return model.sampling(data=data, warmup=200, iter=700)
def compile_stan_models(target_dir, model_dir=MODEL_DIR):
"""Pre-compile the stan models that are used by the module."""
from pystan import StanModel
names = ["simple_model.stan", "model_with_prior.stan"]
targets = ["simple_model.pkl", "prior_model.pkl"]
for (name, target) in zip(names, targets):
sm = StanModel(file=os.path.join(model_dir, name))
with open(os.path.join(target_dir, target), "wb") as f:
pickle.dump(sm, f, protocol=pickle.HIGHEST_PROTOCOL)
def compile_stan_models(target_dir, model_dir=MODEL_DIR):
"""Pre-compile the stan models that are used by the module."""
from pystan import StanModel
print("Compiling Stan player model, and putting pickle in {}".format(
target_dir))
sm = StanModel(file=os.path.join(model_dir, "player_forecasts.stan"))
with open(os.path.join(target_dir, "player_forecasts.pkl"),
"wb") as f_stan:
pickle.dump(sm, f_stan, protocol=pickle.HIGHEST_PROTOCOL)
def test_matrix_param_order_optimizing():
model_code = """
data {
int<lower=2> K;
}
parameters {
matrix[K,2] beta;
}
model {
for (k in 1:K)
beta[k,1] ~ normal(0,1);
for (k in 1:K)
beta[k,2] ~ normal(100,1);
}"""
sm = StanModel(model_code=model_code)
op = sm.optimizing(data=dict(K=3))
beta = op['par']['beta']
assert beta.shape == (3, 2)
beta_colmeans = np.mean(beta, axis=0)
assert beta_colmeans[0] < 4
assert beta_colmeans[1] > 100 - 4
import pandas as pd
from pystan import StanModel
import matplotlib.pyplot as plt
import pickle
d = pd.read_csv('input/data-attendance-1.txt')
d.Score /= 200
data = d.to_dict('list')
data.update({'N':len(d)})
stanmodel = StanModel(file='model/model5-3.stan')
# NUTS (No U-Turn Sampler)
fit_nuts = stanmodel.sampling(data=data, n_jobs=1)
mcmc_sample = fit_nuts.extract()
mu_est = mcmc_sample['mu']
# ADVI (Automatic Differentiation Variational Inference)
fit_vb = stanmodel.vb(data=data)
vb_sample = pd.read_csv(fit_vb['args']['sample_file'].decode('utf-8'), comment='#')
vb_sample = vb_sample.drop([0,1])
mu_est = vb_sample.filter(regex='mu\.\d+')
with open('output/model_and_result.pkl', 'wb') as f:
pickle.dump(stanmodel, f)
pickle.dump(fit_nuts, f)
def test8schools():
model_name = "_8chools"
sfile = os.path.join(os.path.dirname(__file__),
"../stan/src/models/misc/eight_schools/eight_schools.stan")
m = StanModel(file=sfile, model_name=model_name, verbose=True)
m.dso
yam = StanModel(file=sfile, model_name=model_name, save_dso=False, verbose=True)
yam.dso
dat = dict(J=8, y=(28, 8, -3, 7, -1, 1, 18, 12),
sigma=(15, 10, 16, 11, 9, 11, 10, 18))
iter = 5020
# HMC
ss1 = m.sampling(data=dat, iter=iter, chains=4, algorithm='HMC', refresh=100)
ss1son = stan(fit=ss1, data=dat, init_r=0.0001)
ss1son = stan(fit=ss1, data=dat, init_r=0)
ainfo1 = ss1.get_adaptation_info()
lp1 = ss1.get_logposterior()
yalp1 = ss1.get_logposterior(inc_warmup=False)
sp1 = ss1.get_sampler_params()
yasp1 = ss1.get_sampler_params(inc_warmup=False)
gm1 = ss1.get_posterior_mean()
print(gm1)
# NUTS 1
ss2 = m.sampling(data=dat, iter=iter, chains=4, refresh=100,
control=dict(metric="unit_e"))
ainfo2 = ss2.get_adaptation_info()
lp2 = ss2.get_logposterior()
yalp2 = ss2.get_logposterior(inc_warmup=False)
sp2 = ss2.get_sampler_params()
yasp2 = ss2.get_sampler_params(inc_warmup=False)
gm2 = ss2.get_posterior_mean()
print(gm2)
# NUTS 2
ss3 = m.sampling(data=dat, iter=iter, chains=4, refresh=100)
ainfo3 = ss3.get_adaptation_info()
lp3 = ss3.get_logposterior()
yalp3 = ss3.get_logposterior(inc_warmup=False)
sp3 = ss3.get_sampler_params()
yasp3 = ss3.get_sampler_params(inc_warmup=False)
gm3 = ss3.get_posterior_mean()
print(gm3)
# Non-diag
ss4 = m.sampling(data=dat, iter=iter, chains=4,
control=dict(metric='dense_e'), refresh=100)
ainfo4 = ss4.get_adaptation_info()
lp4 = ss4.get_logposterior()
yalp4 = ss4.get_logposterior(inc_warmup=False)
sp4 = ss4.get_sampler_params()
yasp4 = ss4.get_sampler_params(inc_warmup=False)
gm4 = ss4.get_posterior_mean()
print(gm4)
print(ss1)
print(ss2)
print(ss3)
ss1.plot()
ss1.traceplot()
ss9 = m.sampling(data=dat, iter=iter, chains=4, refresh=10)
iter = 52012
ss = stan(sfile, data=dat, iter=iter, chains=4, sample_file='8schools.csv')
print(ss)
ss_inits = ss.inits
ss_same = stan(sfile, data=dat, iter=iter, chains=4,
seed=ss.stan_args[0]['seed'], init=ss_inits,
sample_file='ya8schools.csv')
b = np.allclose(ss.extract(permuted=False), ss_same.extract(permuted=False))
# b is not true as ss is initialized randomly while ss.same is not.
s = ss_same.summary(pars="mu", probs=(.3, .8))
# not in python: print(ss.same, pars='theta', probs=c(.4, .8))
print(ss_same)
N = len(x_data)
# Introduce noise
x_data = np.random.normal(x_data, 7)
y_data = np.random.normal(y_data, 8)
# plot the data
pyplot.plot(x_data, y_data, 'o')
stan_data_mappings = {
'x': x_data,
'y': y_data,
'N': N,
}
model = StanModel(file='models/univariate_regression.stan')
fit = model.sampling(data=stan_data_mappings)
params = fit.extract()
a_pred = params['a']
b_pred = params['b']
sigma_pred = params['sigma']
# Draw 100 points from where x_data is.
xfit = np.linspace(-10 + min(x_data), 10 + max(x_data), 100)
# Number of samples.
M = len(a_pred)
yfit = a_pred.reshape((M, 1)) + b_pred.reshape((M, 1)) * xfit
'sc_mean_vec': sc_mean_vec,
'sc_var_vec': sc_var_vec,
'mp_mean_prior_mean': 1,
'mp_mean_prior_var': 2,
'mp_var_prior_shape': 3,
'mp_var_prior_scale': 4,
'mp_corr_prior_conc': 3,
'exponent_prior_mean': exponent,
'base_rate_prior_mean': base_rate,
'threshold_prior_mean': threshold,
'n_samples': n_samp_est,
'stdnorm_samples': stdnorm_samples
}
if recompile:
sm = StanModel(file='corr_rate.stan', verbose=False)
with open('corr_rate.pkl', 'wb') as f:
pickle.dump(sm, f)
else:
sm = pickle.load(open('corr_rate.pkl', 'rb'))
fit = sm.sampling(data=corr_dat, iter=2000, chains=3)
estimation = fit.extract(permuted=True)
cm = estimation['mp_corr_mat']
pickle.dump(cm, open('corr_mat_samples.pkl', 'wb'))
savemat('corr_mat_samples.mat', {'cm': cm})
mp_col = 'r'
sc_true_col = 'y'
sc_obs_col = 'g'
import numpy as np
import pickle
import pystan
from matplotlib import pyplot as plt
print 'test'
from pystan import StanModel
sm = StanModel(file='model.stan')
with open('model.pkl','wb') as f:
pickle.dump(sm, f)
import scipy as sc
def phi(x,mu=0,sd=1):
return 0.5 * (1 + sc.special.erf((x - mu) / (sd * np.sqrt(2))))
N = 300
df = 2*(np.random.random(N)-0.5)*0.6
d1 = 2*(np.random.random(N)-0.5)
A = lambda sc,de : lambda d : sc*d*np.exp(-np.abs(d)/de)
alpha = A(5,1)
sigma = 0.06
y = (np.random.rand(N)<phi(df/sigma-alpha(d1))).astype(int)
plt.plot(d1,alpha(d1),'rx',)
plt.plot(d1,df/sigma,'gx',)
sm = pickle.load(open('model.pkl','rb'))
def test_optimizing_basic():
sm = StanModel(model_code='parameters {real y;} model {y ~ normal(0,1);}')
op = sm.optimizing()
assert op['par']['y'].shape == ()
assert abs(op['par']['y']) < 1
// We will do this in separate dimensions (teff, logg) because we are not considering
// the case that the outliers are covariant in the same way we believe the measurements
// are
increment_log_prob(log_sum_exp(
log1m_alpha + normal_log(sp_vector[1], outlier_teff_mu, outlier_teff_sigma),
log1m_alpha + normal_log(sp_vector[2], outlier_teff_mu, outlier_teff_sigma)
));
}
}"""
# Ok, here is our toy data:
with open("toy.data", "r") as fp:
data = json.load(fp)
model = StanModel(model_code=model_code)
print("Optimizing...")
op = model.optimizing(data=data)
print("Fitting...")
fit = model.sampling(data=data, pars=op["par"], iter=20000)
subplots_adjust = { "left": 0.10, "bottom": 0.05, "right": 0.95, "top": 0.95,
"wspace": 0.20, "hspace": 0.45
}
nodes = range(2)
dimensions = ("teff", "logg")
# Plot the m, b parameters for each node
'C': C,
'z_shape': z_shape,
'z_scale': z_scale,
'g_shape': g_shape,
'g_scale': g_scale,
'Var_u': Var_u
}
if model_type == 1:
fname = "csm"
elif model_type == 2:
fname = "csm2"
elif model_type == 3:
fname = "msm"
if recompile:
sm = StanModel(file=fname + '_inference.stan')
with open(fname + '_inference.pkl', 'wb') as f:
pickle.dump(sm, f)
else:
sm = pickle.load(open(fname + '_inference.pkl', 'rb'))
fit = sm.sampling(data=gsm_dat, iter=2000, chains=2)
estimation = fit.extract(permuted=True)
g_est_mean = np.mean(estimation["g"], 0)
print('g est', g_est_mean)
print('g true', g_synth)
z_est_mean = np.mean(estimation["z"], 0).T
print('z est', z_est_mean)
print('z true', z_synth)
parameters {
real mu;
real<lower=0> tau;
real eta[J];
}
transformed parameters {
real theta[J];
for (j in 1:J)
theta[j] <- mu + tau * eta[j];
}
model {
eta ~ normal(0, 1);
y ~ normal(theta, sigma);
}
'''
m = StanModel(model_code=schools_code, model_name=model_name, verbose=True)
J = 8
y = (28, 8, -3, 7, -1, 1, 18, 12)
sigma = (15, 10, 16, 11, 9, 11, 10, 18)
iter = 1000
dat = dict(J=J, y=y, sigma=sigma)
ss1 = m.sampling(data=dat, iter=iter, chains=4, refresh=100)
print(ss1)
ss1.traceplot()
ss = stan(model_code=schools_code, data=dat, iter=iter, chains=4,
sample_file='8schools.csv')
print(ss)
yield obsid, odata
standata = StanData(datafile, samplefile, obssel)
N = standata.Noutcomes()
K = standata.Npredictors()
matrix = standata.predictors()
print "Predictor matix (", K, "X", N, "):"
for i in range(min(K, 5)):
print "\t".join( [str(matrix[j,i]) for j in range(min(N, 10))] )
from pystan import StanModel
smfile = modelfile + ".pkl"
if not os.path.exists(smfile):
modelname = os.path.splitext(os.path.basename(modelfile))[0] + "_" + os.path.splitext(os.path.basename(datafile))[0]
stanmodel = StanModel(file=modelfile, model_name=modelname)
with open(smfile, 'wb') as f:
pickle.dump(stanmodel, f)
else:
stanmodel = pickle.load(open(smfile, 'rb'))
def get_median(sample_array):
sample_array.sort()
n = len(sample_array)
medianvalue = sample_array[n/2] if (n % 2) == 0 else (sample_array[n/2] + sample_array[n/2 + 1]) / 2.0
return medianvalue
pdf = bp.PdfPages(betapdffile)
results = {}
for obsid, odata in standata.iter_observations():
sample_outfile = os.path.join(sampledir, obsid + "_samples.txt") if sampledir != "" else None
import matplotlib.pyplot as pl
# x = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
x = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
# x = [1, 1, 1]
cf_dat = {
'N': len(x),
'x': x,
'prior_width': 0.2
}
recompile = False
if recompile:
sm = StanModel(file='coinflip.stan')
with open('coinflip.pkl', 'wb') as f:
pickle.dump(sm, f)
else:
sm = pickle.load(open('coinflip.pkl', 'rb'))
# fit = sm.sampling(data=cf_dat, iter=2000, chains=2)
fit = sm.sampling(data=cf_dat, iter=20, chains=1, seed='random', init=[{'beta': 0.5}], warmup=10)
estimation = fit.extract(permuted=True)
print(estimation['beta'])
pl.hist(estimation['beta'], bins=40)
pl.xlim([0, 1])
pl.show()
for i in range(N):
act_u = u_synth[i, :].T
act_mean = z_synth[i] * A.dot(act_u)
x_synth[i, :] = multivariate_normal(act_mean, sigma_x)
gsm_dat = {
"N": N,
"d_x": d_x,
"d_u": d_u,
"sigma_x": sigma_x,
"x": x_synth,
"A": A,
"C": C,
"z_shape": z_shape,
"z_scale": z_scale,
}
if recompile:
sm = StanModel(file="gsm_inference.stan")
with open("gsm_inference.pkl", "wb") as f:
pickle.dump(sm, f)
else:
sm = pickle.load(open("gsm_inference.pkl", "rb"))
fit = sm.sampling(data=gsm_dat, iter=100, chains=8)
estimation = fit.extract(permuted=True)
z_est_mean = mean(estimation["z"], 0).T
print(z_est_mean)
print(z_synth)