def execute():
data = read_data(
"sqlite:///../data/isrid-master.db", Subject.age, Subject.sex, Incident.search_hours, Subject.survived
)
data = data[data.search_hours > 0]
time_max = 1000
time_ticks = np.linspace(0, time_max, time_max + 1)[:, None]
data = data[(21 <= data.age) & (data.age < 30) & (data.sex == 1)]
# Preprocessing
# The anomaly detection is slow and memory-intensive
# There is probably a smarter way to calculate the distances
times = data["search_hours"].as_matrix()
lof = local_outlier_factors(times)
indices, threshold = [], 100 # Threshold is arbitrary
# There is an extension to map the LOF on a
# closed range from 0 to 1
for index, time in enumerate(times):
if time > time_max:
p = lof(index)
if p > threshold:
print("t = {:.3f} h, LOF = {:.3f}".format(time, p))
indices.append(index)
data.drop(data.index[indices], inplace=True)
# Fitting
lines = []
for cutoff in [1000, float("inf")]:
label = "Cutoff at {} h".format(cutoff)
alpha, beta_samples = fit(data, label, data.search_hours < cutoff)
beta_mean = np.mean(beta_samples)
data_ = data.copy()
predictions = sigmoid(data_["search_hours"], alpha, beta_mean)
bs = brier_score(data_["survived"], predictions)
print(" BS = {:.3f}".format(bs))
y = sigmoid(time_ticks.T, alpha, beta_samples)
line, *_ = plt.plot(time_ticks, y.mean(axis=0), label=label + " ({:.3f})".format(bs), alpha=0.8)
lines.append(line)
quantiles = mquantiles(y, [0.025, 0.975], axis=0)
plt.fill_between(time_ticks[:, 0], *quantiles, alpha=0.6, color=line.get_color())
# Empirical Distribution
start, end, width = 0, time_max, time_max // 10
probabilities = []
for left in range(start, end, width):
right = left + width
cases = data[(data.search_hours >= left) & (data.search_hours < right)]
print(len(cases))
if len(cases) > 0:
probabilities.append(sum(cases["survived"]) / len(cases))
else:
probabilities.append(float("nan"))
plt.scatter([x + width / 2 for x in range(start, end, width)], probabilities)
plt.legend(handles=lines)
plt.title("Survival Curves Over Time (Male Subjects, 21 - 30 Years Old)")
plt.xlabel("Search Duration (hours)")
plt.ylabel("Probability of Survival")
plt.xlim(0, time_max)
plt.ylim(0, 1)
plt.grid(True)
# plt.savefig('../doc/figures/survival-curves-male-empirical.svg',
# transparent=True)
plt.show()
for column in range(3):
category = categories[row*3 + column]
ax = axes[row, column]
print(category)
subquery = query.filter(func.upper(Group.category) == category)
subquery = subquery.filter(Incident.total_hours > 0)
subquery = subquery.order_by(Incident.total_hours.asc())
times = subquery.from_self(Incident.total_hours).all()
times = list(map(lambda t: t[0].total_seconds()/3600, times))
survivals = subquery.from_self(Subject.survived).all()
survivals = [survival for survival, *_ in survivals]
indices = []
lof = local_outlier_factors(times)
for index, time in enumerate(times):
if time > 21*24:
indices.append(index)
elif lof(index) > 100:
indices.append(index)
print('Removing {} outliers'.format(len(indices)))
times = [time for index, time in enumerate(times)
if index not in indices]
survivals = [survival for index, survival in enumerate(survivals)
if index not in indices]
alpha = np.log(1/0.99 - 1)
beta = pm.Beta('beta', 1, 2, 1e-3)
prob = pm.Lambda('prob', lambda t=times, a=alpha, b=beta: