def apply(self, sim: cv.Sim):
''' Perform testing '''
t = sim.t
if self.n_tests[t]:
# Compute weights for people who would test positive or negative
positive_tests = np.zeros((sim.n, ))
for i, person in enumerate(sim.people.values()):
if person.infectious:
positive_tests[i] = 1
negative_tests = 1 - positive_tests
# Select the people to test in each category
positive_inds = cv.choose_weighted(probs=positive_tests,
n=min(sum(positive_tests),
self.n_positive[t]),
normalize=True)
negative_inds = cv.choose_weighted(
probs=negative_tests,
n=min(sum(negative_tests),
self.n_tests[t] - len(positive_inds)),
normalize=True)
# Todo - assess performance and optimize e.g. to reduce dict indexing
for ind in positive_inds:
person = sim.get_person(ind)
person.test(
t, test_sensitivity=1.0
) # Sensitivity is 1 because the person is guaranteed to test positive
sim.results['new_diagnoses'][t] += 1
for ind in negative_inds:
person = sim.get_person(ind)
person.test(t, test_sensitivity=1.0)
sim.results['new_tests'][t] += self.n_tests[t]
return
def apply(self, sim: cv.Sim):
t = sim.t
# Check that there are still tests
if t < len(self.daily_tests):
n_tests = self.daily_tests[t] # Number of tests for this day
sim.results['new_tests'][t] += n_tests
else:
return
# If there are no tests today, abort early
if not (n_tests and pl.isfinite(n_tests)):
return
test_probs = np.ones(sim.n)
for i, person in enumerate(sim.people.values()):
# Adjust testing probability based on what's happened to the person
# NB, these need to be separate if statements, because a person can be both diagnosed and infectious/symptomatic
if person.symptomatic:
test_probs[i] *= self.sympt_test # They're symptomatic
if person.known_contact:
test_probs[
i] *= self.trace_test # They've had contact with a known positive
if person.diagnosed:
test_probs[i] = 0.0
test_inds = cv.choose_weighted(probs=test_probs,
n=n_tests,
normalize=True)
for test_ind in test_inds:
person = sim.get_person(test_ind)
person.test(t, self.sensitivity)
if person.diagnosed:
sim.results['new_diagnoses'][t] += 1
return