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perf: Use Python builtin RNG to generate Bernoulli samples #36

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Jul 25, 2022
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perf: Use Python builtin RNG to generate Bernoulli samples #36

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57 changes: 33 additions & 24 deletions covidmodel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,15 @@
from database import Database


def bernoulli_rvs(p):
# Return a sample from a Bernoulli-distributed random source
# We convert from a Uniform(0, 1)
r = random.random()
if r >= p:
return 1
return 0


class Stage(Enum):
SUSCEPTIBLE = 1
EXPOSED = 2
Expand Down Expand Up @@ -127,7 +136,7 @@ def test_contact_trace(self):
elif self.stage == Stage.EXPOSED:
self.agent_data.tested_traced = True

if bernoulli.rvs(self.model.model_data.prob_asymptomatic):
if bernoulli_rvs(self.model.model_data.prob_asymptomatic):
self.stage = Stage.ASYMPDETECTED
else:
self.stage = Stage.SYMPDETECTED
Expand All @@ -154,7 +163,7 @@ def general_vaccination_chance(self):
eligible_count = compute_age_group_count(self.model, self.agent_data.age_group)
vaccination_chance = 1/eligible_count
if self.stage == Stage.ASYMPTOMATIC or self.stage == Stage.SUSCEPTIBLE or self.stage == Stage.EXPOSED:
if bernoulli.rvs(vaccination_chance):
if bernoulli_rvs(vaccination_chance):
return True
return False
return False
Expand Down Expand Up @@ -198,16 +207,16 @@ def step(self):
# In 60 days, this is equivalent to a probability of 1% unemployment filings.
if self.agent_data.employed:
if self.agent_data.isolated:
if bernoulli.rvs(32*0.00018/self.model.model_data.dwell_15_day):
if bernoulli_rvs(32*0.00018/self.model.model_data.dwell_15_day):
self.agent_data.employed = False
else:
if bernoulli.rvs(8*0.00018/self.model.model_data.dwell_15_day):
if bernoulli_rvs(8*0.00018/self.model.model_data.dwell_15_day):
self.agent_data.employed = False

# We also compute the probability of re-employment, which is at least ten times
# as smaller in a crisis.
if not(self.agent_data.employed):
if bernoulli.rvs(0.000018/self.model.model_data.dwell_15_day):
if bernoulli_rvs(0.000018/self.model.model_data.dwell_15_day):
self.agent_data.employed = True


Expand All @@ -234,7 +243,7 @@ def step(self):
#Will process based on whether all older agents in an older group are vaccinated
if (not(self.agent_data.vaccinated) or self.agent_data.dosage_eligible) and self.model.model_data.vaccination_now and (not(self.agent_data.fully_vaccinated) and (self.agent_data.vaccine_count < self.model.model_data.vaccine_dosage)):
if self.should_be_vaccinated() and self.model.model_data.vaccine_count > 0 and self.agent_data.vaccine_willingness:
if not (bernoulli.rvs(0.1)): # Chance that someone doesnt show up for the vaccine/ vaccine expires.
if not (bernoulli_rvs(0.1)): # Chance that someone doesnt show up for the vaccine/ vaccine expires.
self.agent_data.vaccinated = True
self.agent_data.vaccination_day = self.model.stepno
self.agent_data.vaccine_count = self.agent_data.vaccine_count + 1
Expand All @@ -259,15 +268,15 @@ def step(self):
if (self.astep >= self.model.model_data.isolation_start):
if (self.stage == Stage.SUSCEPTIBLE) or (self.stage == Stage.EXPOSED) or \
(self.stage == Stage.ASYMPTOMATIC):
if bool(bernoulli.rvs(self.model.model_data.isolation_rate)):
if bool(bernoulli_rvs(self.model.model_data.isolation_rate)):
self.agent_data.isolated = True
else:
self.agent_data.isolated = False
self.agent_data.in_isolation = True
elif (self.astep >= self.model.model_data.isolation_end):
if (self.stage == Stage.SUSCEPTIBLE) or (self.stage == Stage.EXPOSED) or \
(self.stage == Stage.ASYMPTOMATIC):
if bool(bernoulli.rvs(self.model.model_data.after_isolation)):
if bool(bernoulli_rvs(self.model.model_data.after_isolation)):
self.agent_data.isolated = True
else:
self.agent_data.isolated = False
Expand Down Expand Up @@ -303,7 +312,7 @@ def step(self):
# Using the model, determine if a susceptible individual becomes infected due to
# being elsewhere and returning to the community
if self.stage == Stage.SUSCEPTIBLE:
# if bernoulli.rvs(self.model.rate_inbound):
# if bernoulli_rvs(self.model.rate_inbound):
# self.stage = Stage.EXPOSED
# self.model.generally_infected = self.model.generally_infected + 1
#
Expand All @@ -316,7 +325,7 @@ def step(self):
# still susceptible.
# We take care of testing probability at the top level step
# routine to avoid this repeated computation
if not(self.agent_data.tested or self.agent_data.tested_traced) and bernoulli.rvs(self.agent_data.test_chance):
if not(self.agent_data.tested or self.agent_data.tested_traced) and bernoulli_rvs(self.agent_data.test_chance):
self.agent_data.tested = True
self.model.model_data.cumul_test_cost = self.model.model_data.cumul_test_cost + self.model.model_data.test_cost
# First opportunity to get infected: contact with others
Expand All @@ -333,7 +342,7 @@ def step(self):
for c in cellmates:
if c.is_contagious() and (c.stage == Stage.SYMPDETECTED or c.stage == Stage.SEVERE) and self.agent_data.variant_immune[c.agent_data.variant] == False:
c.add_contact_trace(self)
if self.agent_data.isolated and bernoulli.rvs(1 - self.model.model_data.prob_isolation_effective):
if self.agent_data.isolated and bernoulli_rvs(1 - self.model.model_data.prob_isolation_effective):
self.agent_data.isolated_but_inefficient = True
infected_contact = 1
variant = c.agent_data.variant
Expand All @@ -344,7 +353,7 @@ def step(self):
break
elif c.is_contagious() and (c.stage == Stage.ASYMPTOMATIC or c.stage == Stage.ASYMPDETECTED) and self.agent_data.variant_immune[c.agent_data.variant] == False:
c.add_contact_trace(self)
if self.agent_data.isolated and bernoulli.rvs(1 - self.model.model_data.prob_isolation_effective):
if self.agent_data.isolated and bernoulli_rvs(1 - self.model.model_data.prob_isolation_effective):
self.agent_data.isolated_but_inefficient = True
infected_contact = 2
variant = c.agent_data.variant
Expand Down Expand Up @@ -381,12 +390,12 @@ def step(self):

if infected_contact > 0:
if self.agent_data.isolated:
if bernoulli.rvs(current_prob) and not(bernoulli.rvs(self.model.model_data.prob_isolation_effective)):
if bernoulli_rvs(current_prob) and not(bernoulli_rvs(self.model.model_data.prob_isolation_effective)):
self.stage = Stage.EXPOSED
self.agent_data.variant = variant
self.model.model_data.generally_infected = self.model.model_data.generally_infected + 1
else:
if bernoulli.rvs(current_prob):
if bernoulli_rvs(current_prob):
#Added vaccination account after being exposed to determine exposure.
self.stage = Stage.EXPOSED
self.agent_data.variant = variant
Expand Down Expand Up @@ -431,8 +440,8 @@ def step(self):


# If testing is available and the date is reached, test
if not(self.agent_data.tested or self.agent_data.tested_traced) and bernoulli.rvs(self.agent_data.test_chance):
if bernoulli.rvs(current_prob_asymptomatic):
if not(self.agent_data.tested or self.agent_data.tested_traced) and bernoulli_rvs(self.agent_data.test_chance):
if bernoulli_rvs(current_prob_asymptomatic):
self.stage = Stage.ASYMPDETECTED
else:
self.stage = Stage.SYMPDETECTED
Expand All @@ -444,7 +453,7 @@ def step(self):
if self.agent_data.curr_incubation < self.agent_data.incubation_time:
self.agent_data.curr_incubation = self.agent_data.curr_incubation + 1
else:
if bernoulli.rvs(current_prob_asymptomatic):
if bernoulli_rvs(current_prob_asymptomatic):
self.stage = Stage.ASYMPTOMATIC
else:
self.stage = Stage.SYMPDETECTED
Expand Down Expand Up @@ -476,7 +485,7 @@ def step(self):
self.agent_data.cumul_private_value = self.agent_data.cumul_private_value + 0
self.agent_data.cumul_public_value = self.agent_data.cumul_public_value - 2*self.model.model_data.stage_value_dist[ValueGroup.PUBLIC][Stage.ASYMPTOMATIC]

if not(self.agent_data.tested or self.agent_data.tested_traced) and bernoulli.rvs(self.agent_data.test_chance):
if not(self.agent_data.tested or self.agent_data.tested_traced) and bernoulli_rvs(self.agent_data.test_chance):
self.stage = Stage.ASYMPDETECTED
self.agent_data.tested = True
self.model.model_data.cumul_test_cost = self.model.model_data.cumul_test_cost + self.model.model_data.test_cost
Expand Down Expand Up @@ -522,7 +531,7 @@ def step(self):
if self.agent_data.curr_incubation + self.agent_data.curr_recovery < self.agent_data.incubation_time + self.agent_data.recovery_time:
self.agent_data.curr_recovery = self.agent_data.curr_recovery + 1

if bernoulli.rvs(current_severe_chance):
if bernoulli_rvs(current_severe_chance):
self.stage = Stage.SEVERE
else:
self.stage = Stage.RECOVERED
Expand Down Expand Up @@ -612,7 +621,7 @@ def step(self):
variant = "Standard"
for c in cellmates:
if c.is_contagious() and self.model.model_data.variant_data_list[c.variant]["Reinfection"] == True and (c.stage == Stage.SYMPDETECTED or c.stage == Stage.SEVERE) and self.agent_data.variant_immune[c.variant] != True:
if self.agent_data.isolated and bernoulli.rvs(1 - self.model.model_data.prob_isolation_effective):
if self.agent_data.isolated and bernoulli_rvs(1 - self.model.model_data.prob_isolation_effective):
self.agent_data.isolated_but_inefficient = True
infected_contact = 1
variant = c.variant
Expand All @@ -623,7 +632,7 @@ def step(self):
break
elif c.is_contagious() and (c.stage == Stage.ASYMPTOMATIC or c.stage == Stage.ASYMPDETECTED) and self.agent_data.variant_immune[c.variant] == False:
c.add_contact_trace(self)
if self.agent_data.isolated and bernoulli.rvs(1 - self.model.model_data.prob_isolation_effective):
if self.agent_data.isolated and bernoulli_rvs(1 - self.model.model_data.prob_isolation_effective):
self.agent_data.isolated_but_inefficient = True
infected_contact = 2
variant = c.variant
Expand All @@ -640,11 +649,11 @@ def step(self):

if infected_contact > 0:
if self.agent_data.isolated:
if bernoulli.rvs(current_prob) and not (bernoulli.rvs(self.model.model_data.prob_isolation_effective)):
if bernoulli_rvs(current_prob) and not (bernoulli_rvs(self.model.model_data.prob_isolation_effective)):
self.stage = Stage.EXPOSED
self.agent_data.variant = variant
else:
if bernoulli.rvs(current_prob):
if bernoulli_rvs(current_prob):
# Added vaccination account after being exposed to determine exposure.
self.stage = Stage.EXPOSED
self.agent_data.variant = variant
Expand Down Expand Up @@ -1561,7 +1570,7 @@ def step(self):
a = CovidAgent(self.i, ag, sg, mort, self)

# Some will be infected
if bernoulli.rvs(self.model_data.new_agent_prop_infected):
if bernoulli_rvs(self.model_data.new_agent_prop_infected):
a.stage = Stage.EXPOSED
self.model_data.generally_infected = self.model_data.generally_infected + 1

Expand Down