def __init__(self, scenario):
if isinstance(scenario, str):
self.scenario = EpiScenario(scenario)
elif isinstance(scenario, EpiScenario):
self.scenario = scenario
self.modelname = self.scenario.modelname
self.total_days = 0
self.r0 = self.scenario.parameters['initial_r0']
self.beta = None
self.population = self.scenario.totalpop
self.susceptible = ProbState(period=0,
count=self.scenario.init_susceptible,
name='susceptible')
self.incubating = ProbState(period=self.scenario.incubation_period,
count=self.scenario.init_infected,
name='incubating')
self.infectious = ProbState(period=self.scenario.prediagnosis,
count=self.scenario.init_infectious,
name='infectious')
self.isolated_holding = ProbState(period=90, name='isolated_holding')
self.incubating.add_exit_state(self.infectious, 1)
self.incubating.normalize_states_over_period()
self.infectious.add_exit_state(self.isolated_holding, 1)
self.infectious.normalize_states_over_period()
self.subgroups = dict()
for key, value in self.scenario.subgrouprates.items():
self.subgroups[key] = AgeGroup(value, name=key)
def __init__(self):
self.r0 = 2.65
self.total_days = 0
self.population = POP_DENVER
self.beta = None
self.susceptible = ProbState(period=0,
count=self.population - 1,
name='susceptible')
self.incubating = ProbState(period=3, name='incubating')
self.infectious = ProbState(period=3.8, count=1, name='infectious')
self.isolated_holding = ProbState(period=90, name='isolated_holding')
self.incubating.add_exit_state(self.infectious, 1)
self.incubating.normalize_states_over_period()
self.infectious.add_exit_state(self.isolated_holding, 1)
self.infectious.normalize_states_over_period()
self.subgroups = dict()
for key, value in AGE_DISTRIBUTION.items():
self.subgroups[key] = AgeGroup(SubgroupRates(ICD[key], value),
name=key)
self.sum_isolated = None
self.sum_noncrit = None
self.sum_icu = None
self.sum_icu_vent = None
self.sum_recovered = None
self.sum_deceased = None
def __init__(self, subgroupstats, name=None):
self.name = name
self.stats = subgroupstats
# Variables to store state changes
# Probability states
if self.name is not None:
self.isolated = ProbState(14, name=f"{self.name}: isolated")
else:
self.isolated = ProbState(14)
self.h_noncrit = ProbState(8)
self.h_post_icu = ProbState(6)
self.h_icu = ProbState(10)
self.h_icu_vent = ProbState(10)
self.recovered = ProbState(1000)
self.deceased = ProbState(1000)
self.isolated.add_exit_state(self.recovered, 1)
self.isolated.normalize_states_over_period()
self.h_noncrit.add_exit_state(self.recovered, 1)
self.h_noncrit.normalize_states_over_period()
self.h_icu.add_exit_state(self.deceased, self.stats.p_icu_death)
self.h_icu.add_exit_state(self.h_post_icu, self.stats.p_icu_recovery)
self.h_icu.normalize_states_over_period()
self.h_icu_vent.add_exit_state(self.deceased, self.stats.p_icu_death)
self.h_icu_vent.add_exit_state(self.h_post_icu, self.stats.p_icu_recovery)
self.h_icu_vent.normalize_states_over_period()
self.h_post_icu.add_exit_state(self.recovered, 1)
self.h_post_icu.normalize_states_over_period()
def __init__(self):
self.r0 = 2.65
self.total_days = 0
self.population = POP_DENVERMETRO - 1
self.beta = None
self.susceptible = ProbState(period=0, count=self.population)
self.incubating = ProbState(period=3)
self.infectious = ProbState(period=3.8, count=1)
self.isolated = ProbState(period=14)
self.unhospitalized = ProbState(period=14)
self.h_noncritical = ProbState(period=8)
self.h_critical = ProbState(period=6)
self.h_icu = ProbState(period=10)
self.recovered = ProbState(period=10000)
self.dead = ProbState(period=10000)
self.incubating.add_exit_state(self.infectious, 1)
self.incubating.normalize_states_over_period()
self.isolated.add_exit_state(self.recovered, 1)
self.isolated.normalize_states_over_period()
self.unhospitalized.add_exit_state(self.recovered, .25)
self.unhospitalized.add_exit_state(self.dead, .75)
self.unhospitalized.normalize_states_over_period()
self.infectious.add_exit_state(self.isolated, .85)
self.infectious.add_exit_state(self.h_noncritical, .11)
self.infectious.add_exit_state(self.h_critical, .4)
self.infectious.normalize_states_over_period()
self.h_noncritical.add_exit_state(self.recovered, 1)
self.h_noncritical.normalize_states_over_period()
self.h_critical.add_exit_state(self.recovered, 1)
self.h_critical.normalize_states_over_period()
self.h_icu.add_exit_state(self.recovered, .75)
self.h_icu.add_exit_state(self.dead, .25)
self.h_icu.normalize_states_over_period()
def __init__(self, subgroupstats, name=None):
self.name = name
self.stats = subgroupstats
# Variables to store state changes
# Probability states
self.isolated = ProbState(TIMINGS['days home isolation'],
name=f"{self.name}: isolated")
self.nevercrit = ProbState(TIMINGS['days noncrit'],
name=f"{self.name}: nevercrit")
self.pre_icu = ProbState(TIMINGS['days preicu'],
name=f"{self.name}: pre_icu")
self.icu_novent = ProbState(TIMINGS['days icu nonvent'],
name=f"{self.name}: icu")
self.icu_vent = ProbState(TIMINGS['days icu vent'],
name=f"{self.name}: icu_vent")
self.post_icu = ProbState(TIMINGS['days posticu'],
name=f"{self.name}: post_icu")
# Recovered and dead are presumed permanent
self.recovered = ProbState(1000, name=f"{self.name}: recovered")
self.deceased = ProbState(1000, name=f"{self.name}: deceased")
self.isolated.add_exit_state(self.recovered, 1)
self.isolated.normalize_states_over_period()
self.nevercrit.add_exit_state(self.recovered, 1)
self.nevercrit.normalize_states_over_period()
self.pre_icu.add_exit_state(self.icu_novent, self.stats.p_icu_nonvent)
self.pre_icu.add_exit_state(self.icu_vent, self.stats.p_icu_vent)
self.pre_icu.normalize_states_over_period()
self.icu_novent.add_exit_state(self.deceased, self.stats.p_icu_death)
self.icu_novent.add_exit_state(self.post_icu,
self.stats.p_icu_recovery)
self.icu_novent.normalize_states_over_period()
self.icu_vent.add_exit_state(self.deceased, self.stats.p_icu_death)
self.icu_vent.add_exit_state(self.post_icu, self.stats.p_icu_recovery)
self.icu_vent.normalize_states_over_period()
self.post_icu.add_exit_state(self.recovered, 1)
self.post_icu.normalize_states_over_period()