Individuals

Supertype for simulation agents

Individual <: Agent

A type to represent individuals, that act as agents inside the simulation.

Fields

• General

  • id::Int32: Unique identifier of the individual
  • sex::Int8: Sex (Female (1), Male(2), Diverse (3))
  • age::Int8: Age
  • education::Int8: Education class (i.e. highest degree)
  • occupation::Int8: Occupation class (i.e. manual labour, office job, etc...)

• Behaviour

  • social_factor::Float32: Parameter for the risk-willingness. Can be anywhere between -1 and 1 with neutral state is 0.
  • mandate_compliance::Float32. Paremeter which influences the probability of complying to mandates. Can be anywhere between -1 and 1 with neutral state is 0.

• Health Status

  • comorbidities::Vector{Bool}: Indicating prevalence of certain health conditions. True, if the individual is preconditioned with the comorbidity associated to the array index.
  • dead::Bool: Flag indicating individual's decease
  • hospital_status::Int8: State in the hopsital (0 = not hospitalized, 1 = hospitalized, 2 = ventilation, 3 = ICU)

• Associated Settings

  • household::Int32: Reference to household id
  • office::Int32: Reference to office id
  • schoolclass::Int32: Reference to schoolclass id
  • municipality::Int32: Reference to municipality id

• Pathogen

  • pathogen_id::Int8: pathogen identifier
  • infection_id::Int32: Current infection id
  • disease_state::Int8: Current State in natural disease history (0 = not infected, 1 = Presymptomatic, 2 = Symptomatic, 3 = Severe, 4 = Critical)
  • symptom_category::Int8: Endstate in current disease progression. The numbers should align with disease_state, but can be interpreted as the symptom category of this case (0 = None, 1 = Asymptomatic, 2 = Mild, 3 = Severe, 4 = Critical)
  • infectiousness::Int8: an individuals infectiousness (1-127), i.e. for superspreaders
  • number_of_infections::Int8: infection count

• Natural Disease History

  • exposed_tick::Int16: Tick of most recent infection
  • infectious_tick::Int16: Tick of most recent change into "infectious" state (considered asymptomatic)
  • onset_of_symptoms::Int16: Tick of the onset of symptoms
  • onset_of_severeness::Int16: Tick of onset of severe symptoms
  • hospitalized_tick::Int16: Tick of hospitalization
  • ventilation_tick::Int16: Tick of ventilation
  • icu_tick::Int16: Tick of ICU (Intensive Care Unit)
  • death_tick::Int16: Tick of Death
  • removed_tick::Int16: Tick of most recent removal event

• Testing

  • last_test::Int16: Tick of last test for pathogen
  • last_test_result::Bool: Flag for positivity of last test
  • last_reported_at::Int16: Tick at which this individual was last reported

• Vaccination

  • vaccine_id::Int8: Vaccine identifier
  • number_of_vaccinations::Int8: Individual's vaccination counter
  • vaccination_tick::Int16: Tick of most recent vaccination

• Interventions

  • quarantine_status::Int8: Status to indicate quarantine (none, household_quarantined, hospitalized, etc...)
  • quarantine_tick::Int16: Start tick of quarantine
  • quarantine_release_tick::Int16: End tick of quarantine

Individual(properties::Dict)

Create an individual with the provided properties. Properties must have at least keys id, sex, age.

Individual(properties::DataFrameRow)

Create an individual with the provided properties. Properties must have at least keys id, sex, age.

age(individual::Individual)

Return an individual's age.

class_id(individual::Individual)

Returns an individual's associated class's ID.

comorbidities(individual::Individual)

Returns an individual's comorbidities.

critical!(individual::Individual)

Marks the individual's condition as critical.

critical(individual::Individual)

Returns wether the individual's condition is critical.

dead(individual::Individual)

Returns an individual's death flag.

death_tick!(individual::Individual, tick::Int16)

Sets an individual's death tick.

death_tick(individual::Individual)

Returns an individual's death tick.

disease_state(individual::Individual)

Returns an individual's disease status (currently infected).

education(individual::Individual)

Return an individual's education class

end_quarantine!(individual::Individual)

Ends an individuals quarantine.

exposed(individual::Individual)

Returns wether the individual is exposed (infected, but not yet infectious).

exposed_tick!(individual::Individual, tick::Int16)

Sets an individual's exposed tick.

exposed_tick(individual::Individual)

Returns an individual's exposed tick (currently infected).

has_municipality(individual::Individual)

Returns true if individual is assigned to an instance of type Municipality.

home_quarantine!(individual::Individual)

Quarantines an individual in their household.

hospital_status(individual::Individual)

Returns the hospital_status of the individual.

hospitalize!(individual::Individual)

Hospitalizes the individual.

hospitalized(individual::Individual)

Returns wether the individual is hospitalized.

hospitalized_tick!(individual::Individual, tick::Int16)

Sets an individual's tick for when it gets hospitalized.

hospitalized_tick(individual::Individual)

Returns an individual's tick for when it gets hospitalized.

household_id(individual::Individual)

Returns an individual's associated household's ID.

icu!(individual::Individual)

Sets the individual to be in ICU.

icu(individual::Individual)

Returns wether the individual is in ICU.

icu_tick!(individual::Individual, tick::Int16)

Sets an individual's tick for when it will be delivered into icu.

icu_tick(individual::Individual)

Returns an individual's tick when it will be delivered into icu.

id(individual::Individual)

Return the unique identifier of the individual.

infected(individual::Individual)

Returns whether an individual is currently infected.

infection_id(individual::Individual)

Returns an individual's infection_id (currently infected).

infectious(individual::Individual)

Returns whether an individual is currently infectious.

infectious_tick!(individual::Individual, tick::Int16)

Sets an individual's infectious tick.

infectious_tick(individual::Individual)

Returns an individual's infectious tick (currently infected).

infectiousness!(individual::Individual, infectiousness)

Assigns a specified infectiousness (0-127) to an individual.

infectiousness(individual::Individual)

Returns an individual's infectiousness (currently infected).

is_student(individual::Individual)

Returns true if individual is assigned to an instance of type SchoolClass.

is_working(individual::Individual)

Returns true if individual is assigned to an instance of type Office.

isdetected(individual::Individual)

Returns true if an individual was currently infected and already reported.

isquarantined(individual::Individual)

Returns wether the individual is in quarantine or not.

isvaccinated(individual::Individual)

Returns wether the individual is vaccinated.

kill!(individual::Individual)

Kills the individual.

last_reported_at!(individual::Individual, report_tick::Int16)

Sets last tick this individual was last reported.

last_reported_at(individual::Individual)

Returns the last tick this individual was a reported case.

last_test!(individual::Individual, tick::Int16)

Sets last test date (tick).

last_test(individual::Individual)

Returns last test date (tick).

last_test_result!(individual::Individual, test_result::Bool)

Sets last test result.

last_test_result(individual::Individual)

Returns whether last test was positive. Defaults to false.

mandate_compliance!(individual::Individual, val::Float32)

Overwrites the individual's mandate_compliance attribute.

mandate_compliance(individual::Individual)

Return an individual's mandate_compliance value.

municipality(i::Individual, sim::Simulation)::Municipality

Returns the Municipality instance referenced in an individual.

municipality_id(individual::Individual)

Returns an individual's associated municipalities ID.

num_of_infected(individuals::Vector{Individual})

Takes a vector of individuals and returns the number of infected individuals.

number_of_infections(individual::Individual)

Returns an individual's number of infections (currently infected).

number_of_vaccinations(individual::Individual)

Returns the number of vaccinations.

occupation(individual::Individual)

Returns an individual's occupation class.

office(i::Individual, sim::Simulation)::Office

Returns the Office instance referenced in an individual.

office_id(individual::Individual)

Returns an individual's associated office's ID.

onset_of_severeness!(individual::Individual, tick::Int16)

Sets an individual's tick for the onset of severe symptoms, if it's a severe case.

onset_of_severeness(individual::Individual)

Returns an individual's tick for the onset of severe symptoms, if it's a severe case.

onset_of_symptoms!(individual::Individual, tick::Int16)

Sets an individual's tick for the onset of symptoms, if symptomatic.

onset_of_symptoms(individual::Individual)

Returns an individual's tick for the onset of symptoms, if symptomatic.

pathogen_id(individual::Individual)

Returns an individual's pathogen (currently infected).

presymptomatic!(individual::Individual)

Marks the individual as asymptomatic, but infectious.

presymptomatic(individual::Individual)

Returns if individual is asymptomatic.

progress_disease!(indiv::Individual, tick::Int16, lookup_dict::Dict = SYMPTOM_CATEGORY_DICT)

Progresses the disease of the (infected) individual. The dictionary lookup_dict can be provided, if custom disease compartements were implemented. The key-value-pairs should align with the meaning of the parameter disease_state or symptom_category. This means, that if disease_state==1 means "Asymptomatic", that status[1]=="Asymptomatic".

This function doesn't kill agents as this is handled a level higher for the simulation to log deaths.

quarantine_release_tick!(individual::Individual, tick::Int16)

Sets an individual's quarantine release tick.

quarantine_release_tick(individual::Individual)

Returns an individual's quarantine release tick.

quarantine_status(individual::Individual)

Returns an individuals quarantine status.

quarantine_tick!(individual::Individual, tick::Int16)

Sets an individual's quarantine tick.

quarantine_tick(individual::Individual)

Returns an individual's quarantine tick.

recover!(individual::Individual)

Recovers the individual from its infection.

removed_tick!(individual::Individual, tick::Int16)

Sets an individual's removed tick (currently infected).

removed_tick(individual::Individual)

Returns an individual's removed tick (currently infected).

reset!(individual::Individual)

Resets all non-static values like the disease progression timing. The individual will get back into a state where it was never infected, vaccinated, tested, etc.

setting_id!(individual::Individual, type::DataType, id::Int32)

Changes the assigned setting id of the individual for the given type of setting to id.

setting_id(individual::Individual, type::DataType)

Returns the id of the setting of type associated with the individual. If the settingtype is unknown or the agent isn't part of a setting of that type, -1 will be returned.

settings(individual::Individual, sim::Simulation)

Return a dictionary with the assigned setting types as keys and the assigned IDs as values.

severe!(individual::Individual)

Marks the individual's disease to be severe.

severe(individual::Individual)

Returns wether the individual's disease is severe.

sex(individual::Individual)

Return an individual's sex.

social_factor!(individual::Individual, val::Float32)

Overwrites the individual's social_factor attribute.

social_factor(individual::Individual)

Returns an individual's social_factor value.

symptom_category!(individual::Individual, category::Int8)

Sets an infected individuals symptom_category.

symptom_category(individual::Individual)

Returns an infected individual's symptom category.

symptomatic!(individual::Individual)

Marks the individual as symptomatic.

symptomatic(individual::Individual)

Returns wether the individual is symptomatic.

vaccination_tick(individual::Individual)

Returns the time of last vaccination.

vaccine_id(individual::Individual)

Returns the id of the vaccine the individual is vaccinated with.

ventilate!(individual::Individual)

Sets the individual to require ventilation.

ventilated(individual::Individual)

Returns wether the individual needs ventilation.

ventilation_tick!(individual::Individual, tick::Int16)

Sets an individual's tick for when it gets ventilated.

ventilation_tick(individual::Individual)

Returns an individual's tick when it gets ventilated.