Settings

Supertype for all simulation settings which act as containers of settings.

Department <: ContainerSetting

Represents a department within a workplace in the simulation.

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

d1 = Department(id = 1)
d2 = Department(id = 2, contains = [13, 14, 15]) # contains IDs of Offices

Parameters

• id::Int32: Unique identifier of the department.
• contains::Vector{Int32} = [] (optional): List of associated Offices
• contained::Int32 = DEFAULT_SETTING_ID (optional): Parent setting id (Workplace)
• type::Int32 = -1 (optional): Numerical code representing the type of department.
• last_infectious::Int16 = -1 (optional): The last simulation tick when an infectious individual was present.
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn.
• isactive::Bool = false (optional): Whether the department is active in the simulation.
• isopen::Bool = true (optional): Whether the setting is open for contacts.

GlobalSetting <: IndividualSetting

A type to a setting that contains all individuals at once (mainly for testing purposes). With this type, each individual can theoretically connect with any other individual.

There should only be one GlobalSetting instance in any simulation.

Fields

• individuals::Vector{Individual}: List of associated individuals
• contact_sampling_method::ContactSamplingMethod: Sampling Method, defining how contacts are drawn.
• isactive::Bool: A flag to represent if the setting is considered active for simulation
• isopen::Bool: Whether the setting is open for contacts. conditions

Household <: Geolocated

A type to represent households with associated individuals as members.

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

h1 = Household(id = 1)
h2 = Household(id = 2, individuals = [i1, i2, i3])

Parameters

• id::Int32: Unique identifier of the household
• individuals::Vector{Individual} = [] (optional): List of associated individuals
• income::Int8 = -1 (optional): Category of income for the household
• dwelling::Int8 = -1 *(optional)*: Category of dwelliung size
• last_infectious::Int16 = -1 (optional): Tick indicating the last presence of an infected individual
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn.
• ags::AGS = AGS() (optional): The Amtlicher Gemeindeschlüssel (AGS) of the Household.
• lon::Float32 = NaN (optional): Longitude of the household
• lat::Float32 = NaN: Latitude of the household
• isactive::Bool = false (optional): A flag to represent if the setting is considered active for simulation
• isopen::Bool = true (optional): Whether the setting is open for contacts.

Supertype for all simulation settings which directly contain individuals.

Municipality <: IndividualSetting

A type to represent (geographical) municipalities.

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

m1 = Municipality(id = 1)
m2 = Municipality(id = 2, individuals = [i1, i2, i3])

Parameters

• id::Int32: Unique identifier of the municipality
• individuals::Vector{Individual} = [] (optional): List of associated individuals
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn.
• ags::AGS = AGS() (optional): The Amtlicher Gemeindeschlüssel (AGS) of the municipality.
• isactive::Bool = false (optional): A flag to represent if the setting is considered active for simulation
• isopen::Bool = true (optional): Whether the setting is open for contacts.

Office <: Geolocated

Represents an office within a department in the simulation.

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

o1 = Office(id = 1)
o2 = Office(id = 2, individuals = [i1, i2, i3])

Parameters

• id::Int32: Unique identifier of the office.
• individuals::Vector{Individual} = [] (optional): List of individuals associated with this office
• contained::Int32 = DEFAULT_SETTING_ID (optional): Parent setting id (Department)
• contained_type::DataType = Department (optional): Parent setting tye (Department)
• type::Int32 = -1 (optional): Numerical code representing the type of office
• last_infectious::Int16 = -1 (optional): The last simulation tick when an infectious individual was present
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn
• ags::AGS = AGS() (optional): The Amtlicher Gemeindeschlüssel (AGS) of the office
• inroom::Int8 = -1 (optional): Describes the amount of indoor work done in the office
• workhome::Int8 = -1 (optional): Describes the amount of work done from home
• lon::Float32 = NaN (optional): Longitude of the office
• lat::Float32 = NaN (optional): Latitude of the office
• isactive::Bool = false (optional): Whether the office is active in the simulation
• isopen::Bool = true (optional): Whether the setting is open for contacts

School <: ContainerSetting

A type to represent a school (which has years and classes).

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

s1 = School(id = 1)
s2 = School(id = 2, contains = [13, 14, 15]) # contains IDs of school years

Parameters

• id::Int32: Unique identifier of the school
• contains::Vector{Int32} = [] (optional): List of associated SchoolYearss
• contained::Int32 = DEFAULT_SETTING_ID (optional): Parent setting id (SchoolComplex)
• type::Int32 = -1 (optional): Type of school (e.g. primary, highschool, ...)
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn.
• isactive::Bool = false (optional): A flag to represent if the setting is considered active for simulation
• isopen::Bool = true (optional): Whether the setting is open for contacts.

SchoolClass <: Geolocated

A type to represent school classes. Should always be part of a school.

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

c1 = SchoolClass(id = 1)
c2 = SchoolClass(id = 2, individuals = [i1, i2, i3])

Parameters

• id::Int32: Unique identifier of the school class
• individuals::Vector{Individual} = [] (optional): List of associated individuals
• type::Int32 = -1 (optional): Type of school class (e.g. grade)
• contained::Int32 = DEFAULT_SETTING_ID (optional): Parent setting id (SchoolYear)
• last_infectious::Int16 = -1 (optional): Tick indicating the last presence of an infected individual
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn.
• ags::Int32 = AGS() (optional): The Amtlicher Gemeindeschlüssel (AGS) of the schoolclass.
• lon::Float32 = NaN (optional): Longitude of the schoolclass
• lat::Float32 = NaN (optional): Latitude of the schoolclass
• isactive::Bool = false (optional): A flag to represent if the setting is considered active for simulation
• isopen::Bool = true (optional): Whether the setting is open for contacts.

SchoolComplex <: ContainerSetting

A type to represent a school complex (which has schools).

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

sc1 = SchoolComplex(id = 1)
sc2 = SchoolComplex(id = 2, contains = [13, 14, 15]) # contains IDs of schools

Parameters

• id::Int32: Unique identifier of the school complex
• contains::Vector{Int32} = [] (optional): List of associated Schools
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn.
• isactive::Bool = false (optional): A flag to represent if the setting is considered active for simulation
• isopen::Bool = true (optional): Whether the setting is open for contacts.

SchoolYear <: ContainerSetting

A type to represent a schoolyear (which has classes).

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

y1 = SchoolYear(id = 1)
y2 = SchoolYear(id = 2, contains = [13, 14, 15]) # contains IDs of school classes

Parameters

• id::Int32: Unique identifier of the schoolyear
• contains::Vector{Int32} = [] (optional): List of associated SchoolClasses
• contained::Int32 = DEFAULT_SETTING_ID (optional): Parent setting id (School)
• type::Int32 = -1 (optional): Type of school year (e.g. grade)
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn.
• isactive::Bool = false (optional): A flag to represent if the setting is considered active for simulation
• isopen::Bool = true (optional): Whether the setting is open for contacts.

Supertype for all simulation settings

SettingsContainer

A container structure for all settings.

Fields

• settings::Dict{DataType, Vector}: A dictionary holding all known settings structured by type. Each value is a concretely-typed Vector{T} where T is the corresponding setting type; the dict value type is widened to Vector to allow this.

Workplace <: ContainerSetting

Represents a workplace in the simulation.

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

ws1 = Workplace(id = 1)
ws2 = Workplace(id = 2, contains = [13, 14, 15]) # contains IDs of Departments

Parameters

• id::Int32: Unique identifier of the workplace.
• contains::Vector{Int32} = [] (optional): List of associated Departments
• contained::Int32 = DEFAULT_SETTING_ID (optional): Parent setting id (WorkplaceSite)
• type::Int32 = -1 (optional): Numerical code representing the type of workplace (e.g., farm, office).
• last_infectious::Int16 -1 (optional): The last simulation tick when an infectious individual was present.
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn.
• isactive::Bool = false (optional): Whether the workplace is active in the simulation.
• isopen::Bool = true (optional): Whether the setting is open for contacts.

WorkplaceSite <: ContainerSetting

Represents a Workplace site in the simulation.

Instantiation

The instantiation requires at least an id that be supplied as a keyword argument. All other fields are optional parameters.

ws1 = WorkplaceSite(id = 1)
ws2 = WorkplaceSite(id = 2, contains = [13, 14, 15]) # contains IDs of Workplaces

Parameters

• id::Int32: Unique identifier of the workplace.
• contains::Vector{Int32} = [] (optional): List of associated Workplaces
• type::Int32 = -1 (optional): Numerical code representing the type of workplace site.
• last_infectious::Int16 = -1 (optional): The last simulation tick when an infectious individual was present.
• contact_sampling_method::ContactSamplingMethod = ContactparameterSampling(0) (optional): Sampling Method, defining how contacts are drawn.
• isactive::Bool = false (optional): Whether the workplace is active in the simulation.
• isopen::Bool = true (optional): Whether the setting is open for contacts.

activate!(setting::Setting)

Sets the setting active for simulation.

activate!(setting::Setting, sim::Simulation)

Activates setting and recursively activates the the containing setting.

add!(container::SettingsContainer, setting::Setting)

Add a setting to the container.

add_member!(setting::IndividualSetting, individual::Individual)

Adds the given individual to the setting and records the membership on the individual. setting_id! is a no-op for setting types without an id field on Individual (GlobalSetting).

Must not be called while the threaded transmission phase is running.

remove_member!(setting::IndividualSetting, individual::Individual)

Removes the given individual from the setting and clears the membership on the individual. Does nothing if it is not a member.

The member is swapped with the last element, so member order is not preserved.

Must not be called while the threaded transmission phase is running.

add_type!(container::SettingsContainer, settingtype::DataType)

Add a settingtype to the container if it is not yet included. Creates a new concretely-typed vector for the provided type in the settings dictionary.

add_types!(container::SettingsContainer, settingtypes::Vector{DataType})

Adds settingtypes to the container if they are not yet included. Calls the add_type! function for each settingtype in the vector.

ags(stng::Setting)

Get the statically computed ags of any Setting.

avg_individuals(stngs::Vector{<:Setting}, simulation::Simulation)

Returns the average number of individuals across all provided settings.

close!(setting::Setting)

Closes the setting.

close!(setting::Setting, simulation::Simulation)

Sets the setting and all settings contained by it as closed (not open).

contact_sampling_method(setting::Setting, csm::ContactSamplingMethod)

Sets the ContactSamplingMethod of this setting to the provided method.

contact_sampling_method(setting::Setting)

Returns ContactSamplingMethod of this setting.

deactivate!(setting::Setting)

Sets the setting as inactive for simulation.

geolocation(stng::ContainerSetting, sim::Simulation)

Get the location of a ContainerSetting by getting the location of the first contained setting.

geolocation(stng::IndividualSetting, sim::Simulation)

Get the location of a IndividualSetting. Fallback for non geolocated settings.

geolocation(stng::IndividualSetting)

Get the location of a IndividualSetting. Fallback for non geolocated settings.

geolocation(stng::IndividualSetting, sim::Simulation)

Get the location of a IndividualSetting.

geolocation(stng::IndividualSetting)

Get the location of a IndividualSetting.

household(i::Individual, sim::Simulation)::Household

Returns the Household instance referenced in an individual.

id(setting::Setting)

Returns the unique identifier of the setting.

individuals!(setting::IndividualSetting, indivs::Vector{Individual}, simulation::Simulation)

Appends the individuals associated with a given IndividualSetting to the provided indivs vector.

Parameters

• setting::IndividualSetting: Setting to get the individuals from
• indivs::Vector{Individual}: List that will be appeneded with the setting's individuals
• simulation::Simulation: Simulation object

individuals!(setting::ContainerSetting, indivs::Vector{Individual}, simulation::Simulation)

Appends the individuals associated with a given ContainerSetting to the provided indivs vector by recursively calling the individuals! function.

Parameters

• setting::ContainerSetting: Setting to get the individuals from
• indivs::Vector{Individual}: List that will be appeneded with the setting's individuals
• simulation::Simulation: Simulation object

individuals(setting::IndividualSetting)

Returns the individuals associated with the given setting.

individuals(setting::IndividualSetting, simulation::Simulation)

Returns the individuals associated with a given IndividualSetting.

individuals(setting::ContainerSetting, indivs::Vector{Individual}, simulation::Simulation)

Returns the individuals associated with a given ContainerSetting by recursively getting the individuals of all contained settings using the individuals! function.

isopen(setting::Setting)

Returns wether the setting is opened (contacts can occur) or not. Without considering its containers.

isactive(setting::Setting)

Returns whether the setting is considered active for simulation, e.g. an infection could spread in the setting.

lat(stng::Geolocated)

Returns latitude of geolocated setting.

lon(stng::Geolocated)

Returns longitude of geolocated setting.

max_individuals(stngs::Vector{<:Setting}, simulation::Simulation)

Returns the maximum number of individuals across all provided settings.

min_individuals(stngs::Vector{<:Setting}, simulation::Simulation)

Returns the minimum number of individuals across all provided settings.

min_max_avg_individuals(stngs::Vector{<:Setting}, simulation::Simulation)

Returns a three-way tuple with (minimum, maximum, mean) number of individuals associated with a setting in the provided stngs vector.

open!(setting::Setting)

Opens the setting.

open!(setting::Setting, simulation::Simulation)

Sets the setting and all settings contained by it as open.

schoolclass(i::Individual, sim::Simulation)::SchoolClass

Returns the SchoolClass instance referenced in an individual.

sample_individuals(individuals::Vector{Individual}, n::Int64; rng::Xoshiro = default_gems_rng())

Returns a subsample of a vector of Individuals of sample size n.

sample_individuals(setting::IndividualSetting, n::Int64; rng::Xoshiro = default_gems_rng())

Returns a subsample of the setting's Individuals of sample size n.

setting(container::SettingsContainer, type::DataType, id::Int32)

Returns a particular setting of a particular type and ID.

settingchar(setting::Setting)

Returns a character that represents the type of setting.

settings(container::SettingsContainer)

Returns a dictionary with all concrete setting types as keys and vectors of all known settings as values.

settingstring(c::Char)

Returns a string that represents the type of setting based on a char that is returned from the function settingchar.

settingtypes(container::SettingsContainer)

Returns all known setting types of the provided container.