Configure activity (contact) scenarios

The DiseasyActivity module is responsible for handling the societal activity. By providing a contact_basis, activity_units and a scenario to the module, the module provides activity matrices throughout the scenario (with flexible age-groupings) as well as the overall "activity" level in society.

The contact_basis contains information about: - contact matrices (contact rates between age groups) - population (size and proportion of population in age groups)

The activity_units projects restrictions, guidelines and other changes in activity into smaller "units" that are independently "opened" or "closed". Opening (closing) a activity unit means the activity described in the unit is (in)active.

The scenario contains information on when different activity_units are opened and closed.

If no scenario is provided, the module will provide non-informative activity information: - Openness is always 1. - The contact matrices are uniform and, when summed, the largest eigenvalue is 1.

See vignette("diseasy-activity") for examples of use.

Value

A new instance of the DiseasyActivity R6 class.

Super class

DiseasyBaseModule -> DiseasyActivity

Active bindings

scenario_matrix: (matrix array)
A reduced view of the internal state of restrictions (showing only used activity units). Read-only.
risk_matrix: (matrix array)
A reduced view of the internal state of overall risk multipliers. Read-only.
contact_basis: (list(list()))
A nested list with all the needed information for the contact_basis
* counts contains the age stratified contact counts across the arenas of the basis (e.g. 'work', 'home', 'school', 'other')
* proportion contains a list of the proportion of population in each age-group
* demography contains a data.frame with the columns
* age (integer()) 1-year age group
* population (numeric()) size of population in age group
* proportion (numeric()) proportion of total population in age group
* description contains information about the source of the contact basis. Read only.

Methods

Public methods

DiseasyActivity$new()
DiseasyActivity$set_activity_units()
DiseasyActivity$set_contact_basis()
DiseasyActivity$change_activity()
DiseasyActivity$change_risk()
DiseasyActivity$crop_scenario()
DiseasyActivity$get_scenario_activities()
DiseasyActivity$get_scenario_openness()
DiseasyActivity$get_scenario_contacts()
DiseasyActivity$map_population()
DiseasyActivity$rescale_contacts_to_rates()
DiseasyActivity$reset_scenario()
DiseasyActivity$plot()
DiseasyActivity$describe()
DiseasyActivity$clone()

Inherited methods

`DiseasyActivity$new()`

Creates a new instance of the DiseasyActivity R6 class.

Usage

DiseasyActivity$new(
  base_scenario = "closed",
  activity_units = NULL,
  contact_basis = NULL,
  ...
)

Arguments

base_scenario: (character(1))
Baseline scenario. Must be either fully "open" or "closed" or "dk_reference"
activity_units: (list(list()))
A nested list of all possible 'units' of activity that can be opened or closed.
contact_basis: (list(list()))
A nested list with all the needed information for the contact_basis
* counts contains the age stratified contact counts across the arenas of the basis (e.g. 'work', 'home', 'school', 'other')
* proportion contains a list of the proportion of population in each age-group
* demography contains a data.frame with the columns
* age (integer()) 1-year age group
* population (numeric()) size of population in age group
* proportion (numeric()) proportion of total population in age group
* description contains information about the source of the contact basis.
...: Parameters sent to DiseasyBaseModule R6 constructor

`DiseasyActivity$set_activity_units()`

Sets the list of all possible "units" of activity that can be opened or closed

Usage

DiseasyActivity$set_activity_units(activity_units)

Arguments

activity_units: (list(list()))
A nested list of all possible 'units' of activity that can be opened or closed.

Details

Each element in the activity_units list should be a list with the following elements:

activity: a programmatic short hand for activity (character, snake_case),
label: a human readable label for activity (character),
home: numeric/vector with number(s) in [0, 1]
work: numeric/vector with number(s) in [0, 1]
school: numeric/vector with number(s) in [0, 1]
other: numeric/vector with number(s) in [0, 1]
risk: numeric greater than zero

If a single number is provider, the number is applied across all age-groups If a vector is provided, the vector must match the number of age groups in the contact_basis

Returns

NULL (called for side effects)

`DiseasyActivity$set_contact_basis()`

Sets the contact matrix basis the activity is computed from

Usage

DiseasyActivity$set_contact_basis(contact_basis)

Arguments

contact_basis: (list(list()))
A nested list with all the needed information for the contact_basis
* counts contains the age stratified contact counts across the arenas of the basis (e.g. 'work', 'home', 'school', 'other')
* proportion contains a list of the proportion of population in each age-group
* demography contains a data.frame with the columns
* age (integer()) 1-year age group
* population (numeric()) size of population in age group
* proportion (numeric()) proportion of total population in age group
* description contains information about the source of the contact basis.

Details

Loads the given contact_basis into the module

Returns

NULL (called for side effects)

`DiseasyActivity$change_activity()`

Adds the specified openings and closings to the scenario

Usage

DiseasyActivity$change_activity(date, opening = NA, closing = NA)

Arguments

date: (Date() | data.frame)
Either a vector of dates when activity changes or a data.frame with columns 'date', 'opening' and 'closing'
opening: (character())
Names of activities to open on given date. Omitted if data.frame is given to date argument
closing: (character())
Names of activities to close on given date. Omitted if data.frame is given to date argument

Returns

NULL (called for side effects)

`DiseasyActivity$change_risk()`

Sets the overall risk of types of activity

Usage

DiseasyActivity$change_risk(date, type = NULL, risk = NULL)

Arguments

date: (Date())
Dates where risk changes. The first argument can also be a data.frame with columns "date", "type" and "risk"
type: (character(1))
Name of activity type to change. Must be in "work", "school", "home" and "other"
risk: (numeric(1))
Relative risk for the given type from the given date

Returns

NULL (called for side effects)

`DiseasyActivity$crop_scenario()`

Helper function to crop the scenario matrix in time

Usage

DiseasyActivity$crop_scenario(first_date = NULL, last_date = NULL)

Arguments

first_date: (Date(1))
New first date in scenario. The column for the lasted prior date will be new first column
last_date: (Date(1))
All columns after this date are deleted

Returns

NULL (called for side effects)

`DiseasyActivity$get_scenario_activities()`

Return list containing the active activity units on dates where there are changes.

Usage

DiseasyActivity$get_scenario_activities()

Returns

(list)
The activity units active in the scenario.

`DiseasyActivity$get_scenario_openness()`

Return openness [0 ; 1] for all age groups and activities on all dates.

Usage

DiseasyActivity$get_scenario_openness(age_cuts_lower = NULL, weights = NULL)

Arguments

age_cuts_lower: (numeric)
vector of ages defining the lower bound for each age group. If NULL, age groups of contact_basis is used.
weights: (numeric(4))
vector of weights for the four types of contacts. If NULL, no weighting is done. The weights are normalized before applying.

Returns

(list())
Returns a list with depth of two: value[date][type]

`DiseasyActivity$get_scenario_contacts()`

Return contacts across age groups and activities on all dates.

Usage

DiseasyActivity$get_scenario_contacts(age_cuts_lower = NULL, weights = NULL)

Arguments

age_cuts_lower: (numeric)
vector of ages defining the lower bound for each age group. If NULL, age groups of contact_basis is used.
weights: (numeric(4))
vector of weights for the four types of contacts. If NULL, no weighting is done.

Returns

If no weights are supplied, a list() of depth of two: value[date][type] is returned. Map population between age groups

`DiseasyActivity$map_population()`

The function computes the proportion of population in the new and old age groups.

Usage

DiseasyActivity$map_population(age_cuts_lower)

Arguments

age_cuts_lower: (numeric)
vector of ages defining the lower bound for each age group. If NULL, age groups of contact_basis is used.

Returns

A data.frame which maps the age groups from their reference in contact_basis to those supplied to the function. Rescale contact matrices to population contact rates

`DiseasyActivity$rescale_contacts_to_rates()`

Re-scale from contacts to rates per individual to fractional population. @details If the contact matrix is $\beta_{i,j}$ and the population is $N_j$, then this function returns the rescaled elements $\left(sum_j N_j\right) \beta_{i,j} / N_j$.

Usage

DiseasyActivity$rescale_contacts_to_rates(input, population)

Arguments

input: (matrix array or list(matrix array))
Contacts to be re-scaled.
population: (numeric)
Population vector to weight contacts by. Must use same age_groups as the contact matrix input.

Returns

Returns an object with the same structure as the input

`DiseasyActivity$reset_scenario()`

Resets the scenario in the module. NOTE: Called automatically when setting/changing activity units.

Usage

DiseasyActivity$reset_scenario()

Returns

NULL (called for side effects)

`DiseasyActivity$plot()`

Plot the first set of contact matrices of the scenario as well as the "openness" over time.

Usage

DiseasyActivity$plot(
  age_cuts_lower = NULL,
  weights = rep(1, 4),
  contacts_date = NULL
)

Arguments

age_cuts_lower: (numeric)
vector of ages defining the lower bound for each age group. If NULL, age groups of contact_basis is used.
weights: (numeric(4))
vector of weights for the four types of contacts. If NULL, no weighting is done.
contacts_date: (Date(1))
The date to plot contact matrix for (default is earliest contact matrix).

Returns

NULL (called for side effects)

`DiseasyActivity$describe()`

Prints a human readable report of the internal state of the module.

Usage

DiseasyActivity$describe()

`DiseasyActivity$clone()`

The objects of this class are cloneable with this method.

Usage

DiseasyActivity$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples

  # Activity module with Danish reference scenario
  act <- DiseasyActivity$new(base_scenario = "dk_reference",
                             activity_units = dk_activity_units,
                             contact_basis = contact_basis %.% DK)

  # Get contact matrices
  contact_matrices <- act$get_scenario_activities()


  # Configuring a custom scenario in another country (using Danish activity units)
  scenario <- data.frame(date = as.Date(character(0)),
                         opening = character(0),
                         closing = character(0)) |>
    dplyr::add_row(date = as.Date("2020-01-01"), opening = "baseline",      closing = NA) |>
    dplyr::add_row(date = as.Date("2020-03-12"), opening = NA,              closing = "baseline") |>
    dplyr::add_row(date = as.Date("2020-03-12"), opening = "lockdown_2020", closing = NA)

  act$set_contact_basis(contact_basis %.% GB) # Use the "Great Britain" contact_basis
  act$set_activity_units(dk_activity_units)
  act$change_activity(scenario)

  # Get societal "openness"
  openness <- act$get_scenario_openness()

  rm(act)

Value

See also

Super class

Active bindings

Methods

Public methods

DiseasyActivity$new()

Usage

Arguments

DiseasyActivity$set_activity_units()

Usage

Arguments

Details

Returns

DiseasyActivity$set_contact_basis()

Usage

Arguments

Details

Returns

DiseasyActivity$change_activity()

Usage

Arguments

Returns

DiseasyActivity$change_risk()

Usage

Arguments

Returns

DiseasyActivity$crop_scenario()

Usage

Arguments

Returns

DiseasyActivity$get_scenario_activities()

Usage

Returns

DiseasyActivity$get_scenario_openness()

Usage

Arguments

Returns

DiseasyActivity$get_scenario_contacts()

Usage

Arguments

Returns

DiseasyActivity$map_population()

Usage

Arguments

Returns

DiseasyActivity$rescale_contacts_to_rates()

Usage

Arguments

Returns

DiseasyActivity$reset_scenario()

Usage

Returns

DiseasyActivity$plot()

Usage

Arguments

Returns

DiseasyActivity$describe()

Usage

DiseasyActivity$clone()

Usage

Arguments

Examples

`DiseasyActivity$new()`

`DiseasyActivity$set_activity_units()`

`DiseasyActivity$set_contact_basis()`

`DiseasyActivity$change_activity()`

`DiseasyActivity$change_risk()`

`DiseasyActivity$crop_scenario()`

`DiseasyActivity$get_scenario_activities()`

`DiseasyActivity$get_scenario_openness()`

`DiseasyActivity$get_scenario_contacts()`

`DiseasyActivity$map_population()`

`DiseasyActivity$rescale_contacts_to_rates()`

`DiseasyActivity$reset_scenario()`

`DiseasyActivity$plot()`

`DiseasyActivity$describe()`

`DiseasyActivity$clone()`