Configure the model population

The DiseasyPopulation module is responsible for handling the population included in the model.

See vignette("diseasy-population").

Value

A new instance of the DiseasyPopulation R6 class.

See also

DiseasyActivity

Super class

DiseasyBaseModule -> DiseasyPopulation

Active bindings

groups

(named character())
The names of the demographic groups that have been configured in the module.

population

(tibble)
The population groups and their sizes configured in the module.

population_proportion

(numeric())
The distribution of individuals across the demography groups defined in the module.

age_cuts_lower

(integer())
vector of ages defining the lower bound for each age group. If NULL, age groups of contact_basis is used. Read only.

activity

(diseasy::DiseasyActivity)
The local copy of an DiseasyActivity module. Read-only.

Methods

Public methods

• DiseasyPopulation$new()

• DiseasyPopulation$stratify_age()

• DiseasyPopulation$per_capita_contact_matrices()

• DiseasyPopulation$describe()

• DiseasyPopulation$clone()

Inherited methods

• DiseasyBaseModule$load_module()
• DiseasyBaseModule$set_moduleowner()

---

DiseasyPopulation$new()

Creates a new instance of the DiseasyPopulation R6 class.

Usage

DiseasyPopulation$new(age_cuts_lower = 0L, ...)

Arguments

age_cuts_lower

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

...

Parameters sent to DiseasyBaseModule R6 constructor

---

DiseasyPopulation$stratify_age()

Sets the age stratification of the model population.

Usage

DiseasyPopulation$stratify_age(age_cuts_lower)

Arguments

age_cuts_lower

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

Returns

NULL (called for side effects)

---

DiseasyPopulation$per_capita_contact_matrices()

Compute the per-capita contact matrices. See vignette("diseasy-activity") for details.

Usage

DiseasyPopulation$per_capita_contact_matrices(weights = rep(1, 4))

Arguments

weights

(numeric(4))
vector of weights for the four types of contacts. If NULL, no weighting is done.

Returns

list(matrix)
A list (with names indicating the dates of changes in contacts) of contact rates (matrix).

---

DiseasyPopulation$describe()

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

Usage

DiseasyPopulation$describe()

---

DiseasyPopulation$clone()

The objects of this class are cloneable with this method.

Usage

DiseasyPopulation$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  # Create population module
  population <- DiseasyPopulation$new()

  # By default a single, non-stratified population is used in the models.
  population
#> # DiseasyPopulation ##########################################
#> No age stratification has been configured

  # Stratification can be added via methods

  # Stratifying by age
  population$stratify_age(age_cuts_lower = c(0, 60)) # 2 age groups
  # NB: Age cuts must be available in demography and disease data.

  population
#> # DiseasyPopulation ##########################################
#> Stratified by age: 00-59, 60+

  rm(population)