Diseasy' variant handler

The DiseasyVariant module is responsible for defining scenarios for disease variants to the models

See vignette("diseasy-variant")

Value

A new instance of the DiseasyVariant R6 class.

Super class

diseasy::DiseasyBaseModule -> DiseasyVariant

Active bindings

variants

(list)
The variants currently in the module. Read-only.

cross_immunity

(matrix)
A matrix indicating the cross immunity interactions of the variants. Index ij indicates the overlap in immunity when variant j infects variant i. Thus, an overlap of 1 means immunisation with variant i protects against infection by variant j. Read-only.

Methods

Public methods

• DiseasyVariant$add_variant()

• DiseasyVariant$describe()

• DiseasyVariant$clone()

Inherited methods

• diseasy::DiseasyBaseModule$finalize()
• diseasy::DiseasyBaseModule$initialize()
• diseasy::DiseasyBaseModule$load_module()
• diseasy::DiseasyBaseModule$set_moduleowner()

---

Method add_variant()

Add a variant to the scenario.

Usage

DiseasyVariant$add_variant(name, characteristics = list())

Arguments

name

(character(1))
The name of the variant.

characteristics

(list)
A named list of characteristics of the variant. Characteristics can be: - relative_infection_risk (numeric(1)): The relative infection risk of the variant. - cross_immunity (named vector): The overlap in immunity of when the named variant attempts to infect a host previously infected by the current variant. If not specified, the default is 1. - introduction_date (Date(1)): The date the variant was introduced into the population.

---

Method describe()

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

Usage

DiseasyVariant$describe()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DiseasyVariant$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  # Create variant module
  var <- DiseasyVariant$new()

  # By default, a no variants are included
  var$variants
#> NULL

  # Add variants via the `$add_variant()` method

  var$add_variant(name = "WT")
  var$add_variant(name = "Mutant", characteristics = list("relative_infection_risk" = 1.2))
  var$variants
#> $WT
#> list()
#> 
#> $Mutant
#> $Mutant$relative_infection_risk
#> [1] 1.2
#> 
#> 

  rm(var)