CompartmentType: CompartmentType

In PoonLab/twt: treeswithintrees

CompartmentType

Description

CompartmentType is an R6 class that defines a type of compartment, such as a class of host individual (risk group) with a specific transmission rate.

Methods

Public methods

• CompartmentType$new()

• CompartmentType$get.bottleneck.size()

• CompartmentType$get.bottleneck.theta()

• CompartmentType$get.name()

• CompartmentType$get.unsampled()

• CompartmentType$get.branching.rates()

• CompartmentType$get.branching.rate()

• CompartmentType$get.migration.rates()

• CompartmentType$get.migration.rate()

• CompartmentType$get.transition.rates()

• CompartmentType$get.transition.rate()

• CompartmentType$get.effective.size()

• CompartmentType$get.popn.growth.dynamics()

• CompartmentType$get.generation.time()

• CompartmentType$get.transmission.times()

• CompartmentType$set.transmission.times()

• CompartmentType$set.migration.rate()

• CompartmentType$clone()

---

Method new()

Usage

CompartmentType$new(
  name = NA,
  unsampled = NA,
  branching.rates = NA,
  transition.rates = NA,
  migration.rates = NA,
  bottleneck.size = NA,
  bottleneck.theta = NA,
  effective.size = NA,
  popn.growth.dynamics = NA,
  generation.time = NA,
  transmission.times = NA
)

---

Method get.bottleneck.size()

Usage

CompartmentType$get.bottleneck.size()

---

Method get.bottleneck.theta()

Usage

CompartmentType$get.bottleneck.theta()

---

Method get.name()

Usage

CompartmentType$get.name()

---

Method get.unsampled()

Usage

CompartmentType$get.unsampled()

---

Method get.branching.rates()

Usage

CompartmentType$get.branching.rates()

---

Method get.branching.rate()

Usage

CompartmentType$get.branching.rate(current.time, name.type)

---

Method get.migration.rates()

Usage

CompartmentType$get.migration.rates()

---

Method get.migration.rate()

Usage

CompartmentType$get.migration.rate(name.type)

---

Method get.transition.rates()

Usage

CompartmentType$get.transition.rates()

---

Method get.transition.rate()

Usage

CompartmentType$get.transition.rate(name.type)

---

Method get.effective.size()

Usage

CompartmentType$get.effective.size()

---

Method get.popn.growth.dynamics()

Usage

CompartmentType$get.popn.growth.dynamics()

---

Method get.generation.time()

Usage

CompartmentType$get.generation.time()

---

Method get.transmission.times()

Usage

CompartmentType$get.transmission.times()

---

Method set.transmission.times()

Usage

CompartmentType$set.transmission.times(vector.transm.times)

---

Method set.migration.rate()

Usage

CompartmentType$set.migration.rate(recipient.type, new.migr.rate)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

CompartmentType$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# load CompartmentTypes from a YAML object
path <- system.file('extdata', 'SI.yaml', package='twt')
settings <- yaml.load_file(path)
mod <- Model$new(settings)
mod$get.types()

# manually specify a CompartmentType object (usually done by YAML)
host <- CompartmentType$new(name='host', branching.rates=c(host=0.1), 
bottleneck.size=1, coalescent.rate=1)

PoonLab/twt documentation built on Nov. 7, 2024, 4:18 a.m.