Compartment: Compartment

In PoonLab/twt: treeswithintrees

Compartment

Description

Compartment is an R6 class for objects that represent the units of an outer tree simulation, such as a host individual or deme.

Methods

Public methods

• Compartment$new()

• Compartment$copy()

• Compartment$get.name()

• Compartment$get.type()

• Compartment$get.source()

• Compartment$get.branching.time()

• Compartment$get.sampling.time()

• Compartment$set.type()

• Compartment$set.source()

• Compartment$set.branching.time()

• Compartment$set.sampling.time()

• Compartment$set.unsampled()

• Compartment$is.unsampled()

• Compartment$get.lineages()

• Compartment$add.lineage()

• Compartment$remove.lineage()

• Compartment$clone()

---

Method new()

Usage

Compartment$new(
  name = NA,
  type = NA,
  source = NA,
  branching.time = NA,
  sampling.time = NA,
  unsampled = FALSE,
  lineages = list()
)

---

Method copy()

Usage

Compartment$copy(deep = FALSE)

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Method get.name()

Usage

Compartment$get.name()

---

Method get.type()

Usage

Compartment$get.type()

---

Method get.source()

Usage

Compartment$get.source()

---

Method get.branching.time()

Usage

Compartment$get.branching.time()

---

Method get.sampling.time()

Usage

Compartment$get.sampling.time()

---

Method set.type()

Usage

Compartment$set.type(new.type)

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Method set.source()

Usage

Compartment$set.source(new.source)

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Method set.branching.time()

Usage

Compartment$set.branching.time(new.branching.time)

---

Method set.sampling.time()

Usage

Compartment$set.sampling.time()

---

Method set.unsampled()

Usage

Compartment$set.unsampled(is.unsampled)

---

Method is.unsampled()

Usage

Compartment$is.unsampled()

---

Method get.lineages()

Usage

Compartment$get.lineages()

---

Method add.lineage()

Usage

Compartment$add.lineage(new.lineage)

---

Method remove.lineage()

Usage

Compartment$remove.lineage(ex.lineage)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Compartment$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

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

# display first Compartment object
host1 <- mod$get.compartments()[[1]]
host1

# manually initialize a new Compartment object
hostN <- Compartment$new(name='newHost', unsampled=TRUE)
hostN$set.type(host1$get.type())

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