Run: Run

In PoonLab/twt: treeswithintrees

Run

Description

Run is an R6 class that is derived from Model. It inherits all simulation model features including CompartmentTypes, Compartments, and Lineages. Unlike Model, a Run object is used to track an outcome of the simulation model and is therefore mutable where Model is immutable. For example, Run tracks which lineages are extant and the numbers of pairs of Lineages that can coalesce over time. In addition, the number of unsampled compartments is stochastic outcome of the model that is tracked at this level.

Public fields

lineages:

list of Lineage objects

extant.lineages:

list of Lineage objects filtered by sampling time

locations:

a named list of Lineage objects keyed by Compartment

counts:

a data frame of population dynamics

Active bindings

lineages:

list of Lineage objects

extant.lineages:

list of Lineage objects filtered by sampling time

locations:

a named list of Lineage objects keyed by Compartment

counts:

a data frame of population dynamics

Methods

Public methods

• Run$new()

• Run$get.eventlog()

• Run$set.eventlog()

• Run$get.counts()

• Run$set.counts()

• Run$get.initial.conds()

• Run$get.fixed.samplings()

• Run$get.types()

• Run$get.compartments()

• Run$get.lineages()

• Run$get.unsampled.hosts()

• Run$get.num.extant()

• Run$get.sampling.times()

• Run$get.extant.lineages()

• Run$add.lineage()

• Run$remove.lineage()

• Run$move.lineage()

• Run$get.locations()

• Run$get.node.ident()

• Run$generate.unsampled()

• Run$clear.unsampled()

• Run$clone()

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Method new()

Usage

Run$new(model)

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Method get.eventlog()

Usage

Run$get.eventlog()

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Method set.eventlog()

Usage

Run$set.eventlog(e)

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Method get.counts()

Usage

Run$get.counts()

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Method set.counts()

Usage

Run$set.counts(df)

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Method get.initial.conds()

Usage

Run$get.initial.conds()

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Method get.fixed.samplings()

Usage

Run$get.fixed.samplings()

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Method get.types()

Usage

Run$get.types()

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Method get.compartments()

Usage

Run$get.compartments()

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Method get.lineages()

Usage

Run$get.lineages()

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Method get.unsampled.hosts()

Usage

Run$get.unsampled.hosts()

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Method get.num.extant()

Usage

Run$get.num.extant(time, location = NA)

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Method get.sampling.times()

Usage

Run$get.sampling.times()

Arguments

time:

reference time point

location:

(optional) name of Compartment object

Returns

integer, number of extant lineages

Retrieves a list of Lineage objects that are extant at the specified time. Note that because Lineages are being added and removed through coalescent and bottleneck events, the output will change over the course of inner tree simulation.

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Method get.extant.lineages()

Usage

Run$get.extant.lineages(time, comp = NA)

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Method add.lineage()

Usage

Run$add.lineage(lineage)

Arguments

time:

coalescent (cumulative time) of the simulation

comp:

R6 object of class Compartment

Returns

a named list of Lineage objects.

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Method remove.lineage()

Usage

Run$remove.lineage(lineage)

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Method move.lineage()

Usage

Run$move.lineage(lineage, comp)

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Method get.locations()

Usage

Run$get.locations()

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Method get.node.ident()

Usage

Run$get.node.ident(prefix = "Node")

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Method generate.unsampled()

Usage

Run$generate.unsampled(type.name)

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Method clear.unsampled()

Usage

Run$clear.unsampled()

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Method clone()

The objects of this class are cloneable with this method.

Usage

Run$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Note

https://github.com/r-lib/roxygen2/issues/415 count the number of Lineages that are extant (has been sampled) more recently than the user-specified time

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