EventLogger: EventLogger

In PoonLab/twt: treeswithintrees

EventLogger

Description

EventLogger is an R6 class for an object that tracks migration, transmission, and coalescent events. Note that bottleneck events are logged as coalescent events.

Methods

Public methods

• EventLogger$new()

• EventLogger$get.all.events()

• EventLogger$get.events()

• EventLogger$add.event()

• EventLogger$clear.events()

• EventLogger$blank.events()

• EventLogger$record.transmission()

• EventLogger$record.migration()

• EventLogger$get.fixed.samplings()

• EventLogger$store.fixed.samplings()

• EventLogger$clone()

---

Method new()

Usage

EventLogger$new(events = NA)

---

Method get.all.events()

Usage

EventLogger$get.all.events()

---

Method get.events()

Usage

EventLogger$get.events(event.type)

---

Method add.event()

Usage

EventLogger$add.event(
  type,
  time,
  line1 = NA,
  line2 = NA,
  comp1 = NA,
  comp2 = NA,
  type1 = NA,
  type2 = NA
)

Arguments

type:

event type, one of 'transmission', 'transition', 'migration', 'coalescence' or 'bottleneck'.

time:

CUMULATIVE time that event has occurred between two compartments in a transmission/migration/coalescent event Record which Lineages are transmitted from source to recipient (should only be one entry with Compartment as recipient)

---

Method clear.events()

Usage

EventLogger$clear.events()

---

Method blank.events()

Usage

EventLogger$blank.events()

---

Method record.transmission()

Usage

EventLogger$record.transmission(recipient, lineages)

Arguments

recipient:

Compartment object

lineages:

a vector of names of Lineages to transfer out of recipient Compartment Record which Lineages are transmitted from source to recipient through a migration event

---

Method record.migration()

Usage

EventLogger$record.migration(recipient, source, time, lineages)

Arguments

recipient:

Compartment object

source:

Compartment object

time:

double, time of migration event

lineages:

a list of Lineage objects

---

Method get.fixed.samplings()

Usage

EventLogger$get.fixed.samplings()

---

Method store.fixed.samplings()

Usage

EventLogger$store.fixed.samplings(model.fixed.samplings)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

EventLogger$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# manually initialize an EventLog object
e <- EventLogger$new()
# note this log entry is not linked to existing Lineage or Compartment objects
e$add.event("transmission", time=1, line1="NA", comp1="host1", comp2="host2")
e$get.all.events()

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