Rtreemix (version 1.34.0)

RtreemixSim-class: Class "RtreemixSim"

Description

This class contains data simulated from the RtreemixModel it extends together with their sampling and waiting times. It also includes the sampling mode and the sampling parameter used for the time simulation.

Objects from the Class

Objects can be created by calls of the form new("RtreemixSim", Model, SimPatterns, SamplingMode, SamplingParam, WaitingTimes, SamplingTimes). The RtreemixSim class specifies patterns (RtreemixData) simulated from the parent RtreemixModel together with their waiting and sampling times resulting from the waiting time simulation along the branchings in the parent model. The Model is an RtreemixModel object used in the data and time simulation process. In other words, this model is used for simulating patterns with their sampling and waiting times. The SimPatterns is an RtreemixData object that contains the patterns simulated from the given Model. The SamplingMode is a character that specifies the sampling mode ("constant" or "exponential") used in the time simulations. The SamplingParam is a numeric that specifies the sampling parameter corresponding to the sampling mode given by SamplingMode. The WaitingTimes is a numeric vector that specifies the waiting times for the simulated patterns. Its length equals the number of patterns in SimPatterns. The SamplingTimes is a numeric vector that specifies the sampling times for the simulated patterns. Its length equals the number of patterns in SimPatterns.

Slots

SimPatterns:

Object of class "RtreemixData".

SamplingMode:

Object of class "character". It can have one of the two possible values: "constant" or "exponential".

SamplingParam:

Object of class "numeric".

WaitingTimes:

Object of class "numeric". The length of WaitingTimes must be equal to the number of patterns in SimPatterns.

SamplingTimes:

Object of class "numeric". The length of SamplingTimes must be equal to the number of patterns in SimPatterns.

Extends

Class "RtreemixModel", directly. Class "RtreemixData", by class "RtreemixModel", distance 2.

Methods

SamplingMode

signature(object = "RtreemixSim"): A method for obtaining the sampling mode ("constant" or "exponential") used for the time simulations.

SamplingParam

signature(object = "RtreemixSim"): A method for obtaining the sampling parameter corresponding to the specified SamplingMode.

SamplingTimes

signature(object = "RtreemixSim"): A method used for obtaining the sampling times of the patterns in SimPatterns.

SimPatterns

signature(object = "RtreemixSim"): A method used for obtaining the patterns simulated from the parent model.

WaitingTimes

signature(object = "RtreemixSim"): A method used for obtaining the waiting times of the patterns in SimPatterns.

getModel

signature(object = "RtreemixSim"): A method for obtaining the mixture model used in the simulations.

noDraws

signature(object = "RtreemixSim"): A method for obtaining the number of simulated patterns, i.e. the size of SimPatterns.

References

Learning multiple evolutionary pathways from cross-sectional data, N. Beerenwinkel et al.

See Also

RtreemixGPS-class, RtreemixData-class, RtreemixModel-class, fit-methods, sim-methods

Examples

## Generate a random RtreemixModel object with 3 components and 9 genetic events.
rand.mod <- generate(K = 3, no.events = 9, noise.tree = TRUE, prob = c(0.2, 0.8))
show(rand.mod)

## Create an RtreemixSim object by simulating patterns with their sampling and waiting times from a given mixture model.
sim.data <- sim(model = rand.mod, sampling.mode = "exponential", sampling.param = 1, no.sim = 200)
show(sim.data)

## See the slots from the RtreemixSim object.
SimPatterns(sim.data)
SamplingMode(sim.data)
SamplingParam(sim.data)
WaitingTimes(sim.data)
SamplingTimes(sim.data)
## See model.
getModel(sim.data)
## See number of simulated patterns.
noDraws(sim.data)