Function to generate a sequence of random CTMC transitions.

Description

The function generates random CTMC transitions as per the provided generator matrix.

Usage

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rctmc(n, ctmc, initDist = numeric(), T = 0, include.T0 = TRUE, out.type = "list")

Arguments

n

The number of samples to generate.

ctmc

The CTMC S4 object.

initDist

The initial distribution of states.

T

The time up to which the simulation runs (all transitions after time T are not returned).

include.T0

Flag to determine if start state is to be included.

out.type

"list" or "df"

Details

In order to use the T0 argument, set n to Inf.

Value

Based on out.type, a list or a data frame is returned. The returned list has two elements - a character vector (states) and a numeric vector (indicating time of transitions). The data frame is similarly structured.

Author(s)

Sai Bhargav Yalamanchi

References

Introduction to Stochastic Processes with Applications in the Biosciences (2013), David F. Anderson, University of Wisconsin at Madison

See Also

generatorToTransitionMatrix,ctmc-class

Examples

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energyStates <- c("sigma", "sigma_star")
byRow <- TRUE
gen <- matrix(data = c(-3, 3,
                       1, -1), nrow = 2,
              byrow = byRow, dimnames = list(energyStates, energyStates))
molecularCTMC <- new("ctmc", states = energyStates, 
                 byrow = byRow, generator = gen, 
                 name = "Molecular Transition Model")   
                 
statesDist <- c(0.8, 0.2)
rctmc(n = Inf, ctmc = molecularCTMC, T = 1)
rctmc(n = 5, ctmc = molecularCTMC, initDist = statesDist, include.T0 = FALSE)

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