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Continuous time Markov chain class

Source: R/ctmcClassesAndMethods.R
ctmc-class.Rd

The S4 class of continuous time Markov chains, described by their generator (rate) matrix.

Slots

states

Names of the states, equal to the row and column names of the generator.

byrow

Logical: are the rates out of each state in its row (rows sum to zero) or in its column?

generator

The square generator matrix: non-negative off-diagonal rates, with rows (or columns) summing to zero.

name

Optional name of the chain.

Note

The validity method checks that the rows (or columns) of the generator sum to zero, rounded to the fifth decimal. If the generator has no state names, the states are named "s1", "s2", ...

Methods

dim

signature(x = "ctmc"): method to get the size

initialize

signature(.Object = "ctmc"): initialize method

states

signature(object = "ctmc"): states method.

steadyStates

signature(object = "ctmc"): method to get the steady state vector.

plot

signature(x = "ctmc", y = "missing"): plot method for ctmc objects

References

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

See also

generatorToTransitionMatrix,rctmc

Examples

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")
steadyStates(molecularCTMC)
#>      sigma sigma_star
#> [1,]  0.25       0.75
plot(molecularCTMC)