R: Continuous time Markov Chains class

ctmc-class {markovchain} | R Documentation

## Continuous time Markov Chains class

### Description

The S4 class that describes `ctmc` (continuous time Markov chain) objects.

### Arguments

`states` | Name of the states. Must be the same of `colnames` and `rownames` of the generator matrix
`byrow` | TRUE or FALSE. Indicates whether the given matrix is stochastic by rows or by columns
`generator` | Square generator matrix
`name` | Optional character name of the Markov chain

### 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

### Note

1. `ctmc` classes are written using S4 classes

2. Validation method is used to assess whether either columns or rows totals to zero. Rounding is used up to 5th decimal. If state names are not properly defined for a generator `matrix`, coercing to `ctmc` object leads to overriding states name with artificial "s1", "s2", ... sequence

### 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)
    ## Not run: plot(molecularCTMC)

[Package markovchain version 0.8.6 Index]