Description Objects from the Class Slots Methods Warning Note Author(s) References See Also Examples

The S4 class that describes `ctmc`

(continuous time Markov chain) objects.

Objects can be created by calls of the form `new("ctmc", states, byrow, generator, ...)`

.

`states`

:Name of the states. Must be the same of

`colnames`

and`rownames`

of the generator matrix`byrow`

:Binary flag.

`generator`

:Square generator matrix

`name`

:Optional character name of the Markov chain

- 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

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

`ctmc`

objects are written using S4 Classes.

Sai Bhargav Yalamanchi, Giorgio Spedicato

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

`generatorToTransitionMatrix`

,`rctmc`

1 2 3 4 5 6 7 8 9 10 11 | ```
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: 0.6.9.8-1
Date: 2017-08-15
BugReport: http://github.com/spedygiorgio/markovchain/issues
sigma sigma_star
[1,] 0.25 0.75
```

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