simulate.mm {smmR}

Simulates k-th order Markov chains

Description

Simulates k-th order Markov chains.

Usage

## S3 method for class 'mm'
simulate(object, nsim = 1, seed = NULL, ...)

Arguments

object

An object of class mm.

nsim

An integer or vector of integers (for multiple sequences) specifying the length of the sequence(s).

seed

Optional. seed for the random number generator. If no seed is given, then seed is set by using the command ⁠set.seed(round(as.numeric(Sys.time()))⁠.

...

further arguments passed to or from other methods.

Details

If nsim is a single integer then a chain of that length is produced. If nsim is a vector of integers, then length(nsim) sequences are generated with respective lengths.

Value

A list of vectors representing the sequences.

See Also

mm, fitmm

Examples

states <- c("a", "c", "g", "t")
s <- length(states)
k <- 2
init <- rep.int(1 / s ^ k, s ^ k)
p <- matrix(0.25, nrow = s ^ k, ncol = s)

# Specify a Markov model of order 1
markov <- mm(states = states, init = init, ptrans = p, k = k)

seqs <- simulate(object = markov, nsim = c(1000, 10000, 2000), seed = 150)