transmatrix2sequence: Sampling function for Markov chains

In localScore: Package for Sequence Analysis by Local Score

Sampling function for Markov chains

Description

Creates Markov chains based on a transition matrix. Can be used as parameter for the Monte Carlo function.

Usage

transmatrix2sequence(matrix, length, initialIndex, score)

Arguments

matrix	transition matrix of Markov process
length	length of sequence to be sampled
initialIndex	(optional) index of matrix which should be initial value of sequence. If none supplied, a value from the stationary distribution is sampled as initial value.
score	(optional) a vector representing the scores (in ascending order) of the matrix index. If supplied, the result will be a vector of these values.

Details

The transition matrix is considered representing the transition from one score to another such that the score in the first row is the lowest and the last row are the transitions from the highest score to another. The matrix must be stochastic (no rows filled up with only '0' values).

It is possible to have the same score for different states of the markov chain. If no score supplied, the function returns a markov chain with state in 1:ncol(matrix)

Value

a Markov chain sampled from the transition matrix

Examples

B <-  matrix (c(0.2, 0.8, 0.4, 0.6), nrow = 2, byrow = TRUE)
transmatrix2sequence(B, length = 10)
transmatrix2sequence(B, length = 10, score = c(-2,1))
transmatrix2sequence(B, length = 10, score = c("A","B"))
MyTransMat <-
   matrix(c(0.3,0.1,0.1,0.1,0.4,
            0.2,0.2,0.1,0.2,0.3,
            0.3,0.4,0.1,0.1,0.1,
            0.3,0.3,0.1,0.0,0.3,
            0.1,0.1,0.2,0.3,0.3),
            ncol = 5, byrow=TRUE)
MySeq.CM <- transmatrix2sequence(matrix = MyTransMat,length=90, score =c(-2,-1,0,2,3))
MySeq.CM

localScore documentation built on April 3, 2025, 5:26 p.m.