Pt {DNAseqtest} | R Documentation |

## Transition Probability Function

### Description

This function calculates the transition probability function for a process during a period of time.

### Usage

`Pt(S, Pi, t)`

### Arguments

`S` |
a 4 x 4 symmetric matrix |

`Pi` |
a diagonal matrix containing the stationary distribution for the process |

`t` |
a period of time describing the length of the process |

### Details

This function needs the 4 x 4 symmetric matrix S, II and the process
length t in order to find the transition probability over that process,
where `P_{ij}(t)`

is the probability that the ith nucleotide changes to the
j-th nucleotide during the period of t.

### Value

A 4 x 4 matrix containing the transition probabilities for a process.

### References

Faisal Ababneh, Lars S Jermiin, Chunsheng Ma, John Robinson (2006). Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics, 22(10), 1225-1231.

### See Also

Smatrix

### Examples

```
Pi<-diag(c(.1,.1,.1,.7))
S<-Smatrix(c(.3,.3,.3,.3,.3,.3),diag(Pi))
t<-1
p<-Pt(S, Pi, t)
p
```

*DNAseqtest*version 1.0 Index]