R: Transition Probabilities of phyclust Given Time

phyclust.Pt {phyclust} | R Documentation

## Transition Probabilities of phyclust Given Time

### Description

This computes transition probabilities of `phyclust` given time.

### Usage

    phyclust.Pt(Q, Tt, substitution.model = .substitution.model$model[1])

### Arguments

`Q` | a list according to the substitution model.
`Tt` | total evolution time, t.
`substitution.model` | substitution model.

### Details

The major models for `Q` are:

Model | Author and Publication | Parameter
JC69 | Jukes and Cantor 1969. | t
K80 | Kimura 1980. | kappa, t
F81 | Felsenstein 1981. | pi, t
HKY85 | Hasegawa, Kishino, and Yano 1985. | kappa, pi, t

A list of `Q` should contains `pi`, `kappa` based on substitution models and code types. `Tt` may be separately stored. Depending on identifiers, `Q`s can be composite to a `QA`, Q matrix array.

### Value

A list with class `Pt` will be returned containing several elements as the following:

`'Pt'` | a transition probability matrix.
`'log.Pt'` | a log transition probability matrix.
`'H'` | a negative entropy, `diag(Pt %*% t(log.Pt))`.

### ToDo(s)

- vectorize `Tt` for repeated computation in C.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

### See Also

`.substitution.model`, `phyclust`, `phyclust.em.step`.

### Examples

    ## Not run:
    library(phyclust, quiet = TRUE)

    Tt <- 0.5

    Q <- list(pi = c(0.25, 0.25, 0.25, 0.25), kappa = 0.5)
    phyclust.Pt(Q, Tt, "HKY85")

    Q <- list(pi = c(0.5, 0.5), kappa = 0.5)
    phyclust.Pt(Q, Tt, "SNP_JC69")

    ## End(Not run)

[Package phyclust version 0.1-30 Index]