phyclust (version 0.1-24)

phyclust.Pt: 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.

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.

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.	\(\pi, \kappa, t\)

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

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")
# }