phyclust (version 0.1-9)

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[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)

• vectorizeTtfor repeated computation in C.

Details

The major models for Q are: lll{ 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: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

See Also

.substitution, phyclust, phyclust.em.step.

Examples

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")