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, |
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. | \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, 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, |
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)