phyclust.update: Update phyclust Results

In snoweye/phyclust: Phylogenetic Clustering (Phyloclustering)

Update phyclust Results

Description

This function will run the EM algorithm on initial parameters specified by users or from other initial procedures. All parameters (Eta, Mu, Q, ...) in this function will be updated.

Usage

phyclust.update(X, EMC = .EMC, ret.phyclust = NULL, K = NULL,
    Eta = NULL, Mu = NULL, pi = NULL, kappa = NULL, Tt = NULL,
    label = NULL, byrow = TRUE)

Arguments

X	nid/sid matrix with N rows/sequences and L columns/sites.
EMC	EM control.
ret.phyclust	an object with the class phyclust.
K	number of clusters.
Eta	proportion of subpopulations, \eta_k, length = K, sum to 1.
Mu	centers of subpopulations, dim = K\times L, each row is a center.
pi	equilibrium probabilities, each row sums to 1.
kappa	transition and transversion bias.
Tt	total evolution time, t.
label	label of sequences for semi-supervised clustering.
byrow	advanced option for X, default = TRUE.

Details

This function is equivalent to run exhaustEM on one specified initial parameters, and no initial procedure is involved. While this function is a little bit different to run phyclust with manual.id where Mu will be reestimated as the new initials. Simply speaking, this function only runs the EM algorithm given the initial parameters.

All the input arguments are the same as the inputs of the functions phyclust and phyclust.em.step.

Value

This function returns an object with class phyclust.

Author(s)

Wei-Chen Chen [e-mail]

References

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

See Also

phyclust, find.best, phyclust.se, phyclust.se.update.

Examples

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

set.seed(1234)
EMC.1 <- .EMC
EMC.1$EM.iter <- 1
# the same as EMC.1 <- .EMControl(EM.iter = 1)
X <- seq.data.toy$org

(ret.1 <- phyclust(X, 2, EMC = EMC.1))
(ret.2 <- phyclust.update(X, ret.phyclust = ret.1))

## End(Not run)

snoweye/phyclust documentation built on Sept. 12, 2023, 5 a.m.