R: Log-Likelihood of phyclust

phyclust.logL {phyclust}

R Documentation

Log-Likelihood of phyclust

Description

This computes a log-likelihood value of phyclust.

Usage

phyclust.logL(X, ret.phyclust = NULL, K = NULL, Eta = NULL,
    Mu = NULL, pi = NULL, kappa = NULL, Tt = NULL,
    substitution.model = NULL, identifier = NULL, code.type = NULL,
    label = NULL)

Arguments

`X`	nid/sid matrix with N rows/sequences and L columns/sites.
`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 = KL*, each row is a center.
`pi`	equilibrium probabilities, each row sums to 1.
`kappa`	transition and transversion bias.
`Tt`	total evolution time, t.
`substitution.model`	substitution model.
`identifier`	identifier.
`code.type`	code type.
`label`	label of sequences for semi-supervised clustering.

Details

X should be a numerical matrix containing sequence data that can be transfered by code2nid or code2sid.

Either input ret.phyclust or all other arguments for this function. ret.phyclust can be obtain either from an EM iteration of phyclust or from a M step of phyclust.m.step.

If label is inputted, the label information will be used to calculate log likelihood (complete-data), even the ret.phyclust is the result of unsupervised clustering.

Value

This function returns a log-likelihood value of phyclust.

Author(s)

Wei-Chen Chen wccsnow@gmail.com

References

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

Examples

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

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)
phyclust.logL(X, ret.phyclust = ret.1)

# For semi-supervised clustering.
semi.label <- rep(0, nrow(X))
semi.label[1:3] <- 1
phyclust.logL(X, ret.phyclust = ret.1, label = semi.label)

## End(Not run)

[Package phyclust version 0.1-18 Index]