phyclust (version 0.1-9)

phyclust.logL: 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 = $K\times L$, each row is a center.

pi

equilibrium probabilities, each row sums to 1.

kappa

transition and transversion bias.

Tt

total evolution time, $t$.

substitution.model

substitution model.

identifier

identifier.

code.type

code type.

label

label of sequences for semi-supervised clustering.

Value

• This function return a log-likelihood value of phyclust.

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 unsuprvised clustering.

References

Phylogenetic Clustering Website: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

See Also

phyclust, phyclust.em.step.

Examples

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)