phyclust (version 0.1-9)

bootstrap.star.trees.seq: Bootstrap sequences from a fitted model.

Description

This function bootstraps sequences from a model fitted by phyclust by combining two functions bootstrap.star.trees and bootstrap.seq. The fitted model can be varied in .identifier.

Usage

bootstrap.star.trees.seq(ret.phyclust, min.n.class = 1)

Arguments

ret.phyclust

a phyclust object in Class phyclust.

min.n.class

minimum number of sequences for a cluster.

Value

• Return a list containing two elements, and both are corresponding to the model of ret.phyclust, including:
• trees
  a list, $K$ star trees according to ret.phyclust
• seq
  a list, sequences in $K$ clusters

Details

ret.phyclust is a phyclust object in Class phyclust which is usually fitted by phyclust, or returned by phyclust.m.step.

min.n.class is a boundary condition to avoid degenerate clusters when some population proportions, $\eta_k$, are small in the fitted model.

References

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

See Also

phyclust, bootstrap.star.trees, bootstrap.seq.

Examples

set.seed(1234)
EMC.1 <- .EMC
EMC.1$EM.iter <- 1
# the same as EMC.1 <- .EMControl(EM.iter = 1)

ret.1 <- phyclust(seq.data.toy$org, 2, EMC = EMC.1)
ret.all <- bootstrap.star.trees.seq(ret.1)