phyclust (version 0.1-9)

bootstrap.seq: Bootstrap sequences from a fitted model and star tree.

Description

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

Usage

bootstrap.seq(ret.phyclust, star.trees)

Arguments

ret.phyclust

a phyclust object in Class phyclust.

star.trees

star trees might be generated by bootstrap.star.trees.

Value

• Return a list containing 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.

star.trees should be corresponding to the ret.phyclust which might be directly bootstrapped from the function bootstrap.star.trees.

References

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

See Also

phyclust, bootstrap.star.trees, bootstrap.star.trees.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.tree <- bootstrap.star.trees(ret.1)
ret.seq <- bootstrap.seq(ret.1, ret.tree)