phyclust (version 0.1-30)

# bootstrap.star.trees: Bootstrap a Star Tree from a Fitted Model.

## Description

This function bootstraps a star tree from a model fitted by phyclust. Each cluster corresponds to a star tree and a center sequence where sequences will evolve from. This function is called by bootstrap.star.trees.seq to generate sequences. The fitted model can be varied in .identifier.

## Usage

bootstrap.star.trees(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 $$K$$ star trees according to ret.phyclust.

## 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: https://snoweye.github.io/phyclust/

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)