phyclust (version 0.1-30)

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

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

Examples

# NOT RUN {
library(phyclust, quiet = TRUE)

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)
# }