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.
bootstrap.star.trees.seq(ret.phyclust, min.n.class = 1)a phyclust object in Class phyclust.
minimum number of sequences for a cluster.
Return a list containing two elements, and both are corresponding to the
model of ret.phyclust, including:
a list, \(K\) star trees according to ret.phyclust
a list, sequences in \(K\) clusters
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.
Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/
# 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)
# }