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) # }