bootstrap.star.trees.seq {phyclust} | R Documentation |
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 |
min.n.class |
minimum number of sequences for a cluster. |
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.
Value
Return a list containing two elements, and both are corresponding to the
model of ret.phyclust
, including:
trees |
a list, |
seq |
a list, sequences in |
Author(s)
Wei-Chen Chen wccsnow@gmail.com
References
Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/
See Also
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)
## End(Not run)