bootstrap.seq: Bootstrap Sequences from a Fitted Model and Star Tree.

In snoweye/phyclust: Phylogenetic Clustering (Phyloclustering)

Bootstrap Sequences from a Fitted Model and Star Tree.

Description

This function bootstraps sequences from a model fitted by phyclust and star trees generated by bootstrap.star.trees. The fitted model can be varied in .identifier.

Usage

bootstrap.seq(ret.phyclust, star.trees)

Arguments

ret.phyclust	a phyclust object in Class phyclust.
star.trees	star trees might be generated by bootstrap.star.trees.

Details

ret.phyclust is a phyclust object in Class phyclust which is usually fitted by phyclust, or returned by phyclust.m.step.

star.trees should be corresponding to the ret.phyclust which might be directly bootstrapped from the function bootstrap.star.trees.

Value

Return a list containing sequences in K clusters.

Author(s)

Wei-Chen Chen [e-mail]

References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

See Also

phyclust, bootstrap.star.trees, bootstrap.star.trees.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.tree <- bootstrap.star.trees(ret.1)
ret.seq <- bootstrap.seq(ret.1, ret.tree)

## End(Not run)

snoweye/phyclust documentation built on Sept. 12, 2023, 5 a.m.