phangorn (version 1.0-2)

bootstrap.pml: Bootstrap

Description

bootstrap.pml performs (non-parametric) bootstrap analysis and bootstrap.phyDat produces a list of bootstrapped data sets. Under Linux the bootstrap is performed in parallel, if the multicore package is loaded. plotBS plots a phylogenetic tree with the with the bootstrap values assigned to the (internal) edges.

Usage

bootstrap.pml(x, bs = 100, trees = TRUE, ...)
bootstrap.phyDat(x, FUN, bs = 100, ...)
plotBS(tree, BStrees, type="unrooted", bs.col="black", bs.adj=c(0.5, 0.5), ...)

Arguments

x

an object of class pml or phyDat.

bs

number of bootstrap samples.

trees

return trees only (default) or whole pml objects.

...

further parameters used by optim.pml or plot.phylo.

FUN

the function to estimate the trees.

tree

The tree on which edges the bootstrap values are plotted.

BStrees

a list of trees (object of class "multiPhylo").

type

the type of tree.

bs.col

color of bootstrap support labels.

bs.adj

one or two numeric values specifying the horizontal and vertical justification of the bootstrap labels.

Value

• returns an object of class multi.phylo or a list where each element is an object of class pml.

See Also

optim.pml, pml, plot.phylo

Examples

data(Laurasiatherian)
dm <- dist.logDet(Laurasiatherian)
tree <- NJ(dm)
fit=pml(tree,Laurasiatherian)
fit = optim.pml(fit,TRUE)

set.seed(1)
bs <- bootstrap.pml(fit, bs=100, optNni=TRUE)
plotBS(fit$tree,bs)