geiger (version 1.2-06)

prune.extinct.taxa: Prune specified taxa from a phylogenetic tree

Description

Prunes a set of taxa from a tree, either a random fraction of all taxa, or just the taxa whos tip branch terminates before the present day (extinct taxa)

Usage

prune.extinct.taxa(phy, tol = .Machine$double.eps^0.5)
prune.random.taxa(phy, n)

Arguments

phy

Phylogenetic tree

tol

Tolerance for taxa that do not reach the present day exactly. This prevents taxa from being pruned just due to rounding error

n

Number of random taxa to prune from the tree

Value

• New tree without these taxa

Examples

# Birth-death tree with extinct taxa
p2<-birthdeath.tree(b=0.2, d=0.1, time.stop=30)
plot(p2)

# Previous tree with extinct taxa removed
prune.extinct.taxa(p2)->p3
if(!is.null(p3)) plot(p3)

p4<-birthdeath.tree(b=0.2, d=0, taxa.stop=100)
p5<-prune.random.taxa(p4, 40)

plot(p5)