birthdeath.tree {geiger}R Documentation

Birth-death tree simulator

Description

Simulates phylogenetic tree under a uniform birth-death process

Usage

birthdeath.tree(b, d, time.stop = 0, taxa.stop = 0, seed = 0)

Arguments

b Per-lineage birth (speciation) rate
d Per-lineage death (extinction) rate
time.stop Stopping time
taxa.stop Maximum number of taxa
seed Random number seed; if seed=0 (default) then random number generator is seeded based on the clock

Details

Value

Phylogenetic tree in ape format

Note

Author(s)

Luke J. Harmon and Jason Wier

References

Geiger

See Also

Examples


# Pure-birth tree
p1<-birthdeath.tree(b=0.1, d=0, time.stop=20)
plot(p1)

# Birth-death tree with extinct taxa
p2<-birthdeath.tree(b=0.2, d=0.05, time.stop=20)
plot(p2)

# Previous tree with extinct taxa removed
prune.extinct.taxa(p2)->p3
if(!is.null(p3)) plot(p3) else cat("No survivors\n")
#Sometimes there are no extant taxa


[Package geiger version 0.2-6 Index]