geiger (version 0.2-6)

birthdeath.tree: 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

Value

• Phylogenetic tree in ape format

References

Geiger

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
")
#Sometimes there are no extant taxa