geiger (version 1.2-13)

birthdeath.tree: Birth-death tree simulator

Description

Simulates phylogenetic trees under a uniform birth-death process.

Usage

birthdeath.tree(b, d, time.stop = 0, taxa.stop = 0, seed = 0, print.seed=FALSE, return.all.extinct=TRUE)

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

print.seed

If T, prints out the random number seed associated with each tree

return.all.extinct

Return trees where all lineages have gone extinct? Otherwise, the function will build trees until it gets one with at least one surviving lineage.

Value

• Phylogenetic tree in ape format. If death rate is non-zero, then the returned tree will likely include some extinct lineages (terminating before the present day). The GEIGER function prune.extinct.taxa can remove these lineages.

Details

Starting from a root node - i.e., two living lineages - this function simulates the growth of a phylogenetic tree under a uniform, time-homogeneous birth-death process. This means that every lineage has a constant probability of speciating, and a constant probability of going extinct, per unit time. If birth is greater than death, then the number of lineages is expected to grow exponentially.

References

Geiger

See Also

BDsim for non-phylogenetic simulations; prune.extinct.taxa

Examples

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

# Birth-death tree with extinct taxa
# The return.all.extinct flag prevents trees with no survivors

p2<-birthdeath.tree(b=0.2, d=0.05, time.stop=20, return.all.extinct=FALSE)
plot(p2)

# Previous tree with extinct taxa removed
prune.extinct.taxa(p2)->p3