Function to convert a table with speciation and extinction events to a set of branching times

Converting a table with speciation and extinction events to a set of branching times

Usage

L2brts(L, dropextinct = T)

Arguments

L

Matrix of events as produced by dd_sim:

- the first column is the time at which a species is born in Mya
- the second column is the label of the parent of the species; positive and negative values indicate whether the species belongs to the left or right crown lineage
- the third column is the label of the daughter species itself; positive and negative values indicate whether the species belongs to the left or right crown lineage
- the fourth column is the time of extinction of the species; if the fourth element equals -1, then the species is still extant.

dropextinct

Sets whether the phylogeny should drop species that are extinct at the present

Value

brts

A set of branching times

References

- Etienne, R.S. et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439
- Etienne, R.S. & B. Haegeman 2012. Am. Nat. 180: E75-E89, doi: 10.1086/667574

Author

Rampal S. Etienne

Examples

sim = dd_sim(c(0.2,0.1,20),10)
phy = L2brts(sim$L)
plot(phy)