Function to convert phylogeny to a table with speciation and extinction events

Converting a phylogeny to a table with speciation and extinction events

Usage

phylo2L(phy)

Arguments

phy

A phylogeny of the phylo type

Value

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.

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

Liang Xu

Examples

sim = dd_sim(c(0.2,0.1,20),10)
phy = sim$tas
L = phylo2L(phy)
phy2 = L2phylo(L, dropextinct = FALSE)
graphics::par(mfrow = c(1,3))
graphics::plot(phy)
graphics::plot(phy2)
graphics::plot(L2phylo(sim$L, dropextinct = FALSE))