L2phylo2: Function to convert a table with speciation and extinction...

In EvoLandEco/eve: Evolution Emulator, phylogenetically dependent

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

Description

Converting a table with speciation and extinction events to a phylogeny (reversed time scale)

Usage

L2phylo2(L, t, dropextinct = FALSE)

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.
t	Simulation time
dropextinct	Sets whether the phylogeny should drop species that are extinct at the present

Value

phy	A phylogeny of the phylo type

Author(s)

Rampal S. Etienne; Tianjian Qin

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

Examples

# do not use this function, use L2phylo() instead

EvoLandEco/eve documentation built on Sept. 14, 2024, 12:04 a.m.