dd_sim: Function to simulate the diversity-dependent diversification process

Description

Simulating the diversity-dependent diversification process

Usage

dd_sim(pars, age, ddmodel = 1)

Arguments

pars

Vector of parameters: pars[1] corresponds to lambda (speciation rate) pars[2] corresponds to mu (extinction rate) pars[3] corresponds to K (clade-level carrying capacity)

age

Sets the crown age for the simulation

ddmodel

Sets the model of diversity-dependence: ddmodel == 1 : linear dependence in speciation rate with parameter K (= diversity where speciation = extinction) ddmodel == 1.3 : linear dependence in speciation rate with parameter K' (= diversity where speciation = 0) ddmodel == 2 : exponential dependence in speciation rate with parameter K (= diversity where speciation = extinction) ddmodel == 2.1 : variant of exponential dependence in speciation rate with offset at infinity ddmodel == 2.2 : 1/n dependence in speciation rate ddmodel == 2.3 : exponential dependence in speciation rate with parameter x (= exponent) ddmodel == 3 : linear dependence in extinction rate ddmodel == 4 : exponential dependence in extinction rate ddmodel == 4.1 : variant of exponential dependence in extinction rate with offset at infinity ddmodel == 4.2 : 1/n dependence in extinction rate with offset at infinity ddmodel == 5 : linear dependence in speciation and extinction rate

Value

out: A list with the following three elements: The first element is the tree of extant species in phylo format The second element is the tree of all species, including extinct species, in phylo format The third element is a matrix of all species where - the first column is the time at which a species is born - the second column is the label of the parent of the species; positive and negative values only 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 only 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