search_tree: Function to search for trees with a given number of tips and...
In EvoLandEco/eve: Evolution Emulator, phylogenetically dependent

search_tree

R Documentation

Function to search for trees with a given number of tips and a given parameter set

Description

Function to search for trees with a given number of tips and a given parameter set

Usage

search_tree(
  pars,
  age,
  model,
  metric,
  offset,
  size = NULL,
  n = 1,
  history = FALSE,
  verbose = FALSE,
  size_limit = 1e+06
)

Arguments

`pars`	Vector of parameters: `pars[1]` corresponds to lambda (speciation rate) `pars[2]` corresponds to mu (extinction rate) `pars[3]` corresponds to beta_num (coefficient for species number effect on speciation) `pars[4]` corresponds to beta_phi (coefficient for evolutionary distinctiveness effect on speciation) `pars[5]` corresponds to gamma_num (coefficient for species number effect on speciation) `pars[6]` corresponds to gamma_phi (coefficient for evolutionary distinctiveness effect on extinction)
`age`	Sets the crown age for the simulation
`model`	Sets the model of diversity-dependence: `model == dsce2` : linear dependence in speciation rate with parameters beta_num and beta-phi `model == dsde2` : linear dependence in both speciation rate and extinction rate with parameters beta_num, beta_phi, gamma_num and gamma_phi
`metric`	"pd" , "ed" or "nnd", Specifies which evolutionary distinctiveness metric should be used.
`offset`	Specifies which method to use to offset the impact of tree age and the collinearity between pd and species richness. "none" for no offset method; "simtime" for deducting tree age from pd value; "spcount" for dividing pd value by species richness; "both" for applying both "simtime" and "spcount", by firstly deducting tree age and then dividing by species richness
`size`	Specifies the number of tips in the tree to be searched for
`n`	Specifies the number of trees to be searched for
`history`	Logical, indicating whether to record the historical states (of the rates and ED/PD values)
`verbose`	Logical, for debugging purpose, indicating whether to print simulation info at each step in the console, and save running time to a file
`size_limit`	Specifies the maximum number of tips in the tree to be
`converter`	Either "cpp" or "r", choose which version of L2phylo to use.