simUltra {cloneRate}

Simulate ultrametric birth and death branching trees

Description

Generates a sampled tree (or a list of many sampled trees) from a supercritial (birth rate > death rate) birth and death branching process according to the coalescent point process described in "Lambert, A. The coalescent of a sample from a binary branching process. (2018)."

Usage

simUltra(
  a,
  b,
  cloneAge,
  n,
  nTrees = 1,
  precBits = 1000,
  addStem = FALSE,
  nCores = 1
)

Arguments

a

Birth rate or vector of birth rates of length 'nTrees'

b

Death rate or vector of death rates of length 'nTrees'

cloneAge

Clone age or vector of clone ages of length 'nTrees'. Make sure it's same time units as birth and death rates

n

Number of samples/tips of the tree to be returned. Can be a vector of length 'nTrees' as well.

nTrees

Integer indicating the number of trees to generate. Default is 1

precBits

Rmpfr param for handling high precision numbers. Needed for drawing the coalescence times. Can be a vector of length 'nTrees', though it is not recommended

addStem

Boolean indicating whether to add stem to tree preceding first split/coalescence. Can also be a vector of length 'nTrees'

nCores

Integer indicating the number of cores to use if parallel pkg is installed. Default is 1.

Value

An ape object of class "phylo" representing the ultrametric phylogenetic tree with edge lengths in units of time. Tree metadata is located in the 'metadata' data.frame included in each "phylo" object. If 'nTrees' param is greater than 1, simUltra returns a list of objects of such objects of class "phylo".

Examples

# Generate a single tree
tree <- simUltra(a = 1, b = 0.5, cloneAge = 20, n = 50)

# Generate a list of trees
tree_list <- simUltra(a = 1, b = 0.5, cloneAge = 20, n = 50, nTrees = 3)