Add poissonian mutations to an ultrametric tree(s)

Takes an ultrametric tree of class "phylo" (or a list of such trees) and draws new edge lengths in units of mutations, with the mean of each new edge length equal to the old edge length multiplied by the mutation rate. Mutation rate can be set or drawn from a uniform distribution.

Usage

ultra2mut(tree, nu)

Arguments

tree: A single tree or list of trees of class "phylo", with edge lengths in units of time
nu: Mutation rate in units of mutations per unit time. Can also be a vector of mutation rates with length equal to the number of input trees. Make sure time units are consistent in nu and tree$edge.length

Value

An ape object of class "phylo" representing the phylogenetic tree with edge lengths in units of mutations. Value of mutation rate will be added to 'metadata' data.frame of output tree if such a data.frame exists in the input tree. Otherwise, mutation rate value will be added to "phylo" object directly. If input is a list of trees, ultra2mut() will return a list of such "phylo" objects.

Examples

# Convert the time-based, ultrametric example trees into mutation-based trees
mutTrees <- ultra2mut(exampleUltraTrees,
  nu = stats::runif(n = length(exampleUltraTrees), min = 10, max = 20)
)