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A phylogeny of all the species of a `roleData`

rolePhylo.Rd

An S4 class to specify a phylogeny for the purpose of the RoLE model

Usage

rolePhylo(n, e, l, alive, tipNames, scale)

Arguments

n
e
l
alive
tipNames

Value

a `rolePhylo` object

Slots

n

the number of tips in the phylogeny

e

the numeric edge matrix of the phylogeny Each row contains an ancestor-child pair where the 1st column is the ancestor and the 2nd is the child

l

a numeric vector of edge lengths The units of l are the time steps (iterations) of the model Each time step unit is equal to 1/J generations where J is the number of individuals in the local community

alive

a logical vector indicating whether each tips is extant or not

tipNames

a character vector of the names of each tip

scale

a single numeric value of time scale translation to years