rolePhylo: A phylogeny of all the species in a 'roleData' object.

In role-model/roleR: Rules of Life Engine

A phylogeny of all the species in a 'roleData' object.

Description

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

Usage

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

Arguments

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 tip is extant or not.
tipNames	A character vector of the tip names.
scale	A single numeric value of time scale translation to years.

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 tip is extant or not.

tipNames

A character vector of the tip names.

scale

A single numeric value of time scale translation to years.

role-model/roleR documentation built on April 3, 2025, 1:06 p.m.