morpho: Morpho object

Description

Create a morpho object.

Usage

morpho(
  sequences = NULL,
  trees = NULL,
  model = NULL,
  transition_history = NULL,
  root.states = NULL,
  fossil = NULL
)
as.morpho(
  sequences,
  trees,
  model = NULL,
  transition_history = NULL,
  root.states = NULL,
  fossil = NULL
)
is.morpho(sequences)

Value

An object of class "morpho" containing the simulated morphological data and associated information. The object includes the simulated sequences, phylogenetic trees and branch rates used for the simulation, model parameters, root states, fossil information (if provided), and the character transition history.

Arguments

sequences: A list containing all of the sequences simulated. This can contain sequences for taxa at the tips or the tree, along the nodes, and if present, for sampled ancestors (SA)
trees: A list containing the trees and branch lengths used for the simulation. EvolTree contains a phylogenetic tree with branch lengths representing evolutionary distance. TimeTree (if present) contains the same tree with branch lengths in unit of time. BrRates can either be a single value, when simulating under a strict clock, or a vector of values representing the rate/branch
model: A list containing all model attributes. Model specifies the components specified to simulate under. RateVar contains the relative values drawn from the specified distribution. RateVarTrait species the rate used to simulate each trait
transition_history: The constant character transitions along the branches
root.states: A vector supplying the root state for each character
fossil: Fossil object used to simulate data