create_default_lambda_transition_matrix: Helper function to create a default lambda list

In secsse: Several Examined and Concealed States-Dependent Speciation and Extinction

Helper function to create a default lambda list

Description

This function generates a generic lambda list, assuming no transitions between states, e.g. a species of observed state 0 generates daughter species with state 0 as well.

Usage

create_default_lambda_transition_matrix(
  state_names = c("0", "1"),
  model = "ETD"
)

Arguments

state_names	vector of names of all observed states.
model	used model, choice of "ETD" (Examined Traits Diversification), "CTD" (Concealed Traits Diversification) or "CR" (Constant Rate).

Examples

lambda_matrix <-
     create_default_lambda_transition_matrix(state_names = c(0, 1),
                                             model = "ETD")
lambda_list <- create_lambda_list(state_names = c(0, 1),
                                  num_concealed_states = 2,
                                  transition_matrix = lambda_matrix,
                                  model = "ETD")

secsse documentation built on June 22, 2024, 11:35 a.m.