create_lambda_list: Helper function to automatically create lambda matrices,...

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

Helper function to automatically create lambda matrices, based on input. When choosing the CTD model, rates associated with observed states are now re-distributed to concealed states. This implicitly assumes that the number of observed and concealed states is identical.

Description

Helper function to automatically create lambda matrices, based on input. When choosing the CTD model, rates associated with observed states are now re-distributed to concealed states. This implicitly assumes that the number of observed and concealed states is identical.

Usage

create_lambda_list(
  state_names = c(0, 1),
  num_concealed_states = 2,
  transition_matrix,
  model = "ETD"
)

Arguments

state_names	vector of names of all observed states.
num_concealed_states	number of concealed states, generally equivalent to the number of examined states in the dataset.
transition_matrix	a matrix containing a description of all speciation events, where the first column indicates the source state, the second and third column indicate the two daughter states, and the fourth column gives the rate indicator used. E.g.: ⁠["SA", "S", "A", 1]⁠ for a trait state "SA" which upon speciation generates two daughter species with traits "S" and "A", where the number 1 is used as indicator for optimization of the likelihood.
model	used model, choice of "ETD" (Examined Traits Diversification), "CTD" (Concealed Traits Diversification) or "CR" (Constant Rate).

Examples

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

secsse documentation built on Aug. 8, 2025, 7:31 p.m.