secsse (version 3.5.0)

id_paramPos: Parameter structure setting Sets the parameters (speciation, extinction and transition) ids. Needed for ML calculation (secsse_ml()).

Description

Parameter structure setting Sets the parameters (speciation, extinction and transition) ids. Needed for ML calculation (secsse_ml()).

Usage

id_paramPos(traits, num_concealed_states)

Value

A list that includes the ids of the parameters for ML analysis.

Arguments

traits

vector with trait states for each tip in the phylogeny. The order of the states must be the same as the tree tips. For help, see vignette("starting_secsse", package = "secsse"). When providing a multiPhylo set of multiple phylognies, traits should be a list where each entry in the list corresponds to the matching phylogeny on that position.

num_concealed_states

number of concealed states, generally equivalent to the number of examined states in the dataset.

Examples

traits <- sample(c(0,1,2), 45,replace = TRUE) #get some traits
num_concealed_states <- 3
param_posit <- id_paramPos(traits,num_concealed_states)