secsse (version 3.0.2)

cla_id_paramPos: Parameter structure setting for cla_secsse It sets the parameters (speciation, extinction and transition) IDs. Needed for ML calculation with cladogenetic options (cla_secsse_ml)

Description

Parameter structure setting for cla_secsse It sets the parameters (speciation, extinction and transition) IDs. Needed for ML calculation with cladogenetic options (cla_secsse_ml)

Usage

cla_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").

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 <- cla_id_paramPos(traits, num_concealed_states)