cla_id_paramPos function

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)

cla_id_paramPos(traits, num_concealed_states)

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.

Returns

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

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)