R/internal.abctaxon.R

In bomeara/treevo: Using ABC to Understand Trait Evolution

#create abctaxon class object


#   abctaxon
#
#   Internal TreEvo function to create a list of objects
#
#
#   @param id Simulation ID
#   @param name Taxon of interest
#   @param timeSinceSpeciation Time since speciation
#   @param states States of taxon
#   @param nextstates States of taxon after mutation
#   @param startTime When this lineage starts
#   @param endTime When this lineage stops
#   @param terminal If TRUE, is a terminal taxon
#   @param ancestorId ID of the ancestor of this node.
#   @author Brian O'Meara and Barb Banbury
# @references O'Meara and Banbury, unpublished
abctaxon <- function(
		id = 0, 
		name = "taxon0", 
		timeSinceSpeciation = 0, 
		states = NA, 
		nextstates = NA, 
		startTime = 0, 
		endTime = Inf, 
		terminal = TRUE, 
		ancestorId = NA
		){
	#########
    taxon <- list(
		id = id, 
		name = name, 
		timeSinceSpeciation = timeSinceSpeciation, 
		states = states, 
        nextstates = nextstates, 
		startTime = startTime, 
		endTime = endTime, 
		terminal = terminal, 
		ancestorId = ancestorId
		)
    class(taxon) <- "abctaxon"
    return(taxon)
	}