RevBayes

characterMapTree(Tree tree, AncestralStateTrace[] ancestral_state_trace_vector, TraceTree tree_trace, String character_file, String posterior_file, String shift_prob_file, Probability burnin, String reconstruction, Integer num_time_slices, Bool verbose)

tree :	Tree (pass by value)
	The input tree to summarize the character history over.
ancestral_state_trace_vector :	AncestralStateTrace[] (pass by value)
	A vector of ancestral state traces.
tree_trace :	TraceTree (pass by value)
	A trace of tree samples.
	Default : NULL
character_file :	String (pass by value)
	The name of the file to store the tree annotated with the MAP character history.
posterior_file :	String (pass by value)
	The name of the file to store the tree annotated with the posterior probabilities for the MAP character history.
shift_prob_file :	String (pass by value)
	The name of the file to store the tree annotated with the shift probabilities of the character.
	Default : NULL
burnin :	Probability (pass by value)
	The fraction/number of samples to discard as burnin.
	Default : 0.25
reconstruction :	String (pass by value)
	'joint' and 'conditional' should only be used to summarize character maps sampled from the joint distribution. 'marginal' can be used for character maps sampled from the joint or marginal distribution.
	Default : marginal
	Options : conditional\|joint\|marginal
num_time_slices :	Integer (pass by value)
	The number of time slices to discretize the character history. Should be the same as used for the numeric ODE.
	Default : 500
verbose :	Bool (pass by value)
	Printing verbose output
	Default : TRUE

Tree

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