Rev Language Reference


characterMapTree

Usage

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

Arguments

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.
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

Return Type