Rev Language Reference



ancestralStateTree(Tree tree, AncestralStateTrace[] ancestral_state_trace_vector, TraceTree tree_trace, Bool include_start_states, String file, Probability burnin, String summary_statistic, String reconstruction, Integer site, Bool verbose, Natural nStates)


tree : Tree (pass by value)
The input tree to summarize ancestral states 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
include_start_states : Bool (pass by value)
Annotate start states as well as end states for each branch. Only applicable for cladogenetic processes.
Default : FALSE
file : String (pass by value)
The name of the file to store the annotated tree.
burnin : Probability (pass by value)
The fraction/number of samples to discard as burnin.
Default : 0.25
summary_statistic : String (pass by value)
The statistic used to summarize ancestral states. 'MAP' displays the 3 states with highest posterior probabilities. 'mean' displays the mean value and 95% CI.
Default : MAP
Options : MAP|mean
reconstruction : String (pass by value)
'joint' and 'conditional' should only be used to summarize ancestral states sampled from the joint distribution. 'marginal' can be used for states sampled from the joint or marginal distribution.
Default : marginal
Options : conditional|joint|marginal
site : Integer (pass by value)
The character site to be summarized.
Default : 1
verbose : Bool (pass by value)
Printing verbose output
Default : TRUE
nStates : Natural (pass by value)
The number of states for which we compute the posterior probability. By default it will be the best three.
Default : 3

Return Type