Rev Language Reference
ancestralStateTree
Usage
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)
Arguments
| 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 |
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