Rev Language Reference
mccTree
Finds the maximum clade credibility (MCC) topology from a trace of trees and summarizes branch lengths.
Usage
mccTree(TraceTree trace, String file, Bool ccAges, Bool ccp, Bool conditionalAges, Probability hpd, Bool mean, Bool sampledAncestors, Bool positiveBranchLengths)
Arguments
| trace : | TraceTree (pass by reference) |
| The samples of trees from the posterior. | |
| file : | String (pass by value) |
| The name of the file where to store the tree. | |
| ccAges : | Bool (pass by value) |
| Annotate conditional clade ages? | |
| Default : FALSE | |
| ccp : | Bool (pass by value) |
| Annotate conditional clade probabilities? | |
| Default : FALSE | |
| conditionalAges : | Bool (pass by value) |
| Annotate node ages conditional on the topology? | |
| Default : FALSE | |
| hpd : | Probability (pass by value) |
| The probability mass of the highest posterior density node age interval. | |
| Default : 0.95 | |
| mean : | Bool (pass by value) |
| Annotate node ages using the mean age instead of the median? | |
| Default : TRUE | |
| sampledAncestors : | Bool (pass by value) |
| Annotate sampled ancestor probs? | |
| Default : TRUE | |
| positiveBranchLengths : | Bool (pass by value) |
| Force negative branch lengths to be short but positive? | |
| Default : FALSE |
Return Type
Example
# Read in tree trace
tree_trace = readTreeTrace("output/my.trees", burnin=0.25)
# Generate the MCC tree
map_tree = mccTree(trace=tree_trace, file="mcc.tree")
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