Description Usage Arguments Value
Create binary dated tree binaryDatedTree class, includes heights for each node and other helper variables like maxSampleTime.
1 2 | binaryDatedTree(phylo, sampleTimes, sampleStates=NULL
, sampleStatesAnnotations=NULL)
|
phylo |
ape::phylo tree |
sampleTimes |
Named vector of sample times for each taxon. Names must correspond to phylo$tip.label |
sampleStates |
Matrix of discrete character information for each taxon. If NULL, this may be inferred from taxon label. Rownames must correspond to phylo$tip.label. Colnames must correspond to names of demes used in subsequent analysis. Each row is a probability vector summing to 1 (the probability that taxon occupies each deme). |
sampleStatesAnnotations |
Vector of possible discrete character states for taxa. If inferring taxon state from label, this provides the possible matches for taxon annotations. The annotations are extracted from all text following '_' at the end of the taxon label. |
A binaryDatedTree object. Includes numeric vector heights for each tip and internal node, the time before most recent sample when each node occurs.
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