binaryDatedTree: Create binary dated tree. The binaryDatedTree class includes...

In rcolgem: statistical inference and modeling of genealogies generated by epidemic and ecological processes

Description

Create binary dated tree binaryDatedTree class, includes heights for each node and other helper variables like maxSampleTime.

Usage

  binaryDatedTree(phylo, sampleTimes, sampleStates=NULL
  , sampleStatesAnnotations=NULL)

Arguments

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.

Value

A binaryDatedTree object. Includes numeric vector heights for each tip and internal node, the time before most recent sample when each node occurs.

rcolgem documentation built on May 2, 2019, 5:28 p.m.