DatedTree: DatedTree function

In emvolz-phylodynamics/phydynR: Model-based coalescent simulation and likelihood for phylodynamic inference

DatedTree function

Description

Create a DatedTree class object; it includes heights for each node and other helper variables

Usage

DatedTree(
  phylo,
  sampleTimes,
  sampleStates = NULL,
  sampleStatesAnnotations = NULL,
  tol = 1e-06,
  minEdgeLength = 0
)

Arguments

phylo	A phylogenetic tree of class ape::phylo
sampleTimes	A numeric vector providing the times of samples. If named, taxon labels will be based on names of the corresponding sample times
sampleStates	For models with more than one deme, a matrix must be supplied describing the probability of sampling from each deme. Each row corresponds to a sample in the same order as sampleTimes. Each column corresponds to probability of sampling each deme. Column names should be defined which correspond to deme names in the model. Rows should sum to one.
sampleStatesAnnotations	Vector of possible discrete character states for taxa. If inferring taxon state from label, this provides the possible matches for taxon annotations.
tol	to do
minEdgeLength	to do

Value

to do

Author(s)

Erik Volz

Examples

to do
#write example

emvolz-phylodynamics/phydynR documentation built on July 28, 2023, 6:06 a.m.