tess.likelihood.bdstp: tess.likelihood.bdstp

In hoehna/TESS: Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events

Description

Computation of the likelihood for a given tree under an episodic fossilized-birth-death model (i.e. piecewise constant rates).

Usage

tess.likelihood.bdstp(
  nodes,
  lambda,
  mu,
  phi,
  r,
  samplingProbability,
  samplingStrategy = "uniform",
  MRCA = TRUE,
  CONDITION = "survival",
  log = TRUE
)

Arguments

nodes	node information from tess.branching.times(phy)
lambda	speciation rate vector
mu	extinction rate vector
phi	serial sampling rate vector
r	conditional probability that a lineage dies upon (serial) sampling
samplingProbability	probability of uniform sampling at present
samplingStrategy	Which strategy was used to obtain the samples (taxa). Options are: uniform|diversified|age
MRCA	does the tree start at the mrca?
CONDITION	do we condition the process on nothing|survival|sampleAtLeastOneLineage?
log	likelhood in log-scale?

Value

log likelihood

Examples

data(conifers)
nodes <- tess.branching.times(conifers)

logL <- tess.likelihood.bdstp(nodes,
                              lambda = 1.0, 
                              mu = 0.5,
                              phi = 0.1,
                              r = 0.0,
                              samplingProbability = 1.0)

hoehna/TESS documentation built on Feb. 3, 2022, 5:59 a.m.