fullMarginalReconstructionWithPE: Reconstruct all marginal ancestral state in a phylogeny

In wu-lab-uva/RasperGade: Reconstructing Ancestral State under Pulsed Evolution in R by Gaussian Decomposition

Reconstruct all marginal ancestral state in a phylogeny

Description

Reconstruct all marginal ancestral states, including those require rerooting, in a phylogeny

Usage

fullMarginalReconstructionWithPE(
  phy,
  x,
  params,
  laplace = FALSE,
  approximate = 1,
  margin = 1e-06,
  numCores = 1,
  asymptotic = 5
)

Arguments

phy	phylo-class object from ape package
x	named vector of tip trait values; names should match the tip labels; NA should not be included
params	a vector of pulsed evolution parameters
laplace	logical, when true, time-independent variation follows Laplace distribution
approximate	number of normal distributions to approximate the uncertainty distribution for internal nodes
margin	total probability mass of the number of jump not taken into account per compound Poisson process
numCores	number of cores to use
asymptotic	threshold of expected number of jumps beyond which the trait change is assumed to be normal

Details

Parameter vector should be in the format of lambda,size,...,sigma,epsilon Currently laplace should always set to be FALSE.

Value

returns a list that contains all the information to calculate the global ancestral states and hidden states

wu-lab-uva/RasperGade documentation built on June 24, 2022, 2:47 p.m.