marginalReconstruction: Reconstruct marginal ancestral state from a node's immediate...

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

Reconstruct marginal ancestral state from a node's immediate descendants

Description

Reconstruct marginal ancestral state using immediate descendants under BM or pulsed evolution model

Usage

marginalReconstruction(x, l)

marginalReconstructionWithPE(
  x,
  l,
  lambdas,
  sizes,
  sigma,
  epsilons,
  margin = 1e-06,
  numCores = 1,
  asymptotic = 5
)

Arguments

x	vector of means of mixed normal distributions
l	vector of standard deviations of mixed normal distributions
lambdas	vector of jump frequencies, has the same length as the number of compound Poisson processes
sizes	vector of variances of trait change per jump, has the same length as the number of compound Poisson processes
sigma	rate of BM, has a length of 1
epsilons	vector of uncertainty not explained by the branches, has the same length as the number of immediate descendants
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

Value

marginalReconstruction returns a vector of the mean variance and the scaling factor

marginalReconstructionWithPE returns a list of the mean, variance and a data frame of the normal mixture

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