fitPE: Fit pulsed evolution model

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

Fit pulsed evolution model

Description

Fit pulsed evolution model in a maximum-likelihood framework

Usage

fitPE(
  x,
  l,
  start.value = NULL,
  min.value = rep(0, 4),
  numCores = 1,
  fixed = list(),
  laplace = TRUE,
  eval.only = FALSE,
  reltol = sqrt(.Machine$double.eps),
  ...
)

fitPE.phy(
  phy,
  x,
  start.value = NULL,
  min.value = rep(0, 4),
  numCores = 1,
  fixed = list(),
  ignore.zero = TRUE,
  laplace = TRUE,
  eval.only = FALSE,
  bootstrap = NULL,
  reltol = sqrt(.Machine$double.eps),
  ...
)

Arguments

x	trait change in fitPE and tip trait values in fitPE.phy
l	branch length of time/divergence
phy	a phylo-class object from the ape package

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