SimulateTips: Simulate trait data

In bomeara/BMhyb: Comparative Methods for Phylogenetic Networks

Description

For a given phylogenetic network generate tip data. Any values not specified use default values

Usage

SimulateTips(
  phy.graph,
  sigma.sq = 1,
  mu = 0,
  bt = 1,
  vh = 0,
  SE = 0,
  measurement.error = 0,
  gamma = 0.5,
  exclude.donors.recipients = TRUE
)

Arguments

phy.graph	An ape::evonet object (a phylogeny stored in phylo format that also includes a reticulation matrix)
sigma.sq	The Brownian motion wiggle rate
mu	The population mean (in the absence of hybridization)
bt	The beta value (multiplier on expected value for each hybridization event)
vh	The burst of variance that comes from a hybridization event
SE	Uniform uncertainty at the tips
measurement.error	Uncertainty at the tips, especially if it varies between species
gamma	In a hybridization event, what proportion of the trait comes from the donating parent. 0.5 means half comes from each parent
exclude.donors.recipients	If TRUE, do not generate for any donors or recipient placeholder taxa

Value

A vector of trait values

Examples

network <- SimulateNetwork(ntax=5, nhybridizations=2)
tips <- SimulateTips(network, mu=1.1, bt=3, vh=1.1, SE=1)

bomeara/BMhyb documentation built on Nov. 11, 2021, 12:37 a.m.