rTraitCauchy: Cauchy Trait Simulation

In cauphy: Trait Evolution on Phylogenies Using the Cauchy Process

Cauchy Trait Simulation

Description

Simulate a continuous trait using the Cauchy Process

Usage

rTraitCauchy(
  n = 1,
  phy,
  model = c("cauchy", "lambda", "kappa", "delta"),
  parameters = NULL
)

Arguments

n	number of independent replicates
phy	a phylogeny in ape phylo format.
model	a phylogenetic model. Default is "cauchy", for the Cauchy process. Alternative are "lambda", "kappa", and "delta".
parameters	list of parameters for the model (see Details).

Details

The default choice of parameters is as follow:

model = cauchy

root.value = 0, disp = 1

model = lambda

root.value = 0, disp = 1, lambda = 1

model = kappa

root.value = 0, disp = 1, kappa = 1

model = delta

root.value = 0, disp = 1, delta = 1

Value

If n=1, a numeric vector with names from the tip labels in the tree. For more than 1 replicate, a matrix with the tip labels as row names, and one column per replicate.

See Also

rTrait, rTraitCont

Examples

set.seed(1289)
phy <- ape::rphylo(40, 0.01, 0)
# One trait
y <- rTraitCauchy(n = 1, phy = phy, model = "cauchy",
                  parameters = list(root.value = 0, disp = 0.1))
y
plot(phy, x.lim = c(0, 750))
phydataplot(y, phy, offset = 150)
# Many trait
y <- rTraitCauchy(n = 10, phy = phy, model = "cauchy",
                  parameters = list(root.value = 0, disp = 0.1))
head(y)

cauphy documentation built on Oct. 1, 2024, 5:08 p.m.