rTraitCauchy function

Cauchy Trait Simulation

Simulate a continuous trait using the Cauchy Process

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).

Returns

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.

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

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)

See Also

rTrait, rTraitCont