posteriorDensityIncrement: Posterior density of an increment

In cauphy: Trait Evolution on Phylogenies Using the Cauchy Process

Posterior density of an increment

Description

Compute the posterior density of a set of branch increments under a Cauchy process on a phylogenetic tree.

Usage

posteriorDensityIncrement(
  node,
  vals,
  tree,
  tipTrait,
  root.value = NULL,
  disp,
  method = c("reml", "random.root", "fixed.root")
)

Arguments

node	the node ending the branch for which to compute the posterior density of the increment.
vals	the table of values where the density should be computed.
tree	a phylogenetic tree of class phylo.
tipTrait	a names vector of tip trait values, with names matching the tree labels.
root.value	the root starting value of the process.
disp	the dispersion value.
method	the method used to compute the likelihood. One of reml (the default), fixed.root or random.root. See Details.

Details

This function is internally called by increment, which is the preferred way of doing ancestral reconstruction on a fitted object.

Value

the posterior density value.

See Also

increment, fitCauchy

Examples

set.seed(1289)
phy <- ape::rphylo(5, 0.1, 0)
dat <- rTraitCauchy(n = 1, phy = phy, model = "cauchy", parameters = list(root.value = 0, disp = 1))
posteriorDensityIncrement(2, 0.1, phy, dat, disp = 1)

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