posteriorDensityIncrement function

Posterior density of an increment

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

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.

Returns

the posterior density value.

Details

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

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)

See Also

increment, fitCauchy