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.

Value

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.

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)
#> [1] 0.1867161