cauphy (version 1.0.3)

posteriorDensityAncestral: Posterior density of a node

Description

Compute the posterior density of a set of node values under a Cauchy process on a phylogenetic tree.

Usage

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

Value

the posterior density value.

Arguments

node

the node for which to compute the posterior density.

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 ancestral, which is the preferred way of doing ancestral reconstruction on a fitted object.

See Also

ancestral, fitCauchy

Examples

phy <- ape::rphylo(5, 0.1, 0)
dat <- rTraitCauchy(n = 1, phy = phy, model = "cauchy", parameters = list(root.value = 0, disp = 1))
posteriorDensityAncestral(7, 0.1, phy, dat, disp = 1)