diversitree (version 0.9-9)

utilities: Utility Functions

Description

These are utility functions that are used internally by diversitree, but which might be more generally useful.

Currently only get.descendants docuemnted here, which determines which species or nodes are descended from a particular node.

Usage

get.descendants(node, tree, tips.only=FALSE, edge.index=FALSE) run.cached(filename, expr, regenerate=FALSE) expand.parameters(p, lik.new, repl=0, target=argnames(lik.new)) get.likelihood(object) drop.likelihood(object)

Arguments

node
A node, either a name in tree$node.label, an integer in 1..tree$Nnode, or in length(tree$tip.label)..(length(tree$tip.label)+tree$Nnode).
tree
A phylogenetic tree, in ape's phylo format.
tips.only
Logical: return only descendant indices of tip species?
edge.index
Logical: return the row indices in the edge matrix?
filename
Name of the file to store cached results
expr
Expression to evaluate
regenerate
Logical: force re-evaluation of expr and regeneration of filename?
object
For drop.likelihood, an object that has a likelihood attribute to be removed (saves space on object save); for get.likelihood, retrieves the function.
p, lik.new, repl, target
Undocumented currently