utils: Utility Functions

In diversitree: Comparative 'Phylogenetic' Analyses of Diversification

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

Author(s)

Richard G. FitzJohn

diversitree documentation built on Oct. 2, 2024, 9:13 a.m.