tree_rescale_exp: Rescale branch lengths following the model

In Caetanods/buddPhy: Trait Evolution and Budding Speciation

Description

Function to rescale branches of a phylogenetic tree following the exponential rate proportional, or inversely-proportional, to lineage-age. This function can be used to simulate a realization of the model for posterior predictive checks among other reasons.

Usage

tree_rescale_exp(
  change_rate = 0.05,
  budding_prob = 0.3,
  tree,
  chunk_fraction = 0.01,
  decay_fn = TRUE
)

Arguments

change_rate	rate for the exponential distribution.
budding_prob	probability of a budding speciation on the internal node.
tree	phylogenetic tree.
chunk_fraction	fraction of the total tree-height for branch length discretization.
decay_fn	whether rates should vary proportional (FALSE) or inversely proportional (TRUE) to lineage age.

Value

a phylogenetic tree with rescaled branch lengths and reordered to "cladewise" order (see 'ape::reorder.phylo').

Caetanods/buddPhy documentation built on Oct. 12, 2021, 12:14 p.m.