fossils.to.BEAST.start.tree: Create a suitable starting tree for a DPPDIV style FBD...

In FossilSim: Simulation and Plots for Fossil and Taxonomy Data

Create a suitable starting tree for a DPPDIV style FBD analysis in BEAST2

Description

If complete = FALSE, only the extant taxa are used to construct the tree, resulting in a DPPDIV style analysis in which the extant topology is fixed and fossils can float in the tree.

Usage

fossils.to.BEAST.start.tree(tree, fossils, complete = FALSE)

Arguments

tree	an object of class "phylo", representing the tree upon which the fossil occurrences were simulated.
fossils	an object of class "fossils" that corresponds to fossil occurrences for the "tree" argument.
complete	logical, if TRUE then the tree are built for the complete tree, if FALSE then the tree is built for the crown clades only.

Value

a string representing the starting tree in newick format.

Examples

t = TreeSim::sim.bd.taxa(10, 1, 0.1, 0.05)[[1]]
f = sim.fossils.poisson(0.1, t, root.edge = FALSE)
fossils.to.BEAST.start.tree(t,f, complete = FALSE)

FossilSim documentation built on Oct. 3, 2024, 1:07 a.m.