FossilSim (version 2.4.1)

fossils.to.BEAST.start.tree: 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)

Value

a string representing the starting tree in newick format.

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.

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)