slice.tree {dispRity}

Time slicing a tree.

Description

Time slicing through a phylogenetic tree.

Usage

slice.tree(tree, age, model, FAD, LAD, keep.all.ancestors = FALSE)

Arguments

tree

A phylo object with a root.time element.

age

A single numeric value indicating where to perform the slice.

model

One of the following models: "acctran", "deltran", "random", "proximity", "equal.split" or "gradual.split". Is ignored if method = "discrete". See chrono.subsets for the models description.

FAD, LAD

The first and last occurrence data.

keep.all.ancestors

Optional, whether to also include the ancestors of the tree slice (TRUE) or just the ones linking the elements present at the slice (FALSE; default)

Author(s)

Thomas Guillerme

References

Guillerme T. & Cooper N. 2018. Time for a rethink: time sub-sampling methods in disparity-through-time analyses. Palaeontology. DOI: 10.1111/pala.12364.

See Also

paleotree::timeSliceTree, chrono.subsets.

Examples

set.seed(1)
## Generate a random ultrametric tree
tree <- rtree(20)

## Add some node labels
tree$node.label <- letters[1:19]

## Add its root time
tree$root.time <- max(tree.age(tree)$ages)

## Slice the tree at age 1.5
tree_slice <- slice.tree(tree, age = 1.5, "deltran")

## The slice at age 0.5 but keeping all the ancestors
deep_slice <- slice.tree(tree, age = 0.5, "deltran",
                            keep.all.ancestors = TRUE)

## Visualising the trees
old_par <- par(mfrow = c(2,2))
plot(ladderize(tree), main = "full tree"); axisPhylo()
abline(v =  tree$root.time - 1.5)
plot(ladderize(tree_slice), main = "tree slice"); axisPhylo()
plot(ladderize(deep_slice), main = "slice with ancestors"); axisPhylo()

par(old_par)