Assign selective regimes to clades

Paints the branches of a tree with selective regimes for traits_ou(): every branch starts in regime "0", and the branches descending from each node in nodes take a new regime ("1", "2", ...). Nodes are painted in order, so a later node nested in an earlier one overrides it.

Usage

paint_regimes(tree, nodes, stem = FALSE)

Arguments

tree

A rooted phylo tree.

nodes

Internal node numbers whose descendant branches get a new regime.

stem

Should the branch leading to each node also take the new regime (the shift happens at the start of the stem rather than at the node)?

Value

Character vector with the regime of each branch, in the order of tree$edge after reordering it "cladewise" (the order traits_ou() uses).

Examples

tr <- ape::read.tree(text = "((a:1,b:1):1,(c:1,d:1):1);")
paint_regimes(tr, nodes = 6)
#> [1] "0" "1" "1" "0" "0" "0"
#> attr(,"order")
#> [1] "cladewise"