PCMBase (version 1.2.10)

PCMTreeSplitAtNode: Slit a tree at a given internal node into a clade rooted at this node and the remaining tree after dropping this clade

Description

Slit a tree at a given internal node into a clade rooted at this node and the remaining tree after dropping this clade

Usage

PCMTreeSplitAtNode(tree, node,
  tableAncestors = PCMTreeTableAncestors(tree), X = NULL)

Arguments

tree

a PCMTree object.

node

an integer or character indicating a root, internal or tip node

tableAncestors

an integer matrix returned by a previous call to PCMTreeTableAncestors(tree) or NULL.

X

an optional k x N matrix with trait value vectors for each tip in tree.

Value

A list containing two named phylo objects:

• clade The subtree (clade) starting at node.

• Xclade The portion of X attributable to the tips in clade; NULL if X is NULL.

• rest The tree resulting after dropping all tips in the clade.

• Xrest The portion of X attributable to the tips in rest; NULL if X is NULL.

Details

In the current implementation, the edge.jump and edge.part members of the tree will be discarded and not present in the clade.

Examples

# NOT RUN {
set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- PCMTree(ape::rtree(25))
# }
# NOT RUN {
PCMTreePlot(tree) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
spl <- PCMTreeSplitAtNode(tree, 28)
# }
# NOT RUN {
PCMTreePlot(PCMTree(spl$clade)) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }
# NOT RUN {
PCMTreePlot(PCMTree(spl$rest)) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }