Extract a clade from phylogenetic tree

PCMTreeExtractClade(tree, cladeRootNode, tableAncestors = NULL,
  X = NULL, returnPhylo = is.null(X))

Arguments

tree

a phylo object

cladeRootNode

a character string denoting the label or an integer denoting a node in the tree.

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.

returnPhylo

logical indicating if only the phylo object associated with the clade should be returned. Defaults to is.null(X)

Value

If returnPhylo is TRUE, a phylo object associated with the clade, otherise, a list with two named members :

  • treethe phylo object associated with the clade

  • Xthe submatrix of X with columns corresponding to the tips in the clade

See also

PCMTreeSpliAtNode PCMTreeDropClade