A list of all possible partitions of a tree with a number of splitting nodes

PCMTreeListCladePartitions(tree, nNodes, minCladeSize = 0,
  tableAncestors = NULL, verbose = FALSE)

Arguments

tree

a phylo object

nNodes

an integer giving the number of partitioning nodes. There would be nNodes+1 blocks in each partition (see details).

minCladeSize

integer indicating the minimum number of tips allowed in a clade.

tableAncestors

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

verbose

a logical indicating if informative messages should be printed to the console.

Value

a list of integer nNodes-vectors.

Details

Each subset of nNodes distinct internal or tip nodes defines a partitioning of the branches of the tree into nNodes+1 blocks. This function generates partitions in which nNode of the blocks are monophyletic complete groups (clades), while the (nNodes+1)'th block is a subtree originating at the root with tips ending at the rooting nodes of the nNode clades, eventually containing a clade of tips.