A list of all possible clade partitions of a tree with a number of splitting nodes
PCMTreeListCladePartitions(tree, nNodes, minCladeSize = 0,
skipNodes = character(0), tableAncestors = NULL, verbose = FALSE)
a phylo object
an integer giving the number of partitioning nodes. There would be
nNodes+1
blocks in each partition (see details).
integer indicating the minimum number of tips allowed in a clade.
an integer or character vector indicating the ids or labels of nodes that should not be used as partition nodes. By default, this is an empty character vector.
NULL (default) or an integer matrix returned by a previous call
to PCMTreeTableAncestors(tree)
.
a logical indicating if informative messages should be printed to the console.
a list of integer nNodes
-vectors. By default a full traversal
of all partitions is done. It is possible to truncate the search to a limited
number of partitions by setting the option PCMBase.MaxLengthListCladePartitions
to a finite positive integer.
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.