PCMTreeListAllPartitions {PCMBase} | R Documentation |
A list of all possible (including recursive) partitions of a tree
Description
A list of all possible (including recursive) partitions of a tree
Usage
PCMTreeListAllPartitions(
tree,
minCladeSize,
skipNodes = character(),
tableAncestors = NULL,
verbose = FALSE
)
Arguments
tree |
a phylo object with set labels for the internal nodes |
minCladeSize |
integer indicating the minimum number of tips allowed in one part. |
skipNodes |
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. |
tableAncestors |
NULL (default) or an integer matrix returned by a
previous call to |
verbose |
a logical indicating if informative messages should be printed to the console. |
Value
a list of integer vectors.
Examples
set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- PCMTree(ape::rtree(10))
if(requireNamespace("ggtree"))
PCMTreePlot(tree) + ggtree::geom_nodelab() + ggtree::geom_tiplab()
# list of all partitions into parts of at least 4 tips
PCMTreeListAllPartitions(tree, 4)
# list of all partitions into parts of at least 3 tips
PCMTreeListAllPartitions(tree, 3)
# list all partitions into parts of at least 3 tips, excluding the partitions
# where node 16 is one of the partition nodes:
PCMTreeListAllPartitions(tree, minCladeSize = 3, skipNodes = "16")
[Package PCMBase version 1.2.14 Index]