# NOT RUN {
tree <- ape::rtree(8)
# the following four are NULLs
tree$node.label
tree$edge.part
tree$part.regime
tree$edge.regime
# In previous version regimes were assigned directly to the edges via
# tree$edge.regime. This is supported but not recommended anymore:
tree$edge.regime <- sample(
letters[1:3], size = PCMTreeNumNodes(tree) - 1, replace = TRUE)
tree.a <- PCMTree(tree)
PCMTreeGetLabels(tree.a)
tree.a$node.label
tree.a$edge.part
tree.a$part.regime
# this is set to NULL - starting from PCMBase 1.2.9 all of the information
# for the regimes is stored in tree$edge.part and tree$part.regime.
tree.a$edge.regime
PCMTreeGetPartition(tree.a)
PCMTreeGetPartNames(tree.a)
PCMTreeGetPartRegimes(tree.a)
# let's see how the tree looks like
# }
# NOT RUN {
PCMTreePlot(tree.a) + ggtree::geom_nodelab() + ggtree::geom_tiplab()
# }
# NOT RUN {
# This is the recommended way to set a partition on the tree
PCMTreeSetPartition(tree.a, c(10, 12))
PCMTreeGetPartition(tree.a)
PCMTreeGetPartNames(tree.a)
PCMTreeGetPartRegimes(tree.a)
# }
# NOT RUN {
PCMTreePlot(tree.a) + ggtree::geom_nodelab() + ggtree::geom_tiplab()
# }
# NOT RUN {
PCMTreeGetPartsForNodes(tree.a, c(11, 15, 12))
PCMTreeGetPartsForNodes(tree.a, c("11", "15", "12"))
PCMTreeSetPartRegimes(tree.a, c(`9` = 'a', `10` = 'b', `12` = 'c'))
PCMTreeGetPartition(tree.a)
PCMTreeGetPartNames(tree.a)
PCMTreeGetPartRegimes(tree.a)
# }
# NOT RUN {
PCMTreePlot(tree.a) + ggtree::geom_nodelab() + ggtree::geom_tiplab()
# }
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