Prune the tree leaving one tip for each or some of its parts

Prune the tree leaving one tip for each or some of its parts

PCMTreeBackbonePartition(tree, partsToKeep = PCMTreeGetPartNames(tree))

Arguments

tree	a PCMTree or a phylo object.
partsToKeep	a character vector denoting part names in the tree to be kept. Defaults to `PCMTreeGetPartNames(tree)`.

Value

a PCMTree object representing a pruned version of tree.

See also

PCMTreeSetPartition

PCMTree

Examples

set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- PCMTree(ape::rtree(25))
# \donttest{
PCMTreePlot(tree) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }
backb <-  PCMTreeBackbonePartition(tree)
# \donttest{
PCMTreePlot(backb) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }

tree2 <- PCMTreeSetPartRegimes(
  tree, c(`26` = "a", `28` = "b"), setPartition = TRUE,
  inplace = FALSE)
# \donttest{
PCMTreePlot(tree2) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }

backb <-  PCMTreeBackbonePartition(tree2)
# \donttest{
PCMTreePlot(backb) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }

tree3 <- PCMTreeSetPartRegimes(
  tree, c(`26` = "a", `28` = "b", `41` = "c"), setPartition = TRUE,
  inplace = FALSE)
# \donttest{
PCMTreePlot(tree3) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }
backb <-  PCMTreeBackbonePartition(tree3)
# \donttest{
PCMTreePlot(backb) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }
backb41 <-  PCMTreeBackbonePartition(tree3, partsToKeep = "41")
# \donttest{
PCMTreePlot(backb41) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)
# }

backbMoreNodes <- PCMTreeInsertSingletonsAtEpoch(
   backb, epoch = 3.7, minLength = 0.001)
PCMTreeGetPartRegimes(backbMoreNodes)
#>  26  28  41 
#> "a" "b" "c" 
# \donttest{
PCMTreePlot(backbMoreNodes) + ggtree::geom_nodelab(angle=45) +
  ggtree::geom_tiplab(angle=45)
# }
backbMoreNodes <- PCMTreeInsertSingletonsAtEpoch(
   backbMoreNodes, epoch = 0.2, minLength = 0.001)
PCMTreeGetPartRegimes(backbMoreNodes)
#>  26  28  41 
#> "a" "b" "c" 
# \donttest{
PCMTreePlot(backbMoreNodes) + ggtree::geom_nodelab(angle=45) +
  ggtree::geom_tiplab(angle=45)
# }
backbMoreNodes <- PCMTreeInsertSingletonsAtEpoch(
   backbMoreNodes, epoch = 1.2, minLength = 0.001)
PCMTreeGetPartRegimes(backbMoreNodes)
#>         26 i_1.2_x_28         41 
#>        "a"        "b"        "c" 

# \donttest{
PCMTreePlot(backbMoreNodes) + ggtree::geom_nodelab(angle=45) +
  ggtree::geom_tiplab(angle=45)
# }