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

In venelin/PCMBase: Simulation and Likelihood Calculation of Phylogenetic Comparative Models

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

Description

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

Usage

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))

if(requireNamespace("ggtree"))
PCMTreePlot(tree) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)

backb <-  PCMTreeBackbonePartition(tree)

if(requireNamespace("ggtree"))
PCMTreePlot(backb) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)


tree2 <- PCMTreeSetPartRegimes(
  tree, c(`26` = "a", `28` = "b"), setPartition = TRUE,
  inplace = FALSE)

if(requireNamespace("ggtree"))
PCMTreePlot(tree2) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)


backb <-  PCMTreeBackbonePartition(tree2)

if(requireNamespace("ggtree"))
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)

if(requireNamespace("ggtree"))
PCMTreePlot(tree3) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)

backb <-  PCMTreeBackbonePartition(tree3)

if(requireNamespace("ggtree"))
PCMTreePlot(backb) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)

backb41 <-  PCMTreeBackbonePartition(tree3, partsToKeep = "41")

if(requireNamespace("ggtree"))
PCMTreePlot(backb41) + ggtree::geom_nodelab(angle = 45) +
  ggtree::geom_tiplab(angle = 45)


backbMoreNodes <- PCMTreeInsertSingletonsAtEpoch(
   backb, epoch = 3.7, minLength = 0.001)
PCMTreeGetPartRegimes(backbMoreNodes)

if(requireNamespace("ggtree"))
PCMTreePlot(backbMoreNodes) + ggtree::geom_nodelab(angle=45) +
  ggtree::geom_tiplab(angle=45)

backbMoreNodes <- PCMTreeInsertSingletonsAtEpoch(
   backbMoreNodes, epoch = 0.2, minLength = 0.001)
PCMTreeGetPartRegimes(backbMoreNodes)

if(requireNamespace("ggtree"))
PCMTreePlot(backbMoreNodes) + ggtree::geom_nodelab(angle=45) +
  ggtree::geom_tiplab(angle=45)

backbMoreNodes <- PCMTreeInsertSingletonsAtEpoch(
   backbMoreNodes, epoch = 1.2, minLength = 0.001)
PCMTreeGetPartRegimes(backbMoreNodes)


if(requireNamespace("ggtree"))
PCMTreePlot(backbMoreNodes) + ggtree::geom_nodelab(angle=45) +
  ggtree::geom_tiplab(angle=45)

venelin/PCMBase documentation built on March 14, 2024, 8:24 p.m.