Drop a clade from a phylogenetic tree

Drop a clade from a phylogenetic tree

PCMTreeDropClade(
  tree,
  cladeRootNode,
  tableAncestors = NULL,
  X = NULL,
  returnList = !is.null(X),
  errorOnMissing = FALSE
)

Arguments

tree

a phylo object
cladeRootNode

a character string denoting the label or an integer denoting a node in the tree
tableAncestors

an integer matrix returned by a previous call to PCMTreeTableAncestors(tree) or NULL.
X

an optional k x N matrix with trait value vectors for each tip in tree.
returnList

logical indicating if a list of the phylo object associated with the tree after dropping the clade and the corresponding entries in X should be returned. Defaults to !is.null(X)
errorOnMissing

logical indicating if an error should be raised if cladeRootNode is not among the nodes in tree. Default FALSE, meaning that if cladeRootNode is not a node in tree the tree (and X if returnList is TRUE) is/are returned unchanged.

Value

If returnList is FALSE, a phylo object associated with the remaining tree after dropping the clade, otherise, a list with two named members :

  • treethe phylo object associated with the remaining tree after dropping the clade

  • Xthe submatrix of X with columns corresponding to the tips in the remaining tree

See also

PCMTreeSpliAtNode PCMTreeExtractClade

Examples

set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
tree <- PCMTree(ape::rtree(25))
PCMTreeSetPartRegimes(
  tree, c(`26`="a", `28`="b", `45`="c"), setPartition = TRUE)
# \donttest{
PCMTreePlot(tree, palette=c(a = "red", b = "green", c = "blue")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
redGreenTree <- PCMTreeDropClade(tree, 45)
PCMTreeGetPartRegimes(redGreenTree)
#>  26  28 
#> "a" "b" 
# \donttest{
PCMTreePlot(redGreenTree, palette=c(a = "red", b = "green", c = "blue")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }
# we need to use the label here, because the node 29 in tree is not the same
# id in redGreenTree:
redGreenTree2 <- PCMTreeDropClade(redGreenTree, "29")
# \donttest{
PCMTreePlot(redGreenTree2, palette=c(a = "red", b = "green", c = "blue")) +
  ggtree::geom_nodelab(angle = 45) + ggtree::geom_tiplab(angle = 45)
# }