tipsubtree: Extract a subtree that contains pre-specified tip names or...
In bcm-uga/apTreeshape: Analyses of Phylogenetic Treeshape

Description Usage Arguments Value Author(s) See Also Examples

tipsubtree returns an object of class "treeshape" that contains pre-specified tip names or labels. The name of the tips are conserved. It extracts the smallest tree that contains the common ancestors of the given tips.

1	tipsubtree(tree, tips, numeric=FALSE)

`tree`	An object of class `"treeshape"`.
`tips`	A vector that contains the names of the tips one want to keep. Warning, the names are case-sensitive.
`numeric`	An object of class `"logical"`. If `FALSE`, the vector `tips` contains the names of the tips. If `TRUE`, it contains the labels of the tips.

An object of class "treeshape"

Michael Blum <michael.blum@imag.fr>
Nicolas Bortolussi <nicolas.bortolussi@imag.fr>
Eric Durand <eric.durand@imag.fr>
Olivier Francois <olivier.francois@imag.fr>

cutreeshape

  
## The universal tree of life provided in the data sets.
data(universal.treeshape)
  
## One might want to extract the tree containing the Animals, the Plants,
##      the Aquifex and the Microsporidia
tree1<-tipsubtree(universal.treeshape,tips=c("Animals", "Aquifex", 
      "Microsporidia", "Plants"))
plot(universal.treeshape, tree1)

## Labels that do not appear in the tree are ignored
tree2<-tipsubtree(universal.treeshape,tips=c("Human", "Animals", "Aquifex", 
      "Microsporidia", "Plants"))
plot(universal.treeshape, tree2)
  
tree3<-tipsubtree(universal.treeshape,tips=c(1,3,7), numeric=TRUE)
plot(universal.treeshape, tree3)