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 |
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 |
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>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
## 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)
|
Loading required package: ape
Attaching package: 'apTreeshape'
The following object is masked from 'package:ape':
is.binary.phylo
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
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