paste.tree: Paste two trees together

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Paste two trees together

Description

Internal function for posterior.evolrate.

Usage

paste.tree(tr1, tr2)

Arguments

tr1	receptor tree.
tr2	donor clade.

Details

Primarily designed as an internal function for posterior.evolrate; however, can be used to graft a clade onto a receptor tree at the "sticky tip" labeled with "NA".

The donor clade needs to have a root edge, even if it is zero length.

Value

A tree.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

Examples

## create two random trees
tr1<-rtree(10)
tr2<-rtree(10)

## make one tip "sticky" by renaming it "NA"
tr1$tip.label[sample(1:10,1)]<-"NA"
tr2$root.edge<-0

## paste the two trees together
tr3<-paste.tree(tr1,tr2)

## plot the results
layout(matrix(c(1,1,2,2,4,3,3,4),2,4,byrow=TRUE))
plotTree(tr1,direction="upwards",
    mar=c(1.1,1.1,3.1,1.1))
add.arrow(tree=tr1,tip=which(tr1$tip.label=="NA"),
    hedl=0.2,arrl=0.2,offset=1)
mtext("a) recipient tree",adj=0)
plotTree(tr2,direction="upwards",plot=FALSE)
pp<-get("last_plot.phylo",envir=.PlotPhyloEnv)
plotTree(tr2,direction="upwards",
    mar=c(1.1,1.1,3.1,1.1),
    ylim=c(-0.2,pp$y.lim[2]),add=TRUE)
arrows(pp$xx[11],pp$yy[11],pp$xx[11],-0.2,
    length=0.1,lwd=2)
mtext("b) donor tree",adj=0)
plotTree(tr3,direction="upwards",
    mar=c(1.1,1.1,3.1,1.1))
mtext("c) grafted tree",adj=0)

## reset par to default
par(mfrow=c(1,1),mar=c(5.1,4.1,4.1,2.1))

phytools documentation built on April 3, 2025, 10:43 p.m.