scaleTree: Phylogenetic tree calibration

View source: R/scaleTree.R

scaleTreeR Documentation

Phylogenetic tree calibration

Description

The function is a wrapper around the functions "scalePhylo", "assign.ages", and "assign.brlen" written by Gene Hunt (http://paleobiology.si.edu/staff/individuals/hunt.cfm). It rescales tree branch lengths according to given calibration dates.

Usage

scaleTree(tree, tip.ages=NULL, node.ages=NULL,min.branch=NULL)

Arguments

tree

a phylogenetic tree. The tree needs not to be ultrametric and fully dichotomous.

tip.ages

a named vector including the ages (i.e. distance from the youngest tip within the tree) of the tips to be changed. If unspecified, the function assumes all the tips are correctly placed with respect to the root.

node.ages

a named vector including the ages (i.e. distance from the youngest tip within the tree) of the nodes to be changed. If no calibration date for nodes is supplied, the tree root is fixed and the function shifts node position only where needed to fit tip ages.

min.branch

has been deprecated.

Value

Rescaled phylogentic tree with tip labels ordered according to their position in the tree.

Author(s)

Silvia Castiglione, Pasquale Raia, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto

See Also

scaleTree vignette

Examples


library(ape)
library(phytools)
# library(geiger)

data("DataFelids")
DataFelids$treefel->tree

max(nodeHeights(tree))->H

#### Example 1 ####
rep(0,4)->tipAges
names(tipAges)<-tips(tree,146)
scaleTree(tree,tipAges)->treeS1

edge.col<-rep("black",nrow(tree$edge))
edge.col[which(treeS1$edge[,2]%in%getDescendants(treeS1,146))]<-"red"

layout(2:1)
plot(tree,edge.color = edge.col,show.tip.label=FALSE)
plot(treeS1,edge.color = edge.col,show.tip.label=FALSE)

#### Example 2 ####
nodeAges<-c(23.5,15.6)
names(nodeAges)<-c(85,139)
scaleTree(tree,node.ages=nodeAges)->treeS2

edge.col<-rep("black",nrow(tree$edge))
edge.col[which(treeS1$edge[,2]%in%c(getDescendants(treeS1,85),
                                    getDescendants(treeS1,139)))]<-"red"

layout(2:1)
plot(tree,edge.color = edge.col,show.tip.label=FALSE)
nodelabels(bg="w",frame="n",node=c(85,139),col="green")
plot(treeS2,edge.color = edge.col,show.tip.label=FALSE)
nodelabels(bg="w",frame="n",node=c(85,139),col="green")

#### Example 3 ####
16->nodeAges
names(nodeAges)<-"145"
tipAges<-19
names(tipAges)<-tree$tip.label[1]
scaleTree(tree,tip.ages = tipAges,node.ages=nodeAges)->treeS3

edge.col<-rep("black",nrow(tree$edge))
edge.col[which(treeS3$edge[,2]%in%c(1,getMommy(tree,1),
                                    getDescendants(treeS3,145)))]<-"red"

layout(2:1)
plot(tree,edge.color = edge.col,show.tip.label=FALSE)
nodelabels(bg="w",frame="n",node=145,col="green")
plot(treeS3,edge.color = edge.col,show.tip.label=FALSE)
nodelabels(bg="w",frame="n",node=145,col="green")


RRphylo documentation built on May 9, 2022, 9:08 a.m.