compareTimescaling: Comparing the Time-Scaling of Trees

Description

These functions take two trees and calculate the changes in node ages (for compareNodeAges) for shared clades or terminal branch lengths leading to shared tip taxa (for compareTermBranches).

Usage

compareNodeAges(tree1,tree2)

compareTermBranches(tree1,tree2)

Arguments

tree1

A time-scaled phylogeny of class 'phylo'

tree2

A time-scaled phylogeny of class 'phylo'

Value

Returns a vector of temporal shifts for nodes or terminal branches, dependent on the function applied. If compareTermBranches is used, the vector will have the tip names as labels.

Details

These functions compare the time-scaling of two trees. Any taxa not-shared on both trees are dropped before analysis, based on tip labels. As with many paleotree functions, calculations relating to time are done with respect to any included $root.time elements. If these are not present, the latest tip is assumed to be at the present day (time=0). compareNodeAges calculates the changes in the clade ages among those clades shared by the two trees, relative to the first tree in absolute time. For example, a shift of +5 means the clade originates 5 time-units later in absolute time on the second tree, while a shift of -5 means the clade originated 5 time-units prior on the second tree. compareTermBranches calculates the changes in the terminal branch lengths attached to tip taxa shared by the two trees, relative to the first tree. Thus, a shift of +5 means that terminal taxon has a terminal branch which is five time-units longer.

Examples

Run this code

set.seed(444)
taxa <- simFossilTaxa(p=0.1,q=0.1,nruns=1,mintaxa=20,maxtaxa=30,maxtime=1000,maxExtant=0)
#get the true tree
tree1 <- taxa2phylo(taxa)
#simulate a fossil record with imperfect sampling with sampleRanges()
rangesCont <- sampleRanges(taxa,r=0.5)
#let's use taxa2cladogram to get the 'ideal' cladogram of the taxa
cladogram <- taxa2cladogram(taxa,plot=TRUE)
#Now let's try timePaleoPhy using the continuous range data
tree2 <- timePaleoPhy(cladogram,rangesCont,type="basic")
#let's look at the distribution of node shifts
hist(compareNodeAges(tree1,tree2))
#let's look at the distribution of terminal branch lengths
hist(compareTermBranches(tree1,tree2))

set.seed(444)
tree1 <- rtree(10)
tree2 <- tree1
tree1$root.time <- 10
compareNodeAges(tree1,tree2)
compareTermBranches(tree1,tree2)