timeSliceTree: Taking a Timeslice of a Tree

Description

Removes the portion of a tree after a set point in time, as if the tree had been sliced at that moment.

Usage

timeSliceTree(ttree, sliceTime, drop.extinct = F, plot = T)

Arguments

ttree

A time-scaled phylogeny of class phylo

sliceTime

Time to 'slice' the tree at. See details below.

drop.extinct

If true, drops tips that go extinct before timeSlice.

plot

If true, plots input and output trees for comparison.

Value

Returns the modified phylogeny as an object of class phylo

Details

The sliceTime is always calculated as on the same as scale as ttree$root.time, which the time before present that the root divergence occurred. In other words, if root.time=100, then timeSlice=80 will slice the tree 20 time units after the root. The function assumes that ttree will generally have an element called $root.time. If $root.time is not present as an element of ttree, then it is assumed the tip furthest from the root is at time 0 (present-day) and a new $root.time is calculated (a warning will be issued in this case). If drop.extinct=T, then extinct tips are dropped and (if present) the $root.time of ttree is adjusted.

Examples

Run this code

set.seed(444)
taxa<-simFossilTaxa(p=0.1,q=0.1,nruns=1,mintaxa=20,maxtaxa=30,maxtime=1000,nExtant=0)
taxicDivCont(taxa[,3:4])
#that's the whole diversity curve
#with timeSliceTree we could look at the lineage accumulation curve we'd get of species sampled at a point in time
tree<-taxa2phylo(taxa)
#use timeSliceTree to make tree of relationships up until time=950 
tree950<-timeSliceTree(tree,sliceTime=950,plot=TRUE,drop.extinct=FALSE)
#use drop.extinct=T to only get the tree of lineages extant at time=950
tree950<-timeSliceTree(tree,sliceTime=950,plot=TRUE,drop.extinct=TRUE)
#now its an ultrametric tree with many fewer tips...
#lets plot the lineage accumulation plot on a log scale
phyloDiv(tree950,plotLogRich=TRUE)